<86>Feb 11 17:09:12 userdel[3639927]: delete user 'rooter'
<86>Feb 11 17:09:12 userdel[3639927]: removed group 'rooter' owned by 'rooter'
<86>Feb 11 17:09:12 userdel[3639927]: removed shadow group 'rooter' owned by 'rooter'
<86>Feb 11 17:09:12 groupadd[3639946]: group added to /etc/group: name=rooter, GID=1286
<86>Feb 11 17:09:12 groupadd[3639946]: group added to /etc/gshadow: name=rooter
<86>Feb 11 17:09:12 groupadd[3639946]: new group: name=rooter, GID=1286
<86>Feb 11 17:09:12 useradd[3639959]: new user: name=rooter, UID=1286, GID=1286, home=/root, shell=/bin/bash
<86>Feb 11 17:09:12 userdel[3639986]: delete user 'builder'
<86>Feb 11 17:09:12 userdel[3639986]: removed group 'builder' owned by 'builder'
<86>Feb 11 17:09:12 userdel[3639986]: removed shadow group 'builder' owned by 'builder'
<86>Feb 11 17:09:12 groupadd[3640010]: group added to /etc/group: name=builder, GID=1287
<86>Feb 11 17:09:12 groupadd[3640010]: group added to /etc/gshadow: name=builder
<86>Feb 11 17:09:12 groupadd[3640010]: new group: name=builder, GID=1287
<86>Feb 11 17:09:12 useradd[3640029]: new user: name=builder, UID=1287, GID=1287, home=/usr/src, shell=/bin/bash
<13>Feb 11 17:09:16 rpmi: libgdbm-1.8.3-alt10 1454943313 installed
<13>Feb 11 17:09:16 rpmi: libexpat-2.4.3-alt1 p9+293696.100.1.1 1643124786 installed
<13>Feb 11 17:09:16 rpmi: libp11-kit-0.23.15-alt2 p9+254920.2400.19.1 1601385869 installed
<13>Feb 11 17:09:16 rpmi: libtasn1-4.14-alt1 p9+235792.100.2.1 1565425233 installed
<13>Feb 11 17:09:16 rpmi: rpm-macros-alternatives-0.5.1-alt1 sisyphus+226946.100.1.1 1554830426 installed
<13>Feb 11 17:09:16 rpmi: alternatives-0.5.1-alt1 sisyphus+226946.100.1.1 1554830426 installed
<13>Feb 11 17:09:16 rpmi: ca-certificates-2021.10.06-alt1 p9+289862.100.1.1 1637033643 installed
<13>Feb 11 17:09:16 rpmi: ca-trust-0.1.2-alt1 p9+233349.100.1.1 1561655062 installed
<13>Feb 11 17:09:16 rpmi: p11-kit-trust-0.23.15-alt2 p9+254920.2400.19.1 1601385869 installed
<13>Feb 11 17:09:17 rpmi: libcrypto1.1-1.1.1u-alt1 p9+322202.100.1.1 1685863283 installed
<13>Feb 11 17:09:17 rpmi: libssl1.1-1.1.1u-alt1 p9+322202.100.1.1 1685863283 installed
<13>Feb 11 17:09:17 rpmi: python3-3.7.11-alt1 p9+273501.10.37.1 1629720188 installed
<13>Feb 11 17:09:17 rpmi: libpython3-3.7.11-alt1 p9+273501.10.37.1 1629720188 installed
<13>Feb 11 17:09:17 rpmi: python3-base-3.7.11-alt1 p9+273501.10.37.1 1629720188 installed
<13>Feb 11 17:09:17 rpmi: tests-for-installed-python3-pkgs-0.1.13.1-alt2 1535450458 installed
<13>Feb 11 17:09:17 rpmi: rpm-build-python3-0.1.13.1-alt2 1535450458 installed
<13>Feb 11 17:09:21 rpmi: libverto-0.3.0-alt1_7 sisyphus+225932.100.1.1 1553994917 installed
<13>Feb 11 17:09:21 rpmi: libkeyutils-1.6-alt2 sisyphus+226520.100.2.1 1554512088 installed
<13>Feb 11 17:09:21 rpmi: libcom_err-1.44.6-alt1 sisyphus+224154.100.1.1 1552091653 installed
<86>Feb 11 17:09:21 groupadd[3665563]: group added to /etc/group: name=_keytab, GID=499
<86>Feb 11 17:09:21 groupadd[3665563]: group added to /etc/gshadow: name=_keytab
<86>Feb 11 17:09:21 groupadd[3665563]: new group: name=_keytab, GID=499
<13>Feb 11 17:09:21 rpmi: libkrb5-1.17.2-alt5 p9+325691.100.1.1 1690460821 installed
<13>Feb 11 17:09:21 rpmi: libtirpc-1.0.3-alt1 1532008015 installed
<13>Feb 11 17:09:21 rpmi: libnsl2-1.1.0-alt1_1 1511548748 installed
<13>Feb 11 17:09:21 rpmi: python-modules-encodings-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Feb 11 17:09:21 rpmi: python-modules-compiler-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Feb 11 17:09:21 rpmi: python-modules-email-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Feb 11 17:09:21 rpmi: python-modules-unittest-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Feb 11 17:09:21 rpmi: python-modules-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Feb 11 17:09:21 rpmi: python-modules-nis-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Feb 11 17:09:21 rpmi: python-modules-ctypes-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Feb 11 17:09:21 rpmi: python-modules-multiprocessing-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Feb 11 17:09:21 rpmi: python-modules-logging-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
<13>Feb 11 17:09:21 rpmi: python-tools-2to3-2.7.16-alt1.M90P.2 p9+260393.40.3.1 1604003646 installed
Building target platforms: x86_64
Building for target x86_64
Wrote: /usr/src/in/nosrpm/python-module-PyDSTool-0.88.121202-alt3.bzr20130716.1.1.nosrc.rpm (w1.gzdio)
Installing python-module-PyDSTool-0.88.121202-alt3.bzr20130716.1.1.src.rpm
Building target platforms: x86_64
Building for target x86_64
Executing(%install): /bin/sh -e /usr/src/tmp/rpm-tmp.12627
+ umask 022
+ /bin/mkdir -p /usr/src/RPM/BUILD
+ cd /usr/src/RPM/BUILD
+ /bin/chmod -Rf u+rwX -- /usr/src/tmp/python-module-PyDSTool-buildroot
+ :
+ /bin/rm -rf -- /usr/src/tmp/python-module-PyDSTool-buildroot
+ PATH=/usr/libexec/rpm-build:/usr/src/bin:/bin:/usr/bin:/usr/X11R6/bin:/usr/games
+ install -d /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages
+ pushd /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages
~/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages ~/RPM/BUILD
+ tar -xzf /usr/src/RPM/SOURCES/PyDSTool-0.88.121202.tar.gz
+ rm -fR .gear
+ install -p -m644 /usr/src/RPM/SOURCES/PyDSTool.pth .
+ popd
~/RPM/BUILD
+ install -d /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages
+ pushd /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages
~/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages ~/RPM/BUILD
+ tar -xzf /usr/src/RPM/SOURCES/PyDSTool-0.88.121202.tar.gz
+ rm -fR .gear
+ find -type f -name '*.py' -exec 2to3 -w -n '{}' +
RefactoringTool: Skipping optional fixer: buffer
RefactoringTool: Skipping optional fixer: idioms
RefactoringTool: Skipping optional fixer: set_literal
RefactoringTool: Skipping optional fixer: ws_comma
RefactoringTool: Refactored ./PyDSTool/utils.py
--- ./PyDSTool/utils.py (original)
+++ ./PyDSTool/utils.py (refactored)
@@ -2,10 +2,10 @@
User utilities.
"""
-from errors import *
-from common import *
-import Redirector as redirc
-from parseUtils import joinStrs
+from .errors import *
+from .common import *
+from . import Redirector as redirc
+from .parseUtils import joinStrs
from numpy import Inf, NaN, isfinite, less, greater, sometrue, alltrue, \
searchsorted, take, argsort, array, swapaxes, asarray, zeros, transpose, \
@@ -51,7 +51,7 @@
# writeout file <name>.m
mfile = open(name+".m", 'w')
mfile.write("function %s = %s(%s)\n"%(name,name,argname))
- for k, v in defs.iteritems():
+ for k, v in defs.items():
if k != name:
mfile.write("%s = %s;\n"%(k,v))
# now the final definition of tau_recip or inf
@@ -68,17 +68,17 @@
if recurseDepth == 1:
if not _repeatFirstTime:
# first time through
- print "Information for " + specName + "\n"
- else:
- print specName + ":",
+ print("Information for " + specName + "\n")
+ else:
+ print(specName + ":", end=' ')
if x.__class__ is type:
return
if hasattr(x, 'iteritems'):
x_keys = sortedDictKeys(x)
if len(x_keys) == 0:
- print "< empty >"
+ print("< empty >")
elif recurseDepth != 1:
- print ""
+ print("")
for k in x_keys:
v = x[k]
kstr = object2str(k)
@@ -111,9 +111,9 @@
if recurseDepth==1 and len(outStrList)>1:
# print an extra space between topmost level entries
# provided those entries occupy more than one line.
- print "\n"
+ print("\n")
for s in outStrList:
- print s
+ print(s)
elif hasattr(x, '__dict__') and recurseDepth <= recurseDepthLimit:
info(x.__dict__, specName, offset, recurseDepth,
recurseDepthLimit, True)
@@ -121,7 +121,7 @@
xstr = repr(x)
if xstr == '':
xstr = '< no information >'
- print xstr
+ print(xstr)
_implicitSolveMethods = ['newton', 'bisect', 'steffe', 'fsolve']
@@ -243,7 +243,7 @@
## rerr.stop()
return res
- except TypeError, e:
+ except TypeError as e:
if solmethod == 'bisect':
infostr = " (did you specify a pair for x0?)"
else:
@@ -254,11 +254,11 @@
return newton_fn
elif solmethod == 'bisect':
if fprime is not None:
- print "Warning: fprime argument unused for bisection method"
+ print("Warning: fprime argument unused for bisection method")
return bisect_fn
elif solmethod == 'steffe':
if fprime is not None:
- print "Warning: fprime argument unused for aitken method"
+ print("Warning: fprime argument unused for aitken method")
return steffe_fn
elif solmethod == 'fsolve':
return fsolve_fn
@@ -311,7 +311,7 @@
ins_off = 0
pta = array([pt]) # extra [] to get compatible shape for concat
- dim_range = range(target.shape[1])
+ dim_range = list(range(target.shape[1]))
# neighborhood
nhood = target[index-lo_off:index+hi_off]
if all(ismonotonic(nhood[:,d]) for d in dim_range):
@@ -369,7 +369,7 @@
curr_tol = [tol] * len(target_array)
est_tol = 0.0
- for i in xrange(len(target_array)):
+ for i in range(len(target_array)):
best_off = 0 # used to adjust closest_indices[i] for best approximating element in input_array
if closest_indices[i] >= input_array_len:
@@ -463,20 +463,20 @@
"""
if evnames is None:
- evnames = edict.keys()
- else:
- assert remain(evnames, edict.keys()) == [], "Invalid event names passed"
+ evnames = list(edict.keys())
+ else:
+ assert remain(evnames, list(edict.keys())) == [], "Invalid event names passed"
# put times as first tuple entry of etuplelist
if nonames:
alltlist = []
- for (evname,tlist) in edict.items():
+ for (evname,tlist) in list(edict.items()):
if evname in evnames:
alltlist.extend(tlist)
alltlist.sort()
return alltlist
else:
etuplelist = []
- for (evname,tlist) in edict.items():
+ for (evname,tlist) in list(edict.items()):
if evname in evnames:
etuplelist.extend([(t,evname) for t in tlist])
# sort by times
@@ -518,7 +518,7 @@
xdict = xdict_base.copy()
if use_gen_params:
def Rhs_wrap(x, t):
- xdict.update(dict(zip(x0_names, x)))
+ xdict.update(dict(list(zip(x0_names, x))))
try:
return take(gen.Rhs(t, xdict, gen.pars), x0_ixs)
except (OverflowError, ValueError):
@@ -526,7 +526,7 @@
else:
def Rhs_wrap(x, t, pdict):
- xdict.update(dict(zip(x0_names, x)))
+ xdict.update(dict(list(zip(x0_names, x))))
try:
return take(gen.Rhs(t, xdict, pdict), x0_ixs)
except (OverflowError, ValueError):
@@ -563,14 +563,14 @@
xdict = xdict_base.copy()
if use_gen_params:
def Jac_wrap(x, t):
- xdict.update(dict(zip(x0_names, x)))
+ xdict.update(dict(list(zip(x0_names, x))))
try:
return take(take(gen.Jacobian(t, xdict, gen.pars), x0_ixs,0), x0_ixs,1)
except (OverflowError, ValueError):
return array([overflow_penalty]*dim)
else:
def Jac_wrap(x, t, pdict):
- xdict.update(dict(zip(x0_names, x)))
+ xdict.update(dict(list(zip(x0_names, x))))
try:
return take(take(gen.Jacobian(t, xdict, pdict), x0_ixs,0), x0_ixs,1)
except (OverflowError, ValueError):
@@ -627,9 +627,9 @@
pickle.dump(obj, pklfile, opt)
except:
if hasattr(obj, 'name'):
- print "Failed to save '%s'"%obj.name
+ print("Failed to save '%s'"%obj.name)
else:
- print "Failed to save object '%s'"%str(obj)
+ print("Failed to save object '%s'"%str(obj))
raise
pklfile.close()
@@ -680,16 +680,16 @@
except EOFError:
notDone = False
except:
- print "Error in un-pickling:"
- print "Was the object created with an old version of PyDSTool?"
+ print("Error in un-pickling:")
+ print("Was the object created with an old version of PyDSTool?")
pklfile.close()
raise
pklfile.close()
if objlist == []:
if getall:
- print "No objects found in file"
- else:
- print "No named objects found in file"
+ print("No objects found in file")
+ else:
+ print("No named objects found in file")
if was_singleton_name:
return objlist[0]
else:
@@ -699,7 +699,7 @@
def intersect(a, b):
"""Find intersection of two lists, sequences, etc.
Returns a list that includes repetitions if they occur in the inputs."""
- return filter(lambda e : e in b, a)
+ return [e for e in a if e in b]
def union(a, b):
"""Find union of two lists, sequences, etc.
@@ -710,7 +710,7 @@
def remain(a, b):
"""Find remainder of two lists, sequences, etc., after intersection.
Returns a list that includes repetitions if they occur in the inputs."""
- return filter(lambda e : e not in b, a)
+ return [e for e in a if e not in b]
def compareList(a, b):
"""Compare elements of lists, ignoring order (like sets)."""
@@ -730,9 +730,9 @@
Deprecated as of v0.89."""
if isinstance(fieldvalues, ndarray):
- return dict(zip(fieldnames, [a.tolist() for a in fieldvalues]))
- else:
- return dict(zip(fieldnames, fieldvalues))
+ return dict(list(zip(fieldnameRefactoringTool: Refactored ./PyDSTool/tests/vode_withJac_test.py
RefactoringTool: Refactored ./PyDSTool/tests/vode_event_test2.py
s, [a.tolist() for a in fieldvalues])))
+ else:
+ return dict(list(zip(fieldnames, fieldvalues)))
# ------------------------
--- ./PyDSTool/tests/vode_withJac_test.py (original)
+++ ./PyDSTool/tests/vode_withJac_test.py (refactored)
@@ -38,8 +38,8 @@
DSargs.name = 'jactest'
testODE = Vode_ODEsystem(DSargs)
-print "Defined the following internal Python function for Jacobian:"
-print testODE.funcspec.auxfns['Jacobian'][0], "\n"
+print("Defined the following internal Python function for Jacobian:")
+print(testODE.funcspec.auxfns['Jacobian'][0], "\n")
tvals = [0.4*10**i for i in range(0,12)]
@@ -47,25 +47,25 @@
for t1 in tvals:
dt = t1-t0
- print "\n============================================\nAt t=",
- print t1, "using dt =", dt
+ print("\n============================================\nAt t=", end=' ')
+ print(t1, "using dt =", dt)
testODE.set(tdata=[t0,t1],
algparams={'init_step': dt}
)
if t0 >0.:
- print testODE._solver.y
+ print(testODE._solver.y)
traj = testODE.compute('test', 'c') # c for continue
testODE.diagnostics.showWarnings()
et = testODE.getEventTimes()['thresh_ev']
if et != []:
- print "\n****** Event found at t =", et, "\n"
+ print("\n****** Event found at t =", et, "\n")
t0 = t1
- print traj(t1)
+ print(traj(t1))
-print "\nCompare results with the output directly from the scipy_ode.py test"
-print "The values from a test integration performed with scipy_ode.py " \
- + "are listed in the comments at the end of the script"
+print("\nCompare results with the output directly from the scipy_ode.py test")
+print("The values from a test integration performed with scipy_ode.py " \
+ + "are listed in the comments at the end of the script")
##At t=0.0 y=[ 1. 0. 0.]
##At t=0.4 y=[ 9.85172114e-001 3.38639538e-005 1.47940221e-002]
--- ./PyDSTool/tests/vode_event_test2.py (original)
+++ ./PyDSTool/tests/vode_event_test2.py (refactored)
@@ -36,22 +36,22 @@
DSargs.algparams = {'init_step':0.01}
DSargs.checklevel = 2
testODE = Vode_ODEsystem(DSargs)
-print "params set => ", testODE.pars
-print "DS defined? => ", testODE.defined
-print "testODE.set(...)"
+print("params set => ", testODE.pars)
+print("DS defined? => ", testODE.defined)
+print("testODE.set(...)")
testODE.set(ics={'w':3.0},
tdata=[0.11,2.1])
-print "traj1 = testODE.compute('traj1')"
+print("traj1 = testODE.compute('traj1')")
traj1 = testODE.compute('traj1')
-print "DS defined now? => ", testODE.defined
-print "traj1(0.5) => ", traj1(0.5)
-print "testODE.diagnostics.showWarnings() => "
+print("DS defined now? => ", testODE.defined)
+print("traj1(0.5) => ", traj1(0.5))
+print("testODE.diagnostics.showWarnings() => ")
testODE.diagnostics.showWarnings()
-print "\ntraj1.indepdomain => ", traj1.indepdomain
-print "traj1(0.2, ['aux_other']) => ", traj1(0.2, ['aux_other'])
+print("\ntraj1.indepdomain => ", traj1.indepdomain)
+print("traj1(0.2, ['aux_other']) => ", traj1(0.2, ['aux_other']))
-print "\nNow adding a terminating co-ordinate threshold event"
-print " and non-terminating timer event"
+print("\nNow adding a terminating co-ordinate threshold event")
+print(" and non-terminating timer event")
# Show off the general-purpose, language-independent event creator:
# 'makeZeroCrossEvent'
ev_args_nonterm = {'name': 'monitor',
@@ -77,12 +77,12 @@
thresh_ev_term = Events.makePythonStateZeroCrossEvent('w',
20, 1, ev_args_term)
testODE.eventstruct.add([thresh_ev_nonterm,thresh_ev_term])
-print "Recomputing trajectory:"
-print "traj2 = testODE.compute('traj2')"
+print("Recomputing trajectory:")
+print("traj2 = testODE.compute('traj2')")
traj2 = testODE.compute('traj2')
-print "\ntestODE.diagnostics.showWarnings() => "
+print("\ntestODE.diagnostics.showWarnings() => ")
testODE.diagnostics.showWarnings()
-print "\ntraj2.indepdomain.get() => ", traj2.indepdomain.get()
+print("\ntraj2.indepdomain.get() => ", traj2.indepdomain.get())
indep1 = traRefactoringTool: Refactored ./PyDSTool/tests/vode_event_test1.py
RefactoringTool: Refactored ./PyDSTool/tests/traj_gt0_test.py
RefactoringTool: Refactored ./PyDSTool/tests/test_variable_traj.py
j2.indepdomain[1]
assert indep1 < 1.17 and indep1 > 1.16
mon_evs_found = testODE.getEvents('monitor')
--- ./PyDSTool/tests/vode_event_test1.py (original)
+++ ./PyDSTool/tests/vode_event_test1.py (refactored)
@@ -69,7 +69,7 @@
# Alternative way to extract events: they are labelled in the
# pointset! These return dictionaries indexing into the pointset.
mon_evs_dict = pts.labels.by_label['Event:monitor']
-mon_ev_points = pts[sort(mon_evs_dict.keys())]
+mon_ev_points = pts[sort(list(mon_evs_dict.keys()))]
assert len(mon_evs_found) == len(mon_ev_points) == 2
assert numpy.all(mon_evs_found == mon_ev_points)
--- ./PyDSTool/tests/traj_gt0_test.py (original)
+++ ./PyDSTool/tests/traj_gt0_test.py (refactored)
@@ -51,4 +51,4 @@
assert all(vals6['t'] == array([2.7, 3.7, 5.7]))
assert vals6[0] == 0.2
-print "\nAll trajectory sampling tests passed"
+print("\nAll trajectory sampling tests passed")
--- ./PyDSTool/tests/test_variable_traj.py (original)
+++ ./PyDSTool/tests/test_variable_traj.py (refactored)
@@ -6,138 +6,138 @@
w_pts = Pointset({'coordarray': array([4.456, 2.34634, 7.3431, 5.443], float64),
'indepvararray': array([0.0, 1.0, 2.0, 3.0], float64)})
w_var = Variable(w_pts)
-print "w_var(0.0) => ", w_var(0.0)
+print("w_var(0.0) => ", w_var(0.0))
-print "\n"
+print("\n")
f2 = interp1d([0., 1., 2.], [5,6,7])
v_var = Variable(f2, 't', 'x')
-print "Use optional 'checklevel' argument to specify degree of bounds/domain checking"
-print "This is useful mainly during initial computation of a variable"
-print "v_var(0.01) => ", v_var(0.01, 2)
+print("Use optional 'checklevel' argument to specify degree of bounds/domain checking")
+print("This is useful mainly during initial computation of a variable")
+print("v_var(0.01) => ", v_var(0.01, 2))
try:
- print "\nv_var(array([0.24,2.566]), 2) =>\n", v_var(array([0.24,2.566]), 2)
-except ValueError, e:
- print " ",e
-print "\nv_var =>\n", v_var
-print "v_var.getDataPoints() => ", v_var.getDataPoints()
+ print("\nv_var(array([0.24,2.566]), 2) =>\n", v_var(array([0.24,2.566]), 2))
+except ValueError as e:
+ print(" ",e)
+print("\nv_var =>\n", v_var)
+print("v_var.getDataPoints() => ", v_var.getDataPoints())
# ------------------------------
-print """Test of domain checking... By making depdomain to be a
+print("""Test of domain checking... By making depdomain to be a
set of integers, and the coordarray to be non-integers, this
object can only be called for indepvar values in [0, 0.5, 1, 1.5,
-..., 4.5]"""
+..., 4.5]""")
-print "\n"
-v_int = Variable(Pointset({'coordarray': array(range(10), float64)*0.1,
- 'indepvararray': array(range(10), float64)*0.5
+print("\n")
+v_int = Variable(Pointset({'coordarray': array(list(range(10)), float64)*0.1,
+ 'indepvararray': array(list(range(10)), float64)*0.5
}))
-print "v_int(0.5) => ", v_int(0.5, 2)
-print "v_int(0.4) => "
+print("v_int(0.5) => ", v_int(0.5, 2))
+print("v_int(0.4) => ")
try:
v_int(0.4, 2)
-except ValueError, e:
- print "Successfully checked domain validation with v_int:"
- print " ... error was "+str(e)
-print "v_int(0) => ", v_int(0)
+except ValueError as e:
+ print("Successfully checked domain validation with v_int:")
+ print(" ... error was "+str(e))
+print("v_int(0) => ", v_int(0))
# ------------------------------
-print "\nTest simple functions in Variable object"
+print("\nTest simple functions in Variable object")
exp_str = """exp_var = Variable(math.exp, 'x', Interval('y', float, [0,Inf]))"""
-print exp_str
+print(exp_str)
exec(exp_str)
-print "exp_var(0.5) => ", exp_var(0.5)
+print("exp_var(0.5) => ", exp_var(0.5))
-print "\nTest wrapped functions in OutputFn class"
-print """The optional Intervals specify the "trajectory" range, but are for
-informational purposes only! They are not checked anywhere."""
+print("\nTest wrapped functions in OutputFn class")
+print("""The optional Intervals specify the "trajectory" range, but are for
+informational purposes only! They are not checked anywhere.""")
sin_str = """sin_opfunc = OutputFn(math.sin, (Interval('t', float, [0,Inf]),
Interval('x', float, [-1.,1.])))"""
-print sin_str
+print(sin_str)
exec(sin_str)
-print """\nThese Intervals specify the valid domains of the indep and dep var
-Deliberately only allow +ve angles (unless specified here they won't be checked)"""
+print("""\nThese Intervals specify the valid domains of the indep and dep var
+Deliberately only allow +ve angles (unless specified here they won't be checked)""")
sin_str2 = """sin_var = Variable(sin_opfunc, Interval('t', float, [0,Inf]),
Interval('x', float, [-1,1]))"""
-print sin_str2
+print(sin_str2)
exec(sin_str2)
-print "sin_var(math.pi) => ", sin_var(math.pi, 2)
-print "sin_var(-math.pi/2) =>"
+print("sin_var(math.pi) => ", sin_var(math.pi, 2))
+print("sin_var(-math.pi/2) =>")
try:
sin_var(-math.pi/2, 2)
-except ValueError, e:
- print " ", e
+except ValueError as e:
+ print(" ", e)
-print "sin_var([0., 0.5*math.pi, math.pi]) => ", sin_var([0., 0.5*math.pi,
- math.pi])
+print("sin_var([0., 0.5*math.pi, math.pi]) => ", sin_var([0., 0.5*math.pi,
+ math.pi]))
# ------------------------------
from utils import makeImplicitFunc
-print "\nTest implicit function routine on half-circle of radius 2"
+print("\nTest implicit function routine on half-circle of radius 2")
cf = """def circ_formula(x,y):
return x*x+y*y-4"""
-print cf
+print(cf)
exec(cf)
nf_str = """newton_halfcirc_fn = makeImplicitFunc(circ_formula, x0=0.75, solmethod='newton')"""
-print nf_str
+print(nf_str)
exec(nf_str)
impl_str = """implicit_halfcirc = OutputFn(newton_halfcirc_fn, (Interval('t',
float, (0,2)), Interval('x', float, (-2,2))))"""
-print impl_str
+print(impl_str)
exec(impl_str)
-print "tval = -1.3"
+print("tval = -1.3")
tval = -1.3
xval = implicit_halfcirc(tval)
-print "xval = implicit_halfcirc(tval) => ", xval
-print "math.sqrt(xval*xval + tval*tval) => ", math.sqrt(xval*xval + \
- tval*tval), " = radius"
-print "As it stands, the OutputFn doesn't understand the bounds on the variables:"
-print "implicit_halfcirc(3.) =>"
+print("xval = implicit_halfcirc(tval) => ", xval)
+print("math.sqrt(xval*xval + tval*tval) => ", math.sqrt(xval*xval + \
+ tval*tval), " = radius")
+print("As it stands, the OutputFn doesn't understand the bounds on the variables:")
+print("implicit_halfcirc(3.) =>")
try:
implicit_halfcirc(3.)
-except RuntimeError,e:
- print " ... returns error: ", e
-except AssertionError,e:
- print " ... returns error: ", e
-print """\nSo we can embed this OutputFn into a variable for x as
-a function of t, with enforcable bounds (using checklevel > 0 second call argument)"""
+except RuntimeError as e:
+ print(" ... returns error: ", e)
+except AssertionError as e:
+ print(" ... returns error: ", e)
+print("""\nSo we can embed this OutputFn into a variable for x as
+a function of t, with enforcable bounds (using checklevel > 0 second call argument)""")
implicit_hc_varstr = """implicit_halfcirc_var = Variable(implicit_halfcirc, Interval('t', float, (0,2)),
Interval('x', float, (-2,2)))"""
-print implicit_hc_varstr
+print(implicit_hc_varstr)
exec(implicit_hc_varstr)
-print "implicit_halfcirc_var(tval) => ", implicit_halfcirc_var(tval), ", as before"
-print "implicit_halfcirc_var(3., 2) =>"
+print("implicit_halfcirc_var(tval) => ", implicit_halfcirc_var(tval), ", as before")
+print("implicit_halfcirc_var(3., 2) =>")
try:
implicit_halfcirc_var(3., 2)
-except ValueError,e:
- print " ... returns error: ", e
+except ValueError as e:
+ print(" ... returns error: ", e)
-print "Tests passed"
+print("Tests passed")
-print "\n\nTest regular Trajectory object"
-v1 = Variable(Pointset({'coordarray': array(range(10), float)*0.1,
- 'indepvaraRefactoringTool: Refactored ./PyDSTool/tests/test_pointsets.py
rray': array(range(10), float)*0.5
+print("\n\nTest regular Trajectory object")
+v1 = Variable(Pointset({'coordarray': array(list(range(10)), float)*0.1,
+ 'indepvararray': array(list(range(10)), float)*0.5
}), name='v1')
-v2 = Variable(Pointset({'coordarray': array(range(10), float64)*0.25+1.0,
- 'indepvararray': array(range(10), float64)*0.5
+v2 = Variable(Pointset({'coordarray': array(list(range(10)), float64)*0.25+1.0,
+ 'indepvararray': array(list(range(10)), float64)*0.5
}), name='v2')
traj = Trajectory('test1', [v1,v2])
-print "print traj(0.5, checklevel=2) => ", traj(0.5, checklevel=2)
-print "print traj([0., 0.5]) => ", traj([0., 0.5], 'v1')
-print "traj(0.4, 0, checklevel=2) =>"
+print("print traj(0.5, checklevel=2) => ", traj(0.5, checklevel=2))
+print("print traj([0., 0.5]) => ", traj([0., 0.5], 'v1'))
+print("traj(0.4, 0, checklevel=2) =>")
try:
traj(0.4, 0, checklevel=2)
-except ValueError, e:
- print " ... raised error: ", e
+except ValueError as e:
+ print(" ... raised error: ", e)
-print "Tests passed."
+print("Tests passed.")
--- ./PyDSTool/tests/test_pointsets.py (original)
+++ ./PyDSTool/tests/test_pointsets.py (refactored)
@@ -4,172 +4,172 @@
from PyDSTool import *
# POINTS
-print "\n****** Point class test ******\n"
-print "x uses Python float type:"
+print("\n****** Point class test ******\n")
+print("x uses Python float type:")
xstr = """x = Point({'coorddict': {'x0': [1.123456789], 'x1': [-0.4],
'x2': [4000]},
'coordtype': float})"""
-print xstr
+print(xstr)
exec(xstr)
# float is equivalent to float64
-print "x => ", repr(x)
-print "x.toarray() = ", x.toarray()
-print "\nprint x => ", x
-print "x.dimension => ", x.dimension, ", x.coordnames => ", x.coordnames
-print "x.coordtype => ", x.coordtype
-print "x.coordtype => ", x.coordtype
-print "x('x1') = ", x('x1')
-print "x(['x1','x0']) = ", x(['x1','x0'])
-print "x([0,1]) = ", x([0,1])
-print "\nChanging x entries is done by x[index] = value:"
-print "x[1] = -0.45"
+print("x => ", repr(x))
+print("x.toarray() = ", x.toarray())
+print("\nprint x => ", x)
+print("x.dimension => ", x.dimension, ", x.coordnames => ", x.coordnames)
+print("x.coordtype => ", x.coordtype)
+print("x.coordtype => ", x.coordtype)
+print("x('x1') = ", x('x1'))
+print("x(['x1','x0']) = ", x(['x1','x0']))
+print("x([0,1]) = ", x([0,1]))
+print("\nChanging x entries is done by x[index] = value:")
+print("x[1] = -0.45")
x[1] = -0.45
-print "\nThe index can also be a name, a list of names, or even a dictionary:"
-print "x[['x0', 'x1']] = [4.11103, -0.56])"
+print("\nThe index can also be a name, a list of names, or even a dictionary:")
+print("x[['x0', 'x1']] = [4.11103, -0.56])")
x[['x0', 'x1']] = [4.11103, -0.56]
-print "\ny is a 1D point (with integer type):"
+print("\ny is a 1D point (with integer type):")
# can also specify as array([4])
ystr = """y = Point({'y': 4})"""
-print ystr
+print(ystr)
exec(ystr)
-print "print y => ", y
-print "y(0) = ", y(0)
-print "type(y(0)) => ", type(y(0))
-print "y([0]) = ", y([0])
-print "y.toarray() = ", y.toarray()
+print("print y => ", y)
+print("y(0) = ", y(0))
+print("type(y(0)) => ", type(y(0)))
+print("y([0]) = ", y([0]))
+print("y.toarray() = ", y.toarray())
assert comparePointCoords(x,(x+0)*1,fussy=True)
### POINTSETS
-print "\n\n****** Pointset test ******\n"
-print "v is a 'singleton' pointset, to make sure this doesn't break the interface"
+print("\n\n****** Pointset test ******\n")
+print("v is a 'singleton' pointset, to make sure this doesn't break the interface")
vstr = """v = Pointset({'coorddict': {'x0': 0.2, 'x1': -1.2},
'indepvardict': {'t': 0.01},
'coordtype': float64,
'indepvartype': float64
})"""
-print vstr
+print(vstr)
exec(vstr)
-print "print v =>", v
-print "\nprint v(0.01) => ", v(0.01)
-print "and v(0.01) is a Point object\n"
-print "print v(0.01, 0) => ", v(0.01, 0)
-print "and v(0.01, 0) is a float\n"
-print "print v(0.01, 'x0') => ", v(0.01, 'x0')
-
-print "\nk tests deprecated syntax for single-point pointset"
+print("print v =>", v)
+print("\nprint v(0.01) => ", v(0.01))
+print("and v(0.01) is a Point object\n")
+print("print v(0.01, 0) => ", v(0.01, 0))
+print("and v(0.01, 0) is a float\n")
+print("print v(0.01, 'x0') => ", v(0.01, 'x0'))
+
+print("\nk tests deprecated syntax for single-point pointset")
kstr = """k = Pointset({'coordarray': array(0.1),
'coordnames': 'k0',
'indepvarname': 't',
'indepvararray': array(0.0)})"""
-print kstr
+print(kstr)
exec(kstr)
assert k.dimension == 1
-print "print k.toarray() => ", k.toarray()
-print "print k['t'] => ", k['t']
-print "print k(0.0) => ", k(0.0)
-print "print k => ", k
-
-print "\nu tests non-parameterized pointset"
+print("print k.toarray() => ", k.toarray())
+print("print k['t'] => ", k['t'])
+print("print k(0.0) => ", k(0.0))
+print("print k => ", k)
+
+print("\nu tests non-parameterized pointset")
ustr = """u = Pointset({'coordarray': array([10., 20., 30., 40.])})"""
exec(ustr)
-print ustr
-print "u.toarray() => ", u.toarray()
-print "isparameterized(u) => ", isparameterized(u)
-print "print u => ", u
-
-print "\nw tests alternative declaration syntax, and other forms of calling"
+print(ustr)
+print("u.toarray() => ", u.toarray())
+print("isparameterized(u) => ", isparameterized(u))
+print("print u => ", u)
+
+print("\nw tests alternative declaration syntax, and other forms of calling")
wstr = """wp = Pointset({'coordarray': array([[4.456, 2.34634, 7.3431, 5.443],
[-10.0336, -5.2235, -3.23221, -0.01],
[3e5, 3.1e5, 3.3e5, 2.8e5]], float64),
'coordnames': ['x0', 'x1', 'x2'],
'indepvarname': 't',
'indepvararray': array([0.0, 1.0, 2.0, 3.0], float64)})"""
-print wstr
+print(wstr)
exec(wstr)
assert type(wp.coordarray)==type(array([1,2],float64))
-print "wp.dimension => ", wp.dimension
-print "print wp(0.0) => ", wp(0.0)
-print "type(wp(0.0)) => ", type(wp(0.0))
-print "print wp(1.0)(0) => ", wp(1.0)(0)
-print "print wp(2.0, 'x1') => ", wp(2.0, 'x1')
-print "\nprint wp(2.0, ['x2', 'x1']) => ", wp(2.0, ['x2', 'x1'])
-print "type(wp(2.0, ['x1', 'x2'])) => ", type(wp(2.0, ['x1', 'x2']))
-print "print wp[['x1','x0']] => ", wp[['x1','x0']]
-print "\nwp.info(1) =>", wp.info(1)
-print "wp(1.0).info(1) =>", wp(1.0).info(1)
-print "wp['t'] => ", wp['t']
-print "\nCall several 't' values at once (explicit values only -- no ellipses):"
-print "wp([1., 2.]) => ", wp([1., 2.])
-print "\nExtract a coordinate (only by name) as a regular array:"
+print("wp.dimension => ", wp.dimension)
+print("print wp(0.0) => ", wp(0.0))
+print("type(wp(0.0)) => ", type(wp(0.0)))
+print("print wp(1.0)(0) => ", wp(1.0)(0))
+print("print wp(2.0, 'x1') => ", wp(2.0, 'x1'))
+print("\nprint wp(2.0, ['x2', 'x1']) => ", wp(2.0, ['x2', 'x1']))
+print("type(wp(2.0, ['x1', 'x2'])) => ", type(wp(2.0, ['x1', 'x2'])))
+print("print wp[['x1','x0']] => ", wp[['x1','x0']])
+print("\nwp.info(1) =>", wp.info(1))
+print("wp(1.0).info(1) =>", wp(1.0).info(1))
+print("wp['t'] => ", wp['t'])
+print("\nCall several 't' values at once (explicit values only -- no ellipses):")
+print("wp([1., 2.]) => ", wp([1., 2.]))
+print("\nExtract a coordinate (only by name) as a regular array:")
w_x0 = wp['x0']
-print "w_x0 = wp['x0'] => ", w_x0
-
-print "\nExtract a point of w as a regular array:"
+print("w_x0 = wp['x0'] => ", w_x0)
+
+print("\nExtract a point of w as a regular array:")
w_at_1 = wp(1.).toarray()
-print "w_at_1 = wp(1.).toarray() => ", w_at_1
-
-print "\nMany forms to access individual values or sub-arrays:"
-print "wp(1., 'x1') => ", wp(1., 'x1')
-print "wp(1.)('x1') => ", wp(1.)('x1')
-print "wp(1., 1)) => ", wp(1., 1)
-print "wp([1.,3.], 1) => ", wp([1.,3.], 1)
-print "wp([1.,3.])('x1') => ", wp([1.,3.])['x1']
-print "wp(1.)([0,1]) => ", wp(1.)([0,1])
-print "but ... wp([1.])(1., [0,1]) => ", wp([1.])(1., [0,1])
-print "... because wp([1.]) is a Pointset and wp(1.) is a Point"
-print "This is why wp(1.).toarray() shows a different array shape to wp([1.]).toarray():"
-print "wp(1.).toarray().shape => ", wp(1.).toarray().shape
-print "wp([1.]).toarray().shape => ", wp([1.]).toarray().shape
-
-print "\nChange a point in w using wp[indepvar_value] = point:"
-print "Old value at t=1.0: wp(1.0) =>", wp(1.0)
-print "wp[1] = x"
+print("w_at_1 = wp(1.).toarray() => ", w_at_1)
+
+print("\nMany forms to access individual values or sub-arrays:")
+print("wp(1., 'x1') => ", wp(1., 'x1'))
+print("wp(1.)('x1') => ", wp(1.)('x1'))
+print("wp(1., 1)) => ", wp(1., 1))
+print("wp([1.,3.], 1) => ", wp([1.,3.], 1))
+print("wp([1.,3.])('x1') => ", wp([1.,3.])['x1'])
+print("wp(1.)([0,1]) => ", wp(1.)([0,1]))
+print("but ... wp([1.])(1., [0,1]) => ", wp([1.])(1., [0,1]))
+print("... because wp([1.]) is a Pointset and wp(1.) is a Point")
+print("This is why wp(1.).toarray() shows a different array shape to wp([1.]).toarray():")
+print("wp(1.).toarray().shape => ", wp(1.).toarray().shape)
+print("wp([1.]).toarray().shape => ", wp([1.]).toarray().shape)
+
+print("\nChange a point in w using wp[indepvar_value] = point:")
+print("Old value at t=1.0: wp(1.0) =>", wp(1.0))
+print("wp[1] = x")
wp[1] = x
-print "w has now been updated for the meshpoint at t=1.0 =>"
-print "New value at t=1.0: wp(1.0) => ", wp(1.0)
-assert type(wp.coordarray)==type(array([1,2],float64))
-
-print "\nWe can test equality between arrays, as usual:"
-print "w_at_1 != wp(1.).toarray() => ", w_at_1 != wp(1.).toarray()
-print "We can also compare with a Pointset object:"
-print "wp(1.) != w_at_1 => ", wp(1.) != w_at_1
-print "But we can't put an array on the left-hand side if a Point or " \
- "Pointset is on the right."
-
-print "\nTo demonstrate appending a Point and Pointset to another Pointset:"
+print("w has now been updated for the meshpoint at t=1.0 =>")
+print("New value at t=1.0: wp(1.0) => ", wp(1.0))
+assert type(wp.coordarray)==type(array([1,2],float64))
+
+print("\nWe can test equality between arrays, as usual:")
+print("w_at_1 != wp(1.).toarray() => ", w_at_1 != wp(1.).toarray())
+print("We can also compare with a Pointset object:")
+print("wp(1.) != w_at_1 => ", wp(1.) != w_at_1)
+print("But we can't put an array on the left-hand side if a Point or " \
+ "Pointset is on the right.")
+
+print("\nTo demonstrate appending a Point and Pointset to another Pointset:")
vw = Pointset({'coorddict': {'x0': [0.1, 0.15], 'x1': [100., 102], 'x2': [0.2, 0.1]},
'indepvardict': {'t': [4.5, 5.0]},
'coordtype': float64,
'indepvartype': float64,
'labels': {1: 'c'}
})
-print "vw.labels -->", vw.labels
-print "wp.append(vw)"
+print("vw.labels -->", vw.labels)
+print("wp.append(vw)")
wp.append(vw)
-print "wp.labels -->", wp.labels
+print("wp.labels -->", wp.labels)
assert type(wp.coordarray)==type(array([1,2],float64))
wp.append(Point({'coorddict': {'t': 6.5, 'x0': 2, 'x1': -300, 'x2': -0.9997}}))
assert type(wp.coordarray)==type(array([1,2],float64))
-print "\nwp.toarray() -->\n", wp.toarray()
-print "\nwp(4.5) -->\n", wp(4.5)
-print "\nwp[[3,6]] -->", wp[[3,6]]
-print "\nwp[3:5] -->", wp[3:5]
-print "\nwp[2:] -->", wp[2:]
+print("\nwp.toarray() -->\n", wp.toarray())
+print("\nwp(4.5) -->\n", wp(4.5))
+print("\nwp[[3,6]] -->", wp[[3,6]])
+print("\nwp[3:5] -->", wp[3:5])
+print("\nwp[2:] -->", wp[2:])
try:
# index out of range
wp[10:]
except ValueError:
pass
-print "\nwp[wp.findIndex(4.5)] -->\n", wp[wp.findIndex(4.5)]
-print "\nwp.labels -->", wp.labels
-print "\nLabels test:"
+print("\nwp[wp.findIndex(4.5)] -->\n", wp[wp.findIndex(4.5)])
+print("\nwp.labels -->", wp.labels)
+print("\nLabels test:")
wp.labels[3] = ('a', {'bif':'SN'})
-print "wp.labels[3] -->", wp.labels[3]
+print("wp.labels[3] -->", wp.labels[3])
wp_part = wp[3:5]
-print "wp_part.labels -->", wp_part.labels
+print("wp_part.labels -->", wp_part.labels)
assert wp_part.labels[0] == wp.labels[3]
wpt = wp(3.)
assert wpt.labels == {RefactoringTool: Refactored ./PyDSTool/tests/test_interval.py
'a': {'bif':'SN'}}
@@ -179,42 +179,42 @@
'indepvartype': float64,
'labels': {2: 'b', 3: {'a': {'bif':'H'}}}
})
-print "\nwp_ins object created to insert into wp:"
-print wp_ins
+print("\nwp_ins object created to insert into wp:")
+print(wp_ins)
wp.insert(wp_ins)
-print "\nwp.insert(wp_ins) -->\n", wp
-
-print "\nTo demonstrate building a Pointset from a list of Point objects:"
+print("\nwp.insert(wp_ins) -->\n", wp)
+
+print("\nTo demonstrate building a Pointset from a list of Point objects:")
codestr = """
pointlist = []
for t in wp['t']:
pointlist.append(wp(t))
w_reconstructed = pointsToPointset(pointlist, 't', wp['t'])
"""
-print codestr
+print(codestr)
exec(codestr)
-print "\nAnd to demonstrate that this yields an identical object:"
-print "w_reconstructed == w => ", w_reconstructed == wp
+print("\nAnd to demonstrate that this yields an identical object:")
+print("w_reconstructed == w => ", w_reconstructed == wp)
try:
w_double = w_reconstructed.append(w_reconstructed)
raise RuntimeError("Internal error with Pointset class!")
except ValueError:
- print "(ensure that any independent variable values to append are well-ordered)"
-
-print "\nTest of non-parameterized use of pointsToPointset:"
+ print("(ensure that any independent variable values to append are well-ordered)")
+
+print("\nTest of non-parameterized use of pointsToPointset:")
wnp = pointsToPointset(pointlist)
-print "(Adding two additional labels to wnp)"
+print("(Adding two additional labels to wnp)")
wnp.labels[0]=('b', {})
wnp.addlabel(4, 'c', {'bif': 'H'}) # preferred syntax
-print wnp
-print "\nwnp[:] -->\n", wnp[:]
-print "-- OK!"
-
-print "\nCan iterate over points and pointsets:"
-print "for p in wnp.bylabel('a'):\n print p\n"
+print(wnp)
+print("\nwnp[:] -->\n", wnp[:])
+print("-- OK!")
+
+print("\nCan iterate over points and pointsets:")
+print("for p in wnp.bylabel('a'):\n print p\n")
for p in wnp.bylabel('a'):
- print p
+ print(p)
wp2 = Pointset({'coorddict': {'x0': [-4.5, 2, 3], 'x1': [54, 62, 64], 'x2': [0.9, 0.8, 0.2]},
@@ -235,7 +235,7 @@
# -----------------------------
-print "\n"
-print "x (point) and wp, wnp (param'd and non-param'd pointsets) are available in the global namespace,", \
- "to play with interactively now that this script has run."
-
+print("\n")
+print("x (point) and wp, wnp (param'd and non-param'd pointsets) are available in the global namespace,", \
+ "to play with interactively now that this script has run.")
+
--- ./PyDSTool/tests/test_interval.py (original)
+++ ./PyDSTool/tests/test_interval.py (refactored)
@@ -3,7 +3,7 @@
"""
from PyDSTool import *
-print '---------- Test for Interval.py ----------'
+print('---------- Test for Interval.py ----------')
a=Interval('a', float, [-1,1], abseps=1e-5)
b=Interval('b', float, [-1.,1.])
c=Interval('c', float, [-3.,-2.])
@@ -21,37 +21,37 @@
assert ([-5, 0, -1] < a) == [True, False, False]
assert (a> array([-5, -4, -1])) == [True, True, False]
-print "m=Interval('test1', float, (0,1))"
+print("m=Interval('test1', float, (0,1))")
m=Interval('test1', float, (0,1))
-print 'm => ', m
-print 'm() => ', m()
-print 'm.info() => ',
+print('m => ', m)
+print('m() => ', m())
+print('m.info() => ', end=' ')
m.info()
-print '0.1 in m => ', 0.1 in m
-print
-print "n=Interval('test2', float, (0,0.4))"
+print('0.1 in m => ', 0.1 in m)
+print()
+print("n=Interval('test2', float, (0,0.4))")
n=Interval('test2', float, (0,0.4))
try:
- print 'n in m => ', n in m, '\n'
+ print('n in m => ', n in m, '\n')
raise RuntimeError("Failed test")
-except PyDSTool_UncertainValueError, e:
- print 'UncertainValueError: ', e
-print "s=Interval('a_singleton', float, 0.4)"
+except PyDSTool_UncertainValueError as e:
+ print('UncertainValueError: ', e)
+print("s=Interval('a_singleton', float, 0.4)")
s=Interval('a_singleton', float, 0.4)
-print 's.get() => ', s.get()
-print "s in m => ", s in m, ' (works for singleton interval s)\n'
+print('s.get() => ', s.get())
+print("s in m => ", s in m, ' (works for singleton interval s)\n')
r=Interval('another_singleton', float, 0.0)
-print "r=Interval('another_singleton', float, 0.0)"
+print("r=Interval('another_singleton', float, 0.0)")
b=Interval('b', int, 0)
-print "b=Interval('b', int, 0)"
+print("b=Interval('b', int, 0)")
try:
- print "b in m => ", b in m
+ print("b in m => ", b in m)
raise RuntimeError("Failed test")
-except PyDSTool_UncertainValueError, e:
- print 'UncertainValueError: ', e
+except PyDSTool_UncertainValueError as e:
+ print('UncertainValueError: ', e)
i=Interval('i', int, (0,1))
-print "i=Interval('i', int, (0,1))"
-print "b in i => ", b in i, " (true because we're comparing integer intervals)"
+print("i=Interval('i', int, (0,1))")
+print("b in i => ", b in i, " (true because we're comparing integer intervals)")
ii=i+3
assert ii[0] == i[0]+3
assert ii[1] == i[1]+3
@@ -73,80 +73,80 @@
ii_neg = 1/i_neg
assert ii_neg.get() == [-1, 1]
-print "\nUse the explicit `contains` method to avoid exceptions, and instead"
-print " get an IntervalMembership type returned..."
-print "m.contains(i) => ", m.contains(i)
-print "m.contains(0.4) => ", m.contains(0.4)
+print("\nUse the explicit `contains` method to avoid exceptions, and instead")
+print(" get an IntervalMembership type returned...")
+print("m.contains(i) => ", m.contains(i))
+print("m.contains(0.4) => ", m.contains(0.4))
j = Interval('test3', float, (0,0.999999999))
-print "j = Interval('test3', float, (0,0.999999999))"
-print "p = m.contains(j)"
+print("j = Interval('test3', float, (0,0.999999999))")
+print("p = m.contains(j)")
p = m.contains(j)
-print "p is uncertain => ", p is uncertain
+print("p is uncertain => ", p is uncertain)
-print "\nBut don't try to compare IntervalMembership objects to booleans..."
-print "q = m.contains(0.9)"
+print("\nBut don't try to compare IntervalMembership objects to booleans...")
+print("q = m.contains(0.9)")
q = m.contains(0.9)
assert q is contained
assert not(q is True)
-print "q is True => ", q is True, " (false because q is not a boolean type)"
-print "... but can use in a statement such as 'if m.contains(0.9): ...etc.'"
+print("q is True => ", q is True, " (false because q is not a boolean type)")
+print("... but can use in a statement such as 'if m.contains(0.9): ...etc.'")
-print "\nElementary `interval logic` can be performed when checking endpoints"
-print " for interval containment."
-print "contained and notcontained => ", contained and notcontained
-print "contained and uncertain => ", contained and uncertain
-print "notcontained and notcontained => ", notcontained and notcontained
+print("\nElementary `interval logic` can be performed when checking endpoints")
+print(" for interval containment.")
+print("contained and notcontained => ", contained and notcontained)
+print("contained and uncertain => ", contained and uncertain)
+print("notcontained and notcontained => ", notcontained and notcontained)
-print "\nm.sample(0.09, strict=False, avoidendpoints=True) => ", \
- m.sample(0.09, strict=False, avoidendpoints=True)
+print("\nm.sample(0.09, strict=False, avoidendpoints=True) => ", \
+ m.sample(0.09, strict=False, avoidendpoints=True))
-print "\nm.sample(0.09, strict=False) => ", \
- m.sample(0.09, strict=False)
+print("\nm.sample(0.09, strict=False) => ", \
+ m.sample(0.09, strict=False))
-print "i2=Interval('i2', int, (0,10))"
+print("i2=Interval('i2', int, (0,10))")
i2=Interval('i2', int, (0,10))
-print "\ni2.sample(2, strict=False, avoidendpoints=True) => ", \
- i2.sample(2, strict=False, avoidendpoints=True)
+print("\ni2.sample(2, strict=False, avoidendpoints=True) => ", \
+ i2.sample(2, strict=False, avoidendpoints=True))
-print "i3=Interval('i3', float, (0.,0.4))"
+print("i3=Interval('i3', float, (0.,0.4))")
i3=Interval('i3', float, (0.,0.4))
-print "\ni3.sample(0.36, strict=False) => ", \
- i3.sample(0.36, strict=False)
+print("\ni3.sample(0.36, strict=False) => ", \
+ i3.sample(0.36, strict=False))
-priRefactoringTool: Refactored ./PyDSTool/tests/test_hybrid_extinputs_Cintegrator.py
RefactoringTool: Refactored ./PyDSTool/tests/test_hybrid_extinputs.py
nt "\ni3.sample(0.36, strict=False, avoidendpoints=True) => ", \
- i3.sample(0.36, strict=False, avoidendpoints=True)
+print("\ni3.sample(0.36, strict=False, avoidendpoints=True) => ", \
+ i3.sample(0.36, strict=False, avoidendpoints=True))
-print "\ni3.sample(0.36, strict=True) => ", \
- i3.sample(0.36, strict=True)
+print("\ni3.sample(0.36, strict=True) => ", \
+ i3.sample(0.36, strict=True))
assert len(i3.sample(0.36, strict=True)) == 3
-print "\nInfinite intervals"
-print "inf1 = Interval('inf1', float, [0,Inf])"
+print("\nInfinite intervals")
+print("inf1 = Interval('inf1', float, [0,Inf])")
inf1 = Interval('inf1', float, [0,Inf], abseps=0)
-print "0 in inf1 => ", 0 in inf1
-print "inf1.contains(inf1) => ", inf1.contains(inf1)
-print "inf2 = Interval('inf2', float, [-Inf,Inf])"
+print("0 in inf1 => ", 0 in inf1)
+print("inf1.contains(inf1) => ", inf1.contains(inf1))
+print("inf2 = Interval('inf2', float, [-Inf,Inf])")
inf2 = Interval('inf2', float, [-Inf,Inf])
-print "inf2.contains(inf2) => ", inf2.contains(inf2)
-print "inf2.contains(inf1) => ", inf2.contains(inf1)
-print "inf3 = Interval('inf3', float, [-Inf,0])"
+print("inf2.contains(inf2) => ", inf2.contains(inf2))
+print("inf2.contains(inf1) => ", inf2.contains(inf1))
+print("inf3 = Interval('inf3', float, [-Inf,0])")
inf3 = Interval('inf3', float, [-Inf,0])
-print "inf3.contains(inf2) => ", inf3.contains(inf2)
+print("inf3.contains(inf2) => ", inf3.contains(inf2))
inf_int = Interval('inf3', int, [-Inf,0])
-print "inf_int = Interval('inf3', int, [-Inf,0])"
-print "inf_int.contains(inf3) => "
+print("inf_int = Interval('inf3', int, [-Inf,0])")
+print("inf_int.contains(inf3) => ")
try:
inf_int.contains(inf3)
-except PyDSTool_TypeError, e:
- print " ",e
-print "inf_int.contains(-Inf) => ", inf_int.contains(-Inf)
+except PyDSTool_TypeError as e:
+ print(" ",e)
+print("inf_int.contains(-Inf) => ", inf_int.contains(-Inf))
assert inf_int.contains(-Inf)
i4 = Interval('i4', int, [-5,5])
-print "i4 = Interval('i4', int, [-5,5])"
-print "inf_int.intersect(i4) => ", inf_int.intersect(i4).get()
-print "Intersection should fail on mixed-type intervals ..."
+print("i4 = Interval('i4', int, [-5,5])")
+print("inf_int.intersect(i4) => ", inf_int.intersect(i4).get())
+print("Intersection should fail on mixed-type intervals ...")
try:
result1 = inf3.intersect(i4).get()
except:
@@ -155,9 +155,9 @@
result2 = j.intersect(i2).get()
except:
result2 = " >> FAILURE"
-print "inf3.intersect(i4) => ", result1
+print("inf3.intersect(i4) => ", result1)
assert result1 == " >> FAILURE"
-print "j.intersect(i2) => ", result2
+print("j.intersect(i2) => ", result2)
assert result2 == " >> FAILURE"
i5 = Interval('i5', int, [4,4])
assert i5.issingleton
@@ -168,4 +168,4 @@
assert 4 in i5
assert 4.0 in i5
-print "Tests passed"
+print("Tests passed")
--- ./PyDSTool/tests/test_hybrid_extinputs_Cintegrator.py (original)
+++ ./PyDSTool/tests/test_hybrid_extinputs_Cintegrator.py (refactored)
@@ -11,10 +11,10 @@
m1 = makeModel('Dopri','Dopri')
m2 = makeModel('Vode','Radau')
-print "Testing dopri integrator"
+print("Testing dopri integrator")
plotData1 = test1(m1)
test2(m1)
-print "Testing vode + radau integrator"
+print("Testing vode + radau integrator")
plotData2 = test1(m2)
test2(m2)
--- ./PyDSTool/tests/test_hybrid_extinputs.py (original)
+++ ./PyDSTool/tests/test_hybrid_extinputs.py (refactored)
@@ -82,7 +82,7 @@
return mc.getModel()
def test1(m):
- print '\nTest 1, integrating... '
+ print('\nTest 1, integrating... ')
m.compute(trajname='test1', tdata=tdomain, ics={'x':1.1, 'state': 1},
verboselevel=2)
assert len(m.trajectories['test1'].trajSeq) == 9, \
@@ -100,7 +100,7 @@
return m.sample('test1')
def test2(m):
- print "\nTest 2, integrating ..."
+ print("\nTest 2, integrating ...")
m.compute(trajname='test2', tdata=tdomain, ics={'x':5.1, 'state': 1})
assert len(m.trajectories['test2'].trajSeq) == 8, \
"Incorrect number of hybrid segments"
@@ -108,7 +108,7 @@RefactoringTool: Refactored ./PyDSTool/tests/test_find_nearby_ball.py
RefactoringTool: Refactored ./PyDSTool/tests/test_context_spikes.py
RefactoringTool: Refactored ./PyDSTool/tests/test_bd_containment.py
RefactoringTool: Refactored ./PyDSTool/tests/splinetest.py
RefactoringTool: Refactored ./PyDSTool/tests/sloppycell_example.py
"Inaccurate hybrid computation"
def doPlot(plotData):
- print 'Preparing plot'
+ print('Preparing plot')
plt.ylabel('x')
plt.xlabel('t')
xline=plot(plotData['t'], plotData['x'])
@@ -118,7 +118,7 @@
if __name__=='__main__':
m = makeModel('Vode','Vode')
- print "Testing vode integrator"
+ print("Testing vode integrator")
plotData = test1(m)
test2(m)
--- ./PyDSTool/tests/test_find_nearby_ball.py (original)
+++ ./PyDSTool/tests/test_find_nearby_ball.py (refactored)
@@ -19,12 +19,12 @@
##swirl = generate_swirl(1000, 1, 0.1, 1.5, 0.0064, 0.00005, 0.000, 2, 0.01)
-print "Generating 2D spiral data with added noise (s.d. 0.05)"
+print("Generating 2D spiral data with added noise (s.d. 0.05)")
spiral = generate_spiral(150, 2, 1., 0.1, 0.1, 1, 0.05)
# test function for radius of data set
diam = find_diameter(spiral, 0.5)
-print "\nDiameter of spiral to within +/- 0.5 is", diam
+print("\nDiameter of spiral to within +/- 0.5 is", diam)
#centre_ix = find_central_point(spiral)
centre_ix = 80 # pick a point out on the arm
@@ -33,13 +33,13 @@
times = 0.1*arange(0, len(spiral))
rec_info = find_recurrences(spiral, centre_ix, diam/3, times)
-print "\nAll data indices in ball: ", rec_info.ball_ixs
+print("\nAll data indices in ball: ", rec_info.ball_ixs)
-print "\nPartitions found (by index): ", rec_info.partitions
+print("\nPartitions found (by index): ", rec_info.partitions)
-print "\nNumber of contiguous traj points in a ball near centre_ix = ", rec_info.partition_lengths
-print "\nRecurrence times for a ball around the black square of radius %.3f"%(diam/3)
-print "for the partitions found are ", rec_info.rec_times
+print("\nNumber of contiguous traj points in a ball near centre_ix = ", rec_info.partition_lengths)
+print("\nRecurrence times for a ball around the black square of radius %.3f"%(diam/3))
+print("for the partitions found are ", rec_info.rec_times)
# x-y projection
--- ./PyDSTool/tests/test_context_spikes.py (original)
+++ ./PyDSTool/tests/test_context_spikes.py (refactored)
@@ -4,7 +4,7 @@
# importPointset or use scipy's text file -> array reading functions
from PyDSTool.Toolbox.neuro_data import *
-print "Test Context class and example of qualitative fitting of spikes"
+print("Test Context class and example of qualitative fitting of spikes")
sigma = 0.05
@@ -46,4 +46,4 @@
assert allclose(is_spike.results.spike_time, 270.5574)
assert allclose(is_spike.results.spike_val, 5117.07697)
-print " ...passed"
+print(" ...passed")
--- ./PyDSTool/tests/test_bd_containment.py (original)
+++ ./PyDSTool/tests/test_bd_containment.py (refactored)
@@ -2,7 +2,7 @@
from PyDSTool import *
-print "Basic tests for boundary containment features..."
+print("Basic tests for boundary containment features...")
vals1 = linspace(-3,3,20)
test_traj1 = numeric_to_traj([vals1],
@@ -85,4 +85,4 @@
ic_disc = numeric_to_traj([[1],[0]], 'test', ['x', 'dxdt'], 0.)
assert disc_dom(ic_disc)
-print " ...passed"
+print(" ...passed")
--- ./PyDSTool/tests/splinetest.py (original)
+++ ./PyDSTool/tests/splinetest.py (refactored)
@@ -81,7 +81,7 @@
PyCont['EQ1'].display(('delta','D'), stability=True, color='green')
-print "Avoiding computing the Hopf curves until C code can be augmented with equivalent spline code"
+print("Avoiding computing the Hopf curves until C code can be augmented with equivalent spline code")
plt.show()
# STOP HERE
1/0
@@ -135,7 +135,7 @@
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
ax1=subplot(111)
PyCont['FO1'].display(('delta','D_max'),axes=ax1, stability=True, color='green')
--- ./PyDSTool/tests/sloppycell_example.py (original)
+++ ./PyDSTool/tests/sloppycell_example.py (refactored)
@@ -313,7 +313,7 @@
# change genTarget to 'Vode_ODEsystem' if your external C compiler doesn't work
-print "Making model"
+print("Making model")
genTarget = 'Radau_ODEsystem'
algparams = {'init_step': 0.1}
@@ -322,23 +322,23 @@
sModel = makeSloppyModel('cplx_eg', sloRefactoringTool: Refactored ./PyDSTool/tests/saveload_test.py
RefactoringTool: Refactored ./PyDSTool/tests/run_all_tests.py
ppyModelEg, genTarget,
algParams=algparams, silent=True)
-print "\nAux spec:\n",
+print("\nAux spec:\n", end=' ')
sModel.showDef('cplx_eg', 'auxspec')
# make some random i.c.s
def uniformICs(varnames, a, b):
- return dict(zip(varnames, [random.uniform(a, b) for v in varnames]))
+ return dict(list(zip(varnames, [random.uniform(a, b) for v in varnames])))
#ics = uniformICs(sModel.allvars, 0, 1)
ics = {}
-for name, val in all_ics_pars.iteritems():
+for name, val in all_ics_pars.items():
if name in sModel.allvars:
ics[name] = val
def compute(trajname='fig2', thi=205, dt=0.1, verboselevel=0):
- print "Computing trajectory"
+ print("Computing trajectory")
sModel.set(algparams={'init_step': dt})
t0=clock()
sModel.compute(trajname=trajname,
@@ -347,7 +347,7 @@
tdata=[0,thi], # time in minutes
verboselevel=verboselevel
)
- print "Finished in %f seconds using initial step size of %f"%(clock()-t0,dt)
+ print("Finished in %f seconds using initial step size of %f"%(clock()-t0,dt))
def doPlots(trajname='test', coords=None, dt=0.1, tlo=None, thi=None):
@@ -356,7 +356,7 @@
for v in coords:
plot(plotdata['t'], plotdata[v])
-print "\nComputing trajectory"
+print("\nComputing trajectory")
compute()
# these plots correspond to the sub-plots of Chen 2004 paper
@@ -371,6 +371,6 @@
# Event2: v['CLB2_20']+v['CLB5_22']-p['KEZ2_172']
# Event3: v['SPN_53']-1
evs=sModel.getTrajEvents('fig2')
-print orderEventData(sModel.getTrajEventTimes('fig2'))
+print(orderEventData(sModel.getTrajEventTimes('fig2')))
show()
--- ./PyDSTool/tests/saveload_test.py (original)
+++ ./PyDSTool/tests/saveload_test.py (refactored)
@@ -5,7 +5,7 @@
# --------------------------------------------------------------------
-print "Test pickling for saving and loading various PyDSTool objects"
+print("Test pickling for saving and loading various PyDSTool objects")
# array
a=array([1,Inf])
@@ -41,16 +41,16 @@
assert objs_pts[0] == x
# Simple Variable
-var1 = Variable(Pointset(coordarray = array(range(10), float)*0.1,
- indepvararray = array(range(10), float)*0.5
+var1 = Variable(Pointset(coordarray = array(list(range(10)), float)*0.1,
+ indepvararray = array(list(range(10)), float)*0.5
), name='v1')
saveObjects(var1, 'temp_objects.pkl', True)
obj_var = loadObjects('temp_objects.pkl')[0]
assert obj_var(1.5) == var1(1.5)
# Trajectory
-var2 = Variable(Pointset(coordarray = array(range(10), float)*0.25+1.0,
- indepvararray = array(range(10), float)*0.5
+var2 = Variable(Pointset(coordarray = array(list(range(10)), float)*0.25+1.0,
+ indepvararray = array(list(range(10)), float)*0.5
), name='v2')
traj = Trajectory('traj1', [var1,var2])
saveObjects(traj, 'temp_objects.pkl', True)
@@ -158,4 +158,4 @@
# delete temp file
os.remove('temp_objects.pkl')
-print " ...passed"
+print(" ...passed")
--- ./PyDSTool/tests/run_all_tests.py (original)
+++ ./PyDSTool/tests/run_all_tests.py (refactored)
@@ -159,20 +159,20 @@
failure = False
for f in flist:
fname = f+'.py'
- print "\n***** Testing script %s ****************************\n"%fname
+ print("\n***** Testing script %s ****************************\n"%fname)
try:
e=os.system(whichpy + ' ' + fname)
except:
- print "\n Testing failed on test file %s"%fname
+ print("\n Testing failed on test file %s"%fname)
failed.append(fname)
if not failure:
res.append("%s: appears to be broken on your system"%infostr)
failure = True
else:
if e in [0,3]:
- print "\n Testing passed on test file %s"%fname
+ print("\n Testing passed on test file %s"%fname)
else:
- print "\n Testing failed on test file %s"%fname
+ print("\n Testing failed on test file %s"%fname)
failed.append(fname)
failure = True
time.sleep(2)
@@ -183,79 +183,79 @@
# ---------------------------------------------------------------------------
-print "***** Running all tests in order...\n"
-print "Note: Depending on your settings, you may have to close matplotlib windows by hand in order to continue to the next test script\n"
+print("***** Running all tests in order...\n")
+print("Note: Depending on your settings, you may have to close matplotlib windows by hand in order to continue to the next test script\n")
if test_general:
- print "Testing general PyDSTool functions...\n"
+ print("Testing general PyDSTool functions...\n")
test(general_list, pythonprogram, "Basic PyDSTool functions")
else:
res.append("Tests of basic PyDSTool functions: SKIPPED")
if test_maps:
- print "Testing map modules...\n"
+ print("Testing map modules...\n")
test(map_list, pythonprogram, "Map related modules")
else:
res.append("Tests of map related modules: SKIPPED")
if test_vode:
- print "Testing modules using VODE integrator...\n"
+ print("Testing modules using VODE integrator...\n")
test(vode_list, pythonprogram, "VODE related modules")
else:
res.append("Tests of VODE related modules: SKIPPED")
if test_symbolic:
- print "Testing symbolic differentiation module...\n"
+ print("Testing symbolic differentiation module...\n")
test(symbolic_list, pythonprogram, "Symbolic differentiation module")
else:
res.append("Tests of symbolic differentiation module: SKIPPED")
if test_param_est:
- print "Testing parameter estimation module, no C compiler dependence...\n"
+ print("Testing parameter estimation module, no C compiler dependence...\n")
test(param_est_list, pythonprogram, "Parameter estimation module")
else:
res.append("Tests of parameter estimation module: SKIPPED")
if test_pycont:
- print "Testing PyCont module, no external compiler dependence...\n"
+ print("Testing PyCont module, no external compiler dependence...\n")
test(pycont_list, pythonprogram, "PyCont")
else:
res.append("Tests of PyCont with no external compiler dependence: SKIPPED")
if do_external:
- print "\n***** Now running tests that use external compilers...\n"
+ print("\n***** Now running tests that use external compilers...\n")
if test_dopri:
- print "Testing dopri integration; external C compiler dependence...\n"
+ print("Testing dopri integration; external C compiler dependence...\n")
test(dopri_list, pythonprogram, "Dopri ODE systems")
else:
res.append("Tests of Dopri ODE systems: SKIPPED")
if test_radau:
- print "Testing radau integration; external C, fortran compiler dependence...\n"
+ print("Testing radau integration; external C, fortran compiler dependence...\n")
test(radau_list, pythonprogram, "Radau ODE systems")
else:
res.append("Tests of Radau ODE systems: SKIPPED")
if test_param_est_C:
- print "Testing parameter estimation module; with C compiler dependence...\n"
+ print("Testing parameter estimation module; with C compiler dependence...\n")
test(param_est_C_list, pythonprogram, "Parameter estimation module with external compilers")
else:
res.append("Tests of parameter estimation module with external compilers: SKIPPED")
if test_pycont_auto:
- print "Testing PyCont continuation with AUTO...\n"
+ print("Testing PyCont continuation with AUTO...\n")
test(pycont_auto_list, pythonprogram, "PyCont interface to AUTO")
else:
res.append("Tests of PyCont interface to AUTO: SKIPPED")
if len(failed) == 0:
- print "No test scripts failed"
-else:
- print "Test scripts that failed:"
+ print("No test scripts failed")
+else:
+ print("Test scripts that failed:")
for fname in failed:
- print "\t%s"%fname
-
-print "Summary:"
+ print("\t%s"%fname)
+
+print("Summary:")
for r in res:
- print RefactoringTool: Refactored ./PyDSTool/tests/radau_event_test.py
RefactoringTool: No changes to ./PyDSTool/tests/poly_interp_test.py
RefactoringTool: Refactored ./PyDSTool/tests/phaseplane_HHtest.py
RefactoringTool: Refactored ./PyDSTool/tests/pest_test4_Cintegrator.py
r
+ print(r)
--- ./PyDSTool/tests/radau_event_test.py (original)
+++ ./PyDSTool/tests/radau_event_test.py (refactored)
@@ -57,13 +57,13 @@
DSargs.events = [thresh_ev_nonterm,thresh_ev_term]
testODE = Radau_ODEsystem(DSargs)
-print "Computing trajectory:"
-print "traj = testODE.compute('traj')"
+print("Computing trajectory:")
+print("traj = testODE.compute('traj')")
traj = testODE.compute('traj')
-print "\ntestODE.diagnostics.showWarnings() => "
+print("\ntestODE.diagnostics.showWarnings() => ")
testODE.diagnostics.showWarnings()
-print "\ntraj.indepdomain.get() => ", traj.indepdomain.get()
+print("\ntraj.indepdomain.get() => ", traj.indepdomain.get())
indep1 = traj.indepdomain[1]
assert indep1 < 1.15 and indep1 > 1.13
mon_evs_found = testODE.getEvents()['monitor']
--- ./PyDSTool/tests/phaseplane_HHtest.py (original)
+++ ./PyDSTool/tests/phaseplane_HHtest.py (refactored)
@@ -53,7 +53,7 @@
ev, ev_helper=make_flow_normal_event('v', 'm', vfn_str, mfn_str,
targetlang='c',
fnspec={'vars': ['v', 'm', 'h', 'n'],
- 'pars': par_args.keys(),
+ 'pars': list(par_args.keys()),
'inputs': [],
'auxfns': auxdict},
evtArgs={'eventtol': 1e-8,
@@ -80,7 +80,7 @@
-print 'Phase Plane test using Hodgkin-Huxley system during action potential'
+print('Phase Plane test using Hodgkin-Huxley system during action potential')
par_args = {'gna': 100, 'gk': 80, 'gl': 0.1,
'vna': 50, 'vk': -100, 'vl': -67,
'I': 1.75, 'C': 1.0}
@@ -93,7 +93,7 @@
HH, ev_helper = makeHHneuron('HH_PP_test', 0.1, par_args, ic_args)
HH.set(tdata=[0, 100], ics={'h':0.7, 'n': 0.2})
-print "Finding analytic Jacobian w.r.t. phase-plane variables v, m..."
+print("Finding analytic Jacobian w.r.t. phase-plane variables v, m...")
jac, new_fnspecs = prepJacobian(HH.funcspec._initargs['varspecs'], ['m', 'v'],
HH.funcspec._initargs['fnspecs'])
@@ -102,8 +102,8 @@
scope.update(new_fnspecs)
jac_fn = expr2fun(jac, ensure_args=['t'], **scope)
-print "Use of Jacobian speeds up finding of nullclines and fixed points by"
-print "nearly a factor of two (not including time to plot results)..."
+print("Use of Jacobian speeds up finding of nullclines and fixed points by")
+print("nearly a factor of two (not including time to plot results)...")
fp_coords = find_fixedpoints(HH, n=4, jac=jac_fn, eps=1e-8,
subdomain={'v':HH.xdomain['v'],'m':HH.xdomain['m'],
'h': HH.initialconditions['h'], 'n': HH.initialconditions['n']})
@@ -116,8 +116,8 @@
N_y = nullcline('v', 'm', nulls_y)
-print "Fixed points for (v,m) phase plane sub-system when h=%.2f and n=%.2f: " % (HH.initialconditions['h'], HH.initialconditions['n'])
-print "For classification and stability, we use the fixedpoint class..."
+print("Fixed points for (v,m) phase plane sub-system when h=%.2f and n=%.2f: " % (HH.initialconditions['h'], HH.initialconditions['n']))
+print("For classification and stability, we use the fixedpoint class...")
fps=[]
fps.append(fixedpoint_2D(HH, Point(fp_coords[0]), coords=['v', 'm'],
@@ -128,8 +128,8 @@
jac=jac_fn, description='top', eps=1e-8))
for fp in fps:
- print "F.p. at (%.5f, %.5f) is a %s and has stability %s" % (fp.point['v'],
- fp.point['m'], fp.classification, fp.stability)
+ print("F.p. at (%.5f, %.5f) is a %s and has stability %s" % (fp.point['v'],
+ fp.point['m'], fp.classification, fp.stability))
plotter.fig_directory = {'PP_large': 1,
'PP_small': 2}
--- ./PyDSTool/tests/pest_test4_Cintegrator.py (original)
+++ ./PyDSTool/tests/pest_test4_Cintegrator.py (refactored)
@@ -44,9 +44,9 @@
result = HH_thresh_ev.searchForEvents(tuple(tdata))
HH_spike_t = result[0][0]
-print "True HH spike time based on threshold evRefactoringTool: Refactored ./PyDSTool/tests/pest_test3_Cintegrator.py
ent is at ", HH_spike_t
-print "but assume the traj is real data so that we have to find the spike"
-print "directly from the noisy data"
+print("True HH spike time based on threshold event is at ", HH_spike_t)
+print("but assume the traj is real data so that we have to find the spike")
+print("directly from the noisy data")
## Set up external interface for the reference trajectory based on spike time
@@ -170,9 +170,9 @@
(geom_interface, int_geom_iface) ])
## Parameter estimation
-print 'Estimating pars gna and vl for fit to non-identical HH cell'
-print 'Goal values are gna =', par_args_HH_goal['gna'], ', gl =', \
- par_args_HH_goal['gl'], ' ...'
+print('Estimating pars gna and vl for fit to non-identical HH cell')
+print('Goal values are gna =', par_args_HH_goal['gna'], ', gl =', \
+ par_args_HH_goal['gl'], ' ...')
pest_pars = LMpest(freeParams=['gna', 'gl'],
@@ -203,11 +203,11 @@
},
verbose=True)
-print '... finished in %.4f seconds\n'%(clock()-t0)
+print('... finished in %.4f seconds\n'%(clock()-t0))
## Finish preparing plots
-print '\nPreparing plots'
+print('\nPreparing plots')
figure()
disp_dt = 0.05
plotData_orig = HH_test_model.sample('orig', ['v'], disp_dt, precise=True)
--- ./PyDSTool/tests/pest_test3_Cintegrator.py (original)
+++ ./PyDSTool/tests/pest_test3_Cintegrator.py (refactored)
@@ -44,7 +44,7 @@
HH_spike_t = HH_goal.getEventTimes()['HH_zerothresh'][0]
-print "HH spike time found at ", HH_spike_t
+print("HH spike time found at ", HH_spike_t)
## Set up test HH model
@@ -160,23 +160,23 @@
pest_context = context([ (spike_interface, int_spike_iface),
(geom_interface, int_geom_iface) ])
-print "Feature evaluation on initial set-up: ", pest_context.evaluate(HH_test_model)
-print "geom feat residual: ", norm(geom_feat.metric.results)
+print("Feature evaluation on initial set-up: ", pest_context.evaluate(HH_test_model))
+print("geom feat residual: ", norm(geom_feat.metric.results))
pts1=geom_feat.ref_traj(tmesh,coords=['v'])
pts2=HH_test_model('test_iface_traj', tmesh, coords=['v'])
#plot(tmesh, pts1['v'])
#plot(tmesh, pts2['v'])
-print "\nResidual norm before feature weighting:"
-print norm(pest_context.residual(HH_test_model))
+print("\nResidual norm before feature weighting:")
+print(norm(pest_context.residual(HH_test_model)))
#pest_context.set_weights({geom_interface: 0.005})
pest_context.set_weights({geom_interface: 0.005, spike_interface: 0.25})
-print "Residual norm after feature weighting:"
-print norm(pest_context.residual(HH_test_model))
+print("Residual norm after feature weighting:")
+print(norm(pest_context.residual(HH_test_model)))
## Parameter estimation
-print '\nEstimating pars gl and vl for fit'
-print 'Goal values are vl =', par_args_HH_goal['vl'], ', gl = ', \
- par_args_HH_goal['gl'], ' ...'
+print('\nEstimating pars gl and vl for fit')
+print('Goal values are vl =', par_args_HH_goal['vl'], ', gl = ', \
+ par_args_HH_goal['gl'], ' ...')
pnames = ['vl', 'gl']
parscales = {'vl': 0.1, 'gl': 0.01}
@@ -203,15 +203,15 @@
parscales=parscales, parseps=parseps)
opt.iterate()
-print '... finished in %.3f seconds\n' % (clock()-start)
+print('... finished in %.3f seconds\n' % (clock()-start))
log_ix = pest2.find_logs()[0]
sol_pars = pest2.log[log_ix].pars
HH_test_model.set(pars=sol_pars) #pestData_par['pars_sol'])
-print "Feature evaluation on solution set-up: ", \
- pest_context.evaluate(HH_test_model)
-print "geom feat residual: ", norm(geom_feat.metric.results)
+print("Feature evaluation on solution set-up: ", \
+ pest_context.evaluate(HH_test_model))
+print("geom feat residual: ", norm(geom_feat.metric.results))
# solution trajectory involving voltage happens to be the second of the
# two trajectories stored in each log (one for each model interface, and
@@ -219,7 +219,7 @@
sol_traj = pest2.log[log_ix].trajectories[-1]
## Finish preparingRefactoringTool: Refactored ./PyDSTool/tests/pest_test3.py
RefactoringTool: Refactored ./PyDSTool/tests/pest_test2.py
plots
-print '\nPreparing plots'
+print('\nPreparing plots')
figure()
disp_dt = 0.05
plotData_orig = HH_test_model.sample('orig', ['v'], disp_dt, precise=True)
--- ./PyDSTool/tests/pest_test3.py (original)
+++ ./PyDSTool/tests/pest_test3.py (refactored)
@@ -44,9 +44,9 @@
result = HH_thresh_ev.searchForEvents(tuple(tdata))
HH_spike_t = result[0][0]
-print "True HH spike time based on threshold event is at ", HH_spike_t
-print "but assume the traj is real data so that we have to find the spike"
-print "directly from the noisy data"
+print("True HH spike time based on threshold event is at ", HH_spike_t)
+print("but assume the traj is real data so that we have to find the spike")
+print("directly from the noisy data")
## Set up external interface for the reference trajectory based on spike time
@@ -162,22 +162,22 @@
pest_context = context([ (spike_interface, int_spike_iface),
(geom_interface, int_geom_iface) ])
-print "Feature evaluation on initial set-up: ", pest_context.evaluate(HH_test_model)
-print "geom feat residual: ", norm(geom_feat.metric.results)
+print("Feature evaluation on initial set-up: ", pest_context.evaluate(HH_test_model))
+print("geom feat residual: ", norm(geom_feat.metric.results))
pts1=geom_feat.ref_traj(tmesh,coords=['v'])
pts2=HH_test_model('test_iface_traj', tmesh, coords=['v'])
#plot(tmesh, pts1['v'])
#plot(tmesh, pts2['v'])
-print "\nResidual norm before feature weighting:"
-print norm(pest_context.residual(HH_test_model))
+print("\nResidual norm before feature weighting:")
+print(norm(pest_context.residual(HH_test_model)))
pest_context.set_weights({geom_interface: 0.005, spike_interface: 0.25})
-print "Residual norm after feature weighting:"
-print norm(pest_context.residual(HH_test_model))
+print("Residual norm after feature weighting:")
+print(norm(pest_context.residual(HH_test_model)))
## Parameter estimation
-print '\nEstimating pars gl and vl for fit'
-print 'Goal values are vl =', par_args_HH_goal['vl'], ', gl = ', \
- par_args_HH_goal['gl'], ' ...'
+print('\nEstimating pars gl and vl for fit')
+print('Goal values are vl =', par_args_HH_goal['vl'], ', gl = ', \
+ par_args_HH_goal['gl'], ' ...')
# Using the built-in least squares optimizer doesn't work
@@ -210,9 +210,9 @@
sol_pars = pest2.log[log_ix].pars
HH_test_model.set(pars=sol_pars) #pestData_par['pars_sol'])
-print "Feature evaluation on solution set-up: ", \
- pest_context.evaluate(HH_test_model)
-print "geom feat residual: ", norm(geom_feat.metric.results)
+print("Feature evaluation on solution set-up: ", \
+ pest_context.evaluate(HH_test_model))
+print("geom feat residual: ", norm(geom_feat.metric.results))
# solution trajectory involving voltage happens to be the second of the
# two trajectories stored in each log (one for each model interface, and
@@ -220,7 +220,7 @@
sol_traj = pest2.log[log_ix].trajectories[-1]
## Finish preparing plots
-print '\nPreparing plots'
+print('\nPreparing plots')
figure()
disp_dt = 0.05
plotData_orig = HH_test_model.sample('orig', ['v'], disp_dt, precise=True)
--- ./PyDSTool/tests/pest_test2.py (original)
+++ ./PyDSTool/tests/pest_test2.py (refactored)
@@ -30,7 +30,7 @@
sample_dt = 0.06
count = 0
countlim = 5
-print "Generating non-uniform samples from HH orbit..."
+print("Generating non-uniform samples from HH orbit...")
tsamples = arange(0, 14, sample_dt)
vsamples = HH_traj(tsamples, ['v']).toarray()
for i in range(len(tsamples)):
@@ -46,7 +46,7 @@
HH_sampleData['t'].append(t)
HH_sampleData['v'].append(v)
count = 0
-print "... done"
+print("... done")
tableArgs = {'tdata': HH_sampleData['t'],
@@ -80,7 +80,7 @@
result = HH_thresh_ev.searchForEvents((0, 15))
HH_spike_t = result[0][0]
-print "HH spike time found at ", HH_spike_t
+print("HH spike time found at ", HH_spike_t)
class IF_spike_feat(qt_feature_leaf):
def _local_init(self):
@@ -128,7 +128,7 @@
## Parameter estimation for spike length
-print "\nParam est. for spike length ..."
RefactoringTool: Refactored ./PyDSTool/tests/pest_test1.py
RefactoringTool: Refactored ./PyDSTool/tests/objectdelete_test.py
RefactoringTool: Refactored ./PyDSTool/tests/numeric_diff_test.py
+print("\nParam est. for spike length ...")
if not pestData_thr['success']:
raise RuntimeError("Failure: will not continue")
@@ -162,7 +162,7 @@
IF_ic = IFmodel_splen('test', t_ic, ['v'])
IFmodel_splen.set(tdata=[t_ic, 12])
-print "\n----------------------"
+print("\n----------------------")
IFmodel_splen.set(ics={'v': IF_ic})
splen_feat = L2_feature_1D('splen', pars=args(t_samples=tmesh_ic,
@@ -192,7 +192,7 @@
ics={'v':-70, 'excited':0})
## Plot data
-print "Acquiring plot data"
+print("Acquiring plot data")
origline=plot(orig_pdata['t'], orig_pdata['v'])
origleg = "Un-fitted IF orbit"
IF_sampleData = []
--- ./PyDSTool/tests/pest_test1.py (original)
+++ ./PyDSTool/tests/pest_test1.py (refactored)
@@ -30,8 +30,8 @@
## Prepare goal ODE trajectory
-print 'Preparing goal trajectory from perturbed system (with k = ', \
- refpars['k'], ') ...'
+print('Preparing goal trajectory from perturbed system (with k = ', \
+ refpars['k'], ') ...')
xfn_refstr = "50-k*w+a*(2-t)*sin_input"
@@ -47,7 +47,7 @@
)
refODE = Generator.Vode_ODEsystem(refDSargs)
reftraj = refODE.compute('goal')
-print '... finished.\n'
+print('... finished.\n')
## Get plot data for goal orbit
@@ -57,8 +57,8 @@
## Parameter estimation
-print 'Estimating parameter k for fit (assuming initial condition for w)'
-print 'Goal value is k = ', refpars['k'], " ..."
+print('Estimating parameter k for fit (assuming initial condition for w)')
+print('Goal value is k = ', refpars['k'], " ...")
xfn_str = "50-k*w"
testDSargs = args(algparams={'init_step':0.02, 'strictopt':True},
@@ -104,13 +104,13 @@
pestData_par = pest_pars.run(parDict={'ftol': ftol,
'xtol':1e-3},
verbose=True)
-print '... finished in %.4f seconds\n' % (time.clock()-start_time)
+print('... finished in %.4f seconds\n' % (time.clock()-start_time))
bestFitModel_par = pestData_par['sys_sol']
## Initial condition estimation
-print "Estimating initial condition for w (assuming k is correct)"
-print "Goal value is w(0) = ", xic['w'], " ..."
+print("Estimating initial condition for w (assuming k is correct)")
+print("Goal value is w(0) = ", xic['w'], " ...")
modelArgs_ic = copy(testDSargs)
modelArgs_ic['ics'] = {'w': 0.0}
@@ -127,11 +127,11 @@
'xtol':1e-3},
verbose=True)
bestFitModel_ic = pestData_ic['sys_sol']
-print '... finished'
+print('... finished')
## Finish preparing plots
-print '\nPreparing plots'
+print('\nPreparing plots')
west_plotData_par = bestFitModel_par.sample('test_iface_traj', dt=0.02,
tlo=min(trange),
thi=max(trange),
--- ./PyDSTool/tests/objectdelete_test.py (original)
+++ ./PyDSTool/tests/objectdelete_test.py (refactored)
@@ -5,16 +5,16 @@
from PyDSTool import *
-print "Test object deletion and deletion of dynamically created class methods"
+print("Test object deletion and deletion of dynamically created class methods")
-var1 = Variable(Pointset(coordarray = array(range(10), float)*0.1,
- indepvararray = array(range(10), float)*0.5
+var1 = Variable(Pointset(coordarray = array(list(range(10)), float)*0.1,
+ indepvararray = array(list(range(10)), float)*0.5
), name='v1')
del var1
try:
- print var1
+ print(var1)
except NameError:
- print " ...passed"
+ print(" ...passed")
else:
raise AssertionError("Variable deletion unsuccessful")
--- ./PyDSTool/tests/numeric_diff_test.py (original)
+++ ./PyDSTool/tests/numeric_diff_test.py (refactored)
@@ -7,7 +7,7 @@
from PyDSTool import _num_types
from numpy import all
-print "Testing numerical differentiation using diff..."
+print("Testing numerical differentiation using diff...")
# Test scalar f
@@ -15,7 +15,7 @@
if isinstance(x, _num_types):
return 3*x*x
else:
- prinRefactoringTool: Refactored ./PyDSTool/tests/mapsystem_test.py
RefactoringTool: Refactored ./PyDSTool/tests/joe_pest.py
RefactoringTool: Refactored ./PyDSTool/tests/interp_vode_test.py
t type(x)
+ print(type(x))
raise TypeError
def f2(x):
@@ -98,5 +98,5 @@
df5_diffd = array(f5(y0pt)) + simplifyMatrixRepr(diff(f5, y0pt)*matrix(y1pt-y0pt).T)
assert alltrue([err < 0.01 for err in abs(df5_taylor-df5_diffd)])
-print " ...passed"
+print(" ...passed")
--- ./PyDSTool/tests/mapsystem_test.py (original)
+++ ./PyDSTool/tests/mapsystem_test.py (refactored)
@@ -30,22 +30,22 @@
DSargs.checklevel = 2
DSargs.inputs = datafn.variables
testmap = MapSystem(DSargs)
-print "params set => ", testmap.pars
-print "DS defined? => ", testmap.defined
-print "testmap.set(...)"
+print("params set => ", testmap.pars)
+print("DS defined? => ", testmap.defined)
+print("testmap.set(...)")
testmap.set(ics={'w': 3.0, 'v': 2.},
tdata=[10,400])
-print "traj1 = testmap.compute('traj1')"
+print("traj1 = testmap.compute('traj1')")
traj1 = testmap.compute('traj1')
-print "DS defined now? => ", testmap.defined
-print "traj1(25) => ", traj1(25)
-print "testmap.diagnostics.showWarnings() => "
+print("DS defined now? => ", testmap.defined)
+print("traj1(25) => ", traj1(25))
+print("testmap.diagnostics.showWarnings() => ")
testmap.diagnostics.showWarnings()
-print "\ntraj1.indepdomain => ", traj1.indepdomain
-print "traj1(30, ['aux_other']) => ", traj1(30, ['aux_other'])
-print "traj1(range(10,40)) => ", traj1(range(10,40))
+print("\ntraj1.indepdomain => ", traj1.indepdomain)
+print("traj1(30, ['aux_other']) => ", traj1(30, ['aux_other']))
+print("traj1(range(10,40)) => ", traj1(list(range(10,40))))
-print "\nNow adding a terminating co-ordinate threshold event at w=58..."
+print("\nNow adding a terminating co-ordinate threshold event at w=58...")
ev_args = {'name': 'threshold',
'eventtol': 1e-4,
'eventdelay': 1e-5,
@@ -55,14 +55,14 @@
'precise': False}
thresh_ev = Events.makePythonStateZeroCrossEvent('w', 58, 1, ev_args)
testmap.eventstruct.add(thresh_ev)
-print "Recomputing trajectory:"
-print "traj2 = testmap.compute('traj2')"
+print("Recomputing trajectory:")
+print("traj2 = testmap.compute('traj2')")
t0=clock()
traj2 = testmap.compute('traj2')
-print "Elapsed time =", clock()-t0
+print("Elapsed time =", clock()-t0)
assert testmap.getEventTimes()['threshold'] == [347.]
-print "\ntestmap.diagnostics.showWarnings() => "
+print("\ntestmap.diagnostics.showWarnings() => ")
testmap.diagnostics.showWarnings()
-print "\ntraj2.indepdomain.get() => ", traj2.indepdomain.get()
-print "traj2(traj2.indepdomain[1],'w') => ", traj2(traj2.indepdomain[1],'w')
-print "Tests passed."
+print("\ntraj2.indepdomain.get() => ", traj2.indepdomain.get())
+print("traj2(traj2.indepdomain[1],'w') => ", traj2(traj2.indepdomain[1],'w'))
+print("Tests passed.")
--- ./PyDSTool/tests/joe_pest.py (original)
+++ ./PyDSTool/tests/joe_pest.py (refactored)
@@ -122,8 +122,8 @@
est_parnames = ['gl', 'vl']
# parameter estimation
-print 'Starting Least Squares parameter estimation'
-print 'Goal pars are gl = ', est_pars_ref['gl'], ' vl = ', est_pars_ref['vl']
+print('Starting Least Squares parameter estimation')
+print('Goal pars are gl = ', est_pars_ref['gl'], ' vl = ', est_pars_ref['vl'])
pest_pars = LMpest(freeParams=est_parnames,
testModel=testModel,
context=c
@@ -135,10 +135,10 @@
'xtol':1e-3},
verbose=True
)
-print ' ... finished in %.3f seconds.\n' % (clock()-start)
+print(' ... finished in %.3f seconds.\n' % (clock()-start))
# Prepare plots
-print '\nPreparing plots'
+print('\nPreparing plots')
disp_dt = 0.05
##plotData_goal = reftraj.sample(['v'], disp_dt)
goalleg = "v original"
--- ./PyDSTool/tests/interp_vode_test.py (original)
+++ ./PyDSTool/tests/interp_vode_test.py (refactored)
@@ -14,28 +14,28 @@
from copy import copy
-print '-------- Test: InterpolateTable'
+print('-------- Test: InterpolateTable')
xnames = ['x1', 'x2']
timeData = array([0., 11., 20., 30.])
x1data = array([10.2, -1.4, 4.1, 6.])
x2data = array([0.1, 0.01, 0.RefactoringTool: Refactored ./PyDSTool/tests/interp_piecewise_test.py
RefactoringTool: Refactored ./PyDSTool/tests/interp_dopri_test.py
4, -0.8])
-print "names for variables: xnames = ", xnames
-print "timeData = ", timeData
-print "x1data = ", x1data
-print "x2data = ", x2data
+print("names for variables: xnames = ", xnames)
+print("timeData = ", timeData)
+print("x1data = ", x1data)
+print("x2data = ", x2data)
xData = makeDataDict(xnames, [x1data, x2data])
interptable = InterpolateTable({'tdata': timeData,
'ics': xData,
'name': 'interp'
})
itabletraj = interptable.compute('interp')
-print "interptable.variables['x1'](0.4) = ", interptable.variables['x1'](0.4), '\n'
-print "itabletraj(11, ['x1']) = ", itabletraj(11, ['x1']), " (preferred syntax)\n"
+print("interptable.variables['x1'](0.4) = ", interptable.variables['x1'](0.4), '\n')
+print("itabletraj(11, ['x1']) = ", itabletraj(11, ['x1']), " (preferred syntax)\n")
# ------------------------------------------------------------
-print '-------- Test: ODE system'
+print('-------- Test: ODE system')
wfn_str = '100 -(1+a)*w*heav(0.2-sin(t+1)) - special_erf(w) -2*itable -k*auxval1(t, w)*auxval2(y)'
yfn_str = '50 - (w/100)*y'
@@ -54,26 +54,26 @@
DSargs.ics = {'w': 30.0, 'y': 80}
DSargs.name = 'ODEtest'
-print "\n"
+print("\n")
info(DSargs)
-print "\n"
+print("\n")
testODE = Vode_ODEsystem(DSargs)
-print 'Integrating...'
+print('Integrating...')
start = clock()
testtraj = testODE.compute('test')
-print ' ... finished in %.3f seconds.\n' % (clock()-start)
+print(' ... finished in %.3f seconds.\n' % (clock()-start))
-print "\nTesting direct call to vector field function:"
-print """testODE.Rhs(0.3, {'w':10., 'y':0.3}, DSargs.pars,
- {'itable': itabletraj.variables['x1'](0.3)}) -->"""
-print testODE.Rhs(0.3, {'w':10., 'y':0.3}, DSargs.pars)
+print("\nTesting direct call to vector field function:")
+print("""testODE.Rhs(0.3, {'w':10., 'y':0.3}, DSargs.pars,
+ {'itable': itabletraj.variables['x1'](0.3)}) -->""")
+print(testODE.Rhs(0.3, {'w':10., 'y':0.3}, DSargs.pars))
plotData = testtraj.sample(dt=0.1)
yaxislabelstr = 'w, y, for k = ' + str(DSargs.pars['k'])
-print "\nTesting continued integration"
+print("\nTesting continued integration")
testODE.set(tdata=[10,20], inputs={'itable': itabletraj.variables['x2']})
testtraj2 = testODE.compute('test2', 'c')
plotData2 = testtraj2.sample(dt=0.1)
@@ -92,12 +92,12 @@
wline2=plot(plotData2['t'], plotData2['w'])
yline2=plot(plotData2['t'], plotData2['y'])
-print "\nContinued integration successfull if only two curves are visible"
-print "(possibly with multiple colours)"
+print("\nContinued integration successfull if only two curves are visible")
+print("(possibly with multiple colours)")
-print "\n--------------------------------------\ntestODE.showSpec() -->"
+print("\n--------------------------------------\ntestODE.showSpec() -->")
testODE.showSpec()
-print "testODE.showAuxFnSpec() -->"
+print("testODE.showAuxFnSpec() -->")
testODE.showAuxFnSpec()
show()
--- ./PyDSTool/tests/interp_piecewise_test.py (original)
+++ ./PyDSTool/tests/interp_piecewise_test.py (refactored)
@@ -8,8 +8,8 @@
from PyDSTool import *
-print 'Test InterpolateTable comparing piecewise-constant and piecewise-'
-print 'linear interpolation of sine function'
+print('Test InterpolateTable comparing piecewise-constant and piecewise-')
+print('linear interpolation of sine function')
timeData = linspace(0, 10, 30)
sindata = sin(timeData)
@@ -41,4 +41,4 @@
# plot(x, sin(x))
# show()
-print " ...passed"
+print(" ...passed")
--- ./PyDSTool/tests/interp_dopri_test.py (original)
+++ ./PyDSTool/tests/interp_dopri_test.py (refactored)
@@ -14,28 +14,28 @@
from copy import copy
-print '-------- Test: InterpolateTable'
+print('-------- Test: InterpolateTable')
xnames = ['x1', 'x2']
timeData = array([0., 11., 20., 30.])
x1data = array([10.2, -1.4, 4.1, 6.])
x2data = array([0.1, 0.01, 0.4, -0.8])
-print "names for variables: xnames = ", xnames
-print "timeData = ", timeData
-print "x1data = ", x1data
-print "x2daRefactoringTool: Refactored ./PyDSTool/tests/imprecise_event_test.py
RefactoringTool: Refactored ./PyDSTool/tests/impfn_test.py
ta = ", x2data
+print("names for variables: xnames = ", xnames)
+print("timeData = ", timeData)
+print("x1data = ", x1data)
+print("x2data = ", x2data)
xData = makeDataDict(xnames, [x1data, x2data])
interptable = InterpolateTable({'tdata': timeData,
'ics': xData,
'name': 'interp'
})
itabletraj = interptable.compute('interp')
-print "interptable.variables['x1'](0.4) = ", interptable.variables['x1'](0.4), '\n'
-print "itabletraj(11, ['x1']) = ", itabletraj(11, ['x1']), " (preferred syntax)\n"
+print("interptable.variables['x1'](0.4) = ", interptable.variables['x1'](0.4), '\n')
+print("itabletraj(11, ['x1']) = ", itabletraj(11, ['x1']), " (preferred syntax)\n")
# ------------------------------------------------------------
-print '-------- Test: ODE system'
+print('-------- Test: ODE system')
wfn_str = '100 -(1+a)*w*heav(0.2-sin(t+1)) -2*x1 -k*auxval1(t, w)*auxval2(y)'
yfn_str = '50 - (w/100)*y'
@@ -55,26 +55,26 @@
DSargs.ics = {'w': 30.0, 'y': 80}
DSargs.name = 'ODEtest'
-print "\n"
+print("\n")
info(DSargs)
-print "\n"
+print("\n")
testODE = Dopri_ODEsystem(DSargs)
-print 'Integrating...'
+print('Integrating...')
start = clock()
testtraj = testODE.compute('test')
-print ' ... finished in %.3f seconds.\n' % (clock()-start)
+print(' ... finished in %.3f seconds.\n' % (clock()-start))
-print "\nTesting direct call to vector field function:"
-print """testODE.Rhs(0.3, {'w':10., 'y':0.3}, DSargs.pars,
- {'itable': itabletraj.variables['x1'](0.3)}) -->"""
-print testODE.Rhs(0.3, {'w':10., 'y':0.3}, DSargs.pars)
+print("\nTesting direct call to vector field function:")
+print("""testODE.Rhs(0.3, {'w':10., 'y':0.3}, DSargs.pars,
+ {'itable': itabletraj.variables['x1'](0.3)}) -->""")
+print(testODE.Rhs(0.3, {'w':10., 'y':0.3}, DSargs.pars))
plotData = testtraj.sample(dt=0.1)
yaxislabelstr = 'w, y, for k = ' + str(DSargs.pars['k'])
-print "\nTesting continued integration -- with different input"
+print("\nTesting continued integration -- with different input")
testODE.set(tdata=[10,20], inputs={'x1': itabletraj.variables['x2']})
testtraj2 = testODE.compute('test2', 'c')
plotData2 = testtraj2.sample(dt=0.1)
@@ -101,9 +101,9 @@
assert allclose(warning[1][0], 14.44, 0.1), \
"Trajectory should have been truncated at approximately t = 14.44"
-print "\n--------------------------------------\ntestODE.showSpec() -->"
+print("\n--------------------------------------\ntestODE.showSpec() -->")
testODE.showSpec()
-print "testODE.showAuxFnSpec() -->"
+print("testODE.showAuxFnSpec() -->")
testODE.showAuxFnSpec()
show()
--- ./PyDSTool/tests/imprecise_event_test.py (original)
+++ ./PyDSTool/tests/imprecise_event_test.py (refactored)
@@ -34,7 +34,7 @@
ode.set(tdata=[0, 80])
traj = ode.compute('test')
-print 'Preparing plot'
+print('Preparing plot')
plotData = traj.sample(dt=0.1)
yaxislabelstr = 'x'
@@ -42,11 +42,11 @@
plt.xlabel('t')
vline=plot(plotData['t'], plotData['x'])
evt=ode.getEventTimes()['thresh_ev_imprec'][0]
-print "Event at", evt, "where x has value", traj(evt)
+print("Event at", evt, "where x has value", traj(evt))
if traj(evt,'x') != 40:
- print "Event occurred away from precise threshold: Test PASSED"
+ print("Event occurred away from precise threshold: Test PASSED")
else:
- print "Event occurred precisely on threshold value: Test FAILED"
+ print("Event occurred precisely on threshold value: Test FAILED")
raise RuntimeError
plot(evt, traj(evt, 'x'), 'ro')
show()
--- ./PyDSTool/tests/impfn_test.py (original)
+++ ./PyDSTool/tests/impfn_test.py (refactored)
@@ -9,7 +9,7 @@
from numpy.linalg import norm
from copy import copy
-print "Test implicit function as variable"
+print("Test implicit function as variable")
# 1D example: a half-circle using newton's method (secant method for estimating derivative)
# Change sign of 'y' initial condition to solve for other half-circle
fvarspecs = {"y": "t*t+y*y-r*r",
@@ -73,4 +RefactoringTool: Refactored ./PyDSTool/tests/imp_load_test.py
RefactoringTool: Refactored ./PyDSTool/tests/funcspec_tests.py
RefactoringTool: Refactored ./PyDSTool/tests/freefinger_noforce_radau.py
73,4 @@
saveObjects([testimp2d, traj2], 'temp_imp.pkl', force=True)
-print " ...passed"
+print(" ...passed")
--- ./PyDSTool/tests/imp_load_test.py (original)
+++ ./PyDSTool/tests/imp_load_test.py (refactored)
@@ -3,7 +3,7 @@
from PyDSTool import *
import os
-print "Implicit trajectory load test"
+print("Implicit trajectory load test")
impgen, imptraj = loadObjects('temp_imp.pkl')
assert impgen.xdomain['y'] == [-2, 2]
@@ -24,4 +24,4 @@
os.remove('temp_imp.pkl')
-print " ...passed"
+print(" ...passed")
--- ./PyDSTool/tests/funcspec_tests.py (original)
+++ ./PyDSTool/tests/funcspec_tests.py (refactored)
@@ -42,8 +42,8 @@
'codeinsert_start': """ print 'code inserted at start'""",
'targetlang': 'python'}
DSfuncspec = RHSfuncSpec(fsargs)
-print DSfuncspec._infostr(verbose=2)
-print "\nDSfuncspec.auxfns['Jacobian'] =>", DSfuncspec.auxfns['Jacobian'],"\n"
+print(DSfuncspec._infostr(verbose=2))
+print("\nDSfuncspec.auxfns['Jacobian'] =>", DSfuncspec.auxfns['Jacobian'],"\n")
## C version
fsargs_C = deepcopy(fsargs)
@@ -53,34 +53,34 @@
del fsargs_C['codeinsert_start']
del fsargs_C['codeinsert_end']
DSfuncspec_C = RHSfuncSpec(fsargs_C)
-print '\nC version of same specifications:\n', DSfuncspec_C._infostr(verbose=2)
-print "Dependencies are not calculated for C code in FuncSpec. If you use ModelSpec"
-print "to generate your models you will have that information there."
+print('\nC version of same specifications:\n', DSfuncspec_C._infostr(verbose=2))
+print("Dependencies are not calculated for C code in FuncSpec. If you use ModelSpec")
+print("to generate your models you will have that information there.")
-print "\nTesting re-targetting of funcspec using 'recreate' method..."
+print("\nTesting re-targetting of funcspec using 'recreate' method...")
dsc=DSfuncspec.recreate('c')
assert dsc.spec[0]==DSfuncspec_C.spec[0], " - FAILED"
-print " - PASSED.\n"
+print(" - PASSED.\n")
-print "\n============================================================="
-print "Test: wrapping delimiters around call arguments"
-print """ ... around first argument: wrapArgInCall(fs, 'initcond', '"')"""
+print("\n=============================================================")
+print("Test: wrapping delimiters around call arguments")
+print(""" ... around first argument: wrapArgInCall(fs, 'initcond', '"')""")
fs = 'initcond(v,p)'
-print fs, " -- wrapped to: ", wrapArgInCall(fs, 'initcond', '"'), "\n"
-print """ ... around second argument: wrapArgInCall(fs,'initcond','"',argnums=[1])"""
-print fs, " -- wrapped to: ", wrapArgInCall(fs, 'initcond', '"', argnums=[1]), "\n"
-print """ ... extra braces to both arguments: wrapArgInCall(fs,'initcond','[',']',[0,1])"""
-print fs, " -- wrapped to: ", wrapArgInCall(fs, 'initcond', '[', ']', [0,1]), "\n"
+print(fs, " -- wrapped to: ", wrapArgInCall(fs, 'initcond', '"'), "\n")
+print(""" ... around second argument: wrapArgInCall(fs,'initcond','"',argnums=[1])""")
+print(fs, " -- wrapped to: ", wrapArgInCall(fs, 'initcond', '"', argnums=[1]), "\n")
+print(""" ... extra braces to both arguments: wrapArgInCall(fs,'initcond','[',']',[0,1])""")
+print(fs, " -- wrapped to: ", wrapArgInCall(fs, 'initcond', '[', ']', [0,1]), "\n")
-print "\nTest combo of addArgToCalls and wrapArgInCall with embedded calls:"
+print("\nTest combo of addArgToCalls and wrapArgInCall with embedded calls:")
fs2 = "1/zeta(y_rel(y,initcond(y)+initcond(z)),z-initcond(x))+zeta(0.)"
-print fs2, "\n"
+print(fs2, "\n")
fs2_p = addArgToCalls(fs2, ['zeta','y_rel','initcond','nothing'], "p")
-print " ** becomes **"
-print fs2_p, "\n"
+print(" ** becomes **")
+print(fs2_p, "\n")
fs2_p = wrapArgInCall(fs2_p, 'initcond', '"')
-print " ** becomes **"
-print fs2_p
+print(" ** becomes **")
+print(fs2_p)
from PyDSTool.parseUtils import proper_match
s='1 +abc13 + abc'
--- ./PyDSTool/tests/freefinger_noforce_radau.py (original)
+++ ./PyDSTool/tests/freefinger_noforce_radau.py (refactored)
@@ -78,7 +78,7 @@
if __name__=='__main__':
- print '-------- Finger Test'
+ print('-------- FingerRefactoringTool: Refactored ./PyDSTool/tests/forced_spring.py
RefactoringTool: Refactored ./PyDSTool/tests/fingermodel_vode.py
RefactoringTool: Refactored ./PyDSTool/tests/fingermodel_auxvartest.py
Test')
# spatial units in mm, angular units in radians
# Ix = 1/12 * mx * lx^2
# radii were 10mm, 8mm, 7mm
@@ -116,21 +116,21 @@
pars['m2'] = m2
pars['m3'] = m3
- print "Making Radau finger model using mass matrix"
+ print("Making Radau finger model using mass matrix")
finger = make_finger_massmatrix('freefinger_noforce_massmatrix', par_args, ic_args)
finger.set(tdata=[0, 3])
# saveObjects(finger, 'fingergen', force=True)
- print 'Integrating...'
+ print('Integrating...')
start = clock()
ftraj = finger.compute('test')
- print 'Computed trajectory in %.3f seconds.\n' % (clock()-start)
+ print('Computed trajectory in %.3f seconds.\n' % (clock()-start))
plotData = ftraj.sample(dt=.001)
exportPointset(plotData, {'varvals': ['phi1','phi2','phi3'], 'tvals':'t'},
ext='dat')
- print 'Preparing plot'
+ print('Preparing plot')
yaxislabelstr = 'angles'
plt.ylabel(yaxislabelstr)
--- ./PyDSTool/tests/forced_spring.py (original)
+++ ./PyDSTool/tests/forced_spring.py (refactored)
@@ -133,6 +133,6 @@
assert abs(evts['sw_ON']['t'][0] - p['t_on']) < evtol, "Event detection was inaccurate"
show()
-print "Red trajectory shows unforced behavior. Green trajectory shows brief forcing..."
-print "Now zoom in closely, to roughly the interval t = [%.3f, %.3f]"%(pars['t_on']-0.1,pars['t_on']+0.1)
-print "The solid trajectory switches within +/-%.5f of the intended switch time\nt_on=%.2f"%(on_event_args['eventtol'],pars['t_on'])
+print("Red trajectory shows unforced behavior. Green trajectory shows brief forcing...")
+print("Now zoom in closely, to roughly the interval t = [%.3f, %.3f]"%(pars['t_on']-0.1,pars['t_on']+0.1))
+print("The solid trajectory switches within +/-%.5f of the intended switch time\nt_on=%.2f"%(on_event_args['eventtol'],pars['t_on']))
--- ./PyDSTool/tests/fingermodel_vode.py (original)
+++ ./PyDSTool/tests/fingermodel_vode.py (refactored)
@@ -69,7 +69,7 @@
'eventdelay': 1e-6,
'starttime': 0,
'term': True,
- 'name': 'deriv'}, ['a'], pd.keys())
+ 'name': 'deriv'}, ['a'], list(pd.keys()))
DSargs = {'varspecs': specdict_contact,
'fnspecs': fnspecs,
'xdomain': {'a': [0, 2*pi], 'incontact': 1},
@@ -83,7 +83,7 @@
'events': [tang_ev, d_ev],
}
ode = embed(Generator.Vode_ODEsystem(DSargs), tdata=[0,200])
- print ode.query('ics')
+ print(ode.query('ics'))
ode_MI = intModelInterface(ode)
@@ -156,15 +156,15 @@
fullmodel = makeModel3(pars, dt=0.01)
-print "Computing trajectory"
-print "Using verboselevel=2 for debug-level info ..."
+print("Computing trajectory")
+print("Using verboselevel=2 for debug-level info ...")
fullmodel.compute(trajname='run1',
tdata=[0, 3.0],
ics={'a': pars['alpha0'],
'incontact': 1},
verboselevel=2)
-print "\nPlotting output"
+print("\nPlotting output")
plotData = fullmodel.sample('run1', coords=['a','ad'],
dt=0.01)
afig = plt.figure()
--- ./PyDSTool/tests/fingermodel_auxvartest.py (original)
+++ ./PyDSTool/tests/fingermodel_auxvartest.py (refactored)
@@ -28,13 +28,13 @@
dtraj1 = decay.compute('testtraj1')
decay.set(ics={'a': 0.5})
dtraj2 = decay.compute('testtraj2')
-print "To test that separate trajectories output from generator actually"
-print " have different values we compare two traj's values"
-print "These should be different:"
+print("To test that separate trajectories output from generator actually")
+print(" have different values we compare two traj's values")
+print("These should be different:")
result = dtraj1.variables['a'](0.2) != dtraj2.variables['a'](0.2)
-print "dtraj1.variables['a'](0.2) != dtraj2.variables['a'](0.2)? =>", \
- result
-print "This demonstrates avoiding an insRefactoringTool: Refactored ./PyDSTool/tests/expfn_test.py
RefactoringTool: Refactored ./PyDSTool/tests/embedded_map_test.py
RefactoringTool: Refactored ./PyDSTool/tests/dopri_event_test.py
RefactoringTool: Refactored ./PyDSTool/tests/basic_gen_tests_C.py
RefactoringTool: Refactored ./PyDSTool/tests/basic_gen_tests.py
ufficiently deep 'copy' of new"
-print " Variables into new trajectories whereby new Variables overwrite"
-print " old ones in other Trajectory objects"
+print("dtraj1.variables['a'](0.2) != dtraj2.variables['a'](0.2)? =>", \
+ result)
+print("This demonstrates avoiding an insufficiently deep 'copy' of new")
+print(" Variables into new trajectories whereby new Variables overwrite")
+print(" old ones in other Trajectory objects")
assert result
--- ./PyDSTool/tests/expfn_test.py (original)
+++ ./PyDSTool/tests/expfn_test.py (refactored)
@@ -10,7 +10,7 @@
from PyDSTool import *
-print "Test of Explicit and Implicit Function generators, global time, and deletion"
+print("Test of Explicit and Implicit Function generators, global time, and deletion")
ev_args = {'name': 'threshold',
'eventtol': 1e-4,
@@ -64,4 +64,4 @@
del sintraj1
assert dv != dir(Variable)
-print " ...passed"
+print(" ...passed")
--- ./PyDSTool/tests/embedded_map_test.py (original)
+++ ./PyDSTool/tests/embedded_map_test.py (refactored)
@@ -84,7 +84,7 @@
map.showSpec()
test_traj = map.compute('test', map_ics)
-print test_traj.sample(), "\n"
+print(test_traj.sample(), "\n")
def return_map(ic):
return map.compute('pdc_shoot', ic)(1)
@@ -96,26 +96,26 @@
## print "\nfp_residual: y0 = ", y0
v = return_map({'y': y0})
## plot(0, y0, 'k.')
- print v
+ print(v)
return v-ic[0]
-print "Finding fixed point of return map as function of initial condition"
+print("Finding fixed point of return map as function of initial condition")
# Equally efficient alternatives to shoot for f.p. solution
y0_guess = map_ics['y']
sol_pdc = minpack.fsolve(fp_residual, array([y0_guess]), xtol=1e-6)
-print "sol_pdc = ", sol_pdc
+print("sol_pdc = ", sol_pdc)
-print "Plotting (x,y) limit cycle of oscillator with Poincare section"
-print " given by x=0"
+print("Plotting (x,y) limit cycle of oscillator with Poincare section")
+print(" given by x=0")
traj, pts = getTraj({'x':0, 'y':-sol_pdc}, {'m':1}, t1=10, termFlag=False)
traj, pts = getTraj({'x':0, 'y':-sol_pdc}, {'m':14}, t1=10, termFlag=False)
map.set(ics={'y':sol_pdc})
-print "Initializing PyCont to follow x=0 crossing as parameter m varied:"
+print("Initializing PyCont to follow x=0 crossing as parameter m varied:")
pc=ContClass(map)
pcargs=args(name='FPu', type='FP-C',
@@ -128,13 +128,13 @@
)
pc.newCurve(pcargs)
-print "\nRunning PyCont forward"
+print("\nRunning PyCont forward")
pc['FPu'].forward()
-print "\n\nSolution is:\n", repr(pc['FPu'].sol)
+print("\n\nSolution is:\n", repr(pc['FPu'].sol))
s=pc['FPu'].sol
-print "Plotting line of fixed points of x vs parameter m ..."
+print("Plotting line of fixed points of x vs parameter m ...")
figure()
plot(s['m'],s['y'])
--- ./PyDSTool/tests/dopri_event_test.py (original)
+++ ./PyDSTool/tests/dopri_event_test.py (refactored)
@@ -57,13 +57,13 @@
DSargs.events = [thresh_ev_nonterm,thresh_ev_term]
testODE = Dopri_ODEsystem(DSargs)
-print "Computing trajectory:"
-print "traj = testODE.compute('traj')"
+print("Computing trajectory:")
+print("traj = testODE.compute('traj')")
traj = testODE.compute('traj')
-print "\ntestODE.diagnostics.showWarnings() => "
+print("\ntestODE.diagnostics.showWarnings() => ")
testODE.diagnostics.showWarnings()
-print "\ntraj.indepdomain.get() => ", traj.indepdomain.get()
+print("\ntraj.indepdomain.get() => ", traj.indepdomain.get())
indep1 = traj.indepdomain[1]
assert indep1 < 1.15 and indep1 > 1.13
mon_evs_found = testODE.getEvents()['monitor']
--- ./PyDSTool/tests/basic_gen_tests_C.py (original)
+++ ./PyDSTool/tests/basic_gen_tests_C.py (refactored)
@@ -1,6 +1,6 @@
from PyDSTool import *
-print "Basic generator tests for C-based vector fields..."
+print("Basic generator tests for C-based vector fields...")
fnspecs = {'testif': (['x'], 'if(x<0.0,0.0,x)'),
@@ -42,4 +42,4 @@
traj = tm2.compute('test')
assert allclose(tm2.Rhs(0, {'y0':0, 'y1': 0.3, 'y2': 5}), array([-11. , 2.3+pi, 0. ]))
-print " ...passed"
+print(" ...passed")
--- ./PyDSTool/RefactoringTool: No changes to ./PyDSTool/tests/Tutorial_linear.py
RefactoringTool: Refactored ./PyDSTool/tests/Tutorial_compneuro.py
RefactoringTool: Refactored ./PyDSTool/tests/Tutorial_VdP.py
RefactoringTool: Refactored ./PyDSTool/tests/Tutorial_SymbolicJac.py
tests/basic_gen_tests.py (original)
+++ ./PyDSTool/tests/basic_gen_tests.py (refactored)
@@ -1,6 +1,6 @@
from PyDSTool import *
-print "Basic generator tests..."
+print("Basic generator tests...")
# Test: InterpolateTable
xnames = ['x1', 'x2']
@@ -28,7 +28,7 @@
# print "ltabletraj(0.4) ="
try:
ltabletraj(0.4)
-except ValueError, e:
+except ValueError as e:
pass
# print "... ltabletraj(0.4) did not succeed because ", e
# print "(0.4 is not in the tdata array)"
@@ -105,11 +105,11 @@
sintraj = sin_gen.compute('sinewave')
assert sintraj(0.0, checklevel=2)['s'] - 0.38941834 < 1e-7
-print "Expect problem calling at t=0.8..."
+print("Expect problem calling at t=0.8...")
try:
sintraj(0.8, checklevel=2)
-except PyDSTool_BoundsError, e:
- print "... correctly raised error: ", e
+except PyDSTool_BoundsError as e:
+ print("... correctly raised error: ", e)
else:
raise AssertionError
# print "Set limits properly now, to [-1., 1.] ..."
@@ -171,4 +171,4 @@
traj = tm3.compute('test')
assert allclose(tm3.Rhs(0, {'x': 0}), 8*pi)
-print " ...passed"
+print(" ...passed")
--- ./PyDSTool/tests/Tutorial_compneuro.py (original)
+++ ./PyDSTool/tests/Tutorial_compneuro.py (refactored)
@@ -163,7 +163,7 @@
HH_model = model_HH.getModel()
verboselevel = 2
-print "Computing trajectory using verbosity level %d..."%verboselevel
+print("Computing trajectory using verbosity level %d..."%verboselevel)
## don't extend tdata past the range given to the ModelConstructor
HH_model.compute(trajname='test',
tdata=[0, 100],
--- ./PyDSTool/tests/Tutorial_VdP.py (original)
+++ ./PyDSTool/tests/Tutorial_VdP.py (refactored)
@@ -98,7 +98,7 @@
traj = vdp.compute('eps_%.4f'%eps)
pts = traj.sample()
event_dict = pts.labels.by_label['Event:event_x_a']
- indices = np.sort(event_dict.keys())
+ indices = np.sort(list(event_dict.keys()))
# assume there are at least 3 indices!
# pick the last two that go through the same point
ix1, ix2, ix3 = indices[-3:]
--- ./PyDSTool/tests/Tutorial_SymbolicJac.py (original)
+++ ./PyDSTool/tests/Tutorial_SymbolicJac.py (refactored)
@@ -52,37 +52,37 @@
'term': True}, [y0])
testODE = Vode_ODEsystem(DSargs)
-print "Defined the following internal Python function for Jacobian:"
-print testODE.funcspec.auxfns['Jacobian'][0]
+print("Defined the following internal Python function for Jacobian:")
+print(testODE.funcspec.auxfns['Jacobian'][0])
-print "\nOutput at exponentially larger subsequent time steps (with event detection!):\n"
+print("\nOutput at exponentially larger subsequent time steps (with event detection!):\n")
tvals = [0.4*10**i for i in range(0,12)]
t0 = 0.
for t1 in tvals:
dt = t1-t0
- print "\n===============================================\nAt t=",
- print t1, "using dt =", dt
+ print("\n===============================================\nAt t=", end=' ')
+ print(t1, "using dt =", dt)
testODE.set(tdata=[t0,t1], algparams={'init_step': dt})
if t0 >0.:
- print testODE._solver.y
+ print(testODE._solver.y)
traj = testODE.compute('test', 'c') # c for continue (acts as f first time)
try:
- print traj(t1)
+ print(traj(t1))
except ValueError:
- print "\n----------"
+ print("\n----------")
testODE.diagnostics.showWarnings()
- print traj(traj.indepdomain[1])
- print "----------\n"
+ print(traj(traj.indepdomain[1]))
+ print("----------\n")
t0 = traj.indepdomain[1]
else:
t0 = t1
-print "\nCompare results with the output directly from the scipy_ode.py test"
-print "(up to the point where the terminal event was found)."
-print "The values from a test integration performed with scipy_ode.py " \
- + "are listed in the comments at the end of this script"
+print("\nCompare results with the output directly from the scipy_ode.py test")
+print("(up to the point where the terminal event was found).")
+print("The values from a test integration performed with scRefactoringTool: Refactored ./PyDSTool/tests/Tutorial_PredatorPrey.py
RefactoringTool: No changes to ./PyDSTool/tests/Tutorial_LorenzMap.py
RefactoringTool: No changes to ./PyDSTool/tests/Tutorial_Calcium.py
RefactoringTool: Refactored ./PyDSTool/tests/Symbolic_test.py
ipy_ode.py " \
+ + "are listed in the comments at the end of this script")
## At t=0.0 y=[ 1. 0. 0.]
## At t=0.4 y=[ 9.85172114e-001 3.38639538e-005 1.47940221e-002]
--- ./PyDSTool/tests/Tutorial_PredatorPrey.py (original)
+++ ./PyDSTool/tests/Tutorial_PredatorPrey.py (refactored)
@@ -62,10 +62,10 @@
PCargs.verbosity = 2
PC.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PC['EQ1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs.name = 'HO1'
PCargs.type = 'H-C2'
@@ -77,10 +77,10 @@
PCargs.SaveEigen = True
PC.newCurve(PCargs)
-print 'Computing Hopf curve...'
+print('Computing Hopf curve...')
start = clock()
PC['HO1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs = args(name = 'FO1', type = 'LP-C')
PCargs.initpoint = 'HO1:ZH1'
@@ -101,14 +101,14 @@
hopfs = Pointset(indepvararray=PC['HO1'].sol['k'], indepvarname='k',
coorddict=hopfs_unparam.todict())
ix0, ix1 = hopfs.find(9)
-print "k values found around 9.0 are %.3f, %.3f" % ( hopfs['k'][ix0], hopfs['k'][ix1] )
+print("k values found around 9.0 are %.3f, %.3f" % ( hopfs['k'][ix0], hopfs['k'][ix1] ))
# Arbitrarily choose closest lower index to check stability
-print "Hopf point found for k = %.3f is stable?" % hopfs['k'][ix0],
+print("Hopf point found for k = %.3f is stable?" % hopfs['k'][ix0], end=' ')
if PC['HO1'].sol[ix0].labels['H']['stab'] == 'N':
- print "No"
+ print("No")
else:
- print "Yes"
+ print("Yes")
# Create interpolatable curve from the pointset
hopfs_curve = pointset_to_traj(hopfs)
--- ./PyDSTool/tests/Symbolic_test.py (original)
+++ ./PyDSTool/tests/Symbolic_test.py (refactored)
@@ -90,7 +90,7 @@
assert testq() == 'a'
assert str(testq.eval(a=3)) == '3'
q = QuantSpec('q', 'zeta(yrel(y,initcond(y)),z)-1')
-print q.eval({})
+print(q.eval({}))
assert 'initcond' in str(q.eval({}))
q2=QuantSpec('q','Exp(-spikeTable+b)/k')
assert 'spikeTable' in q2.freeSymbols
@@ -125,21 +125,21 @@
assert c.isDefined() == False
c.add(x)
-print c.freeSymbols, c.isDefined()
+print(c.freeSymbols, c.isDefined())
c.add(az)
-print c.freeSymbols, c.isDefined()
+print(c.freeSymbols, c.isDefined())
c.add(w)
-print c.freeSymbols, c.isDefined()
-
-print "\n"
+print(c.freeSymbols, c.isDefined())
+
+print("\n")
c.compileFuncSpec()
-print c.funcSpecDict
-
-print "\n"
+print(c.funcSpecDict)
+
+print("\n")
empty_fn = Fun('1+exp(1)', [], 'dumb_fn')
-print empty_fn()
+print(empty_fn())
q = Par('qpar')
y = Var(QuantSpec('rel', 'v+p'), domain=[0,1])
@@ -165,160 +165,160 @@
a = myNode('sys1')
a.add([f,p,y])
-print a.isDefined(True)
+print(a.isDefined(True))
a.add(c)
-print a.freeSymbols, a.isDefined(), a.isComplete()
+print(a.freeSymbols, a.isDefined(), a.isComplete())
a.add(d)
-print a.freeSymbols, a.isDefined(), a.isComplete()
+print(a.freeSymbols, a.isDefined(), a.isComplete())
a.add(d2)
-print a.freeSymbols, a.isDefined(), a.isComplete()
+print(a.freeSymbols, a.isDefined(), a.isComplete())
a.add(v)
-print "Added v"
-print a.freeSymbols, a.isDefined(), a.isComplete()
-print "Removed v"
+print("Added v")
+print(a.freeSymbols, a.isDefined(), a.isComplete())
+print("Removed v")
a.remove(v)
-print a.freeSymbols, a.isDefined(), a.isComplete()
+print(a.freeSymbols, a.isDefined(), a.isComplete())
a.add([z,ipar])
-print a.freeSymbols, a.isDefined(), a.isComplete()
-print "\na._registry --> "
-print a._registry
-print "Re-added v"
+print(a.freeSymbols, a.isDefined(), a.isComplete())
+print("\na._registry --> ")
+print(a._registry)
+print("Re-added v")
a.add(v)
-print a.freeSymbols, a.isDefined(), a.isComplete()
-print "\nv in a -->", v in a
-
-print "\n"
+print(a.freeSymbols, a.isDefined(), a.isComplete())
+print("\nv in a -->", v in a)
+
+print("\n")
try:
a.compileFuncSpec()
test = True
- print "\nWas able to add a non-parameter as a free name to an"
- print "auxiliary function definition! This should not have happened!"
-except TypeError, errinfo:
- print "\nSuccessfully could not add a non-parameter as a free name"
- print "in an auxiliary function"
- print "Error was: ", errinfo
+ print("\nWas able to add a non-parameter as a free name to an")
+ print("auxiliary function definition! This should not have happened!")
+except TypeError as errinfo:
+ print("\nSuccessfully could not add a non-parameter as a free name")
+ print("in an auxiliary function")
+ print("Error was: ", errinfo)
test = False
assert not test
a.remove(['leaf2.qfunc_dummy', 'leaf2.q_notpar'])
-print "--------- sys1: funcSpecDict ---------------------"
+print("--------- sys1: funcSpecDict ---------------------")
a.compileFuncSpec()
info(a.funcSpecDict)
-print "\n\n------------- Flatten spec with unravelling\n"
-print "\n\ninfo(a.flattenSpec()) --> \n"
+print("\n\n------------- Flatten spec with unravelling\n")
+print("\n\ninfo(a.flattenSpec()) --> \n")
info(a.flattenSpec(globalRefs=['t']), "Model specification")
-print "\n\n------------- Flatten spec with no unravelling\n"
-print "\n\ninfo(a.flattenSpec(False, globalRefs=['t'])) --> \n"
+print("\n\n------------- Flatten spec with no unravelling\n")
+print("\n\ninfo(a.flattenSpec(False, globalRefs=['t'])) --> \n")
info(a.flattenSpec(False, globalRefs=['t']), "Model specification")
-print "\n\nDemos for functions (results are strings):\n"
+print("\n\nDemos for functions (results are strings):\n")
h = f(p, -x)
z = QuantSpec('zero','0')
-print "h = f(p, -x) --> ", h
-print "z = QuantSpec('zero','0') --> ", z
-print "f(g(3)*1,h) --> ", f(g(3)*1,h)
-print "f(g(p),h) --> ", f(g(p),h)
-print "f(g(p),0*h) --> ", f(g(p),0*h)
-print "f(g(x),h+z) --> ", f(g(x),h+z)
+print("h = f(p, -x) --> ", h)
+print("z = QuantSpec('zero','0') --> ", z)
+print("f(g(3)*1,h) --> ", f(g(3)*1,h))
+print("f(g(p),h) --> ", f(g(p),h))
+print("f(g(p),0*h) --> ", f(g(p),0*h))
+print("f(g(x),h+z) --> ", f(g(x),h+z))
# e is the math constant, but it doesn't evaluate to a float!
-print "f(g(x()),(e+h)/2) --> ", f(g(x()),(e+h)/2)
-print "f(g(x()),-h) --> ", f(g(x()),-h)
-print "f(g(x()),.5-h+0) --> ", f(g(x()),.5-h+0)
-print "Sin(pi+q) --> ", Sin(pi+q)
+print("f(g(x()),(e+h)/2) --> ", f(g(x()),(e+h)/2))
+print("f(g(x()),-h) --> ", f(g(x()),-h))
+print("f(g(x()),.5-h+0) --> ", f(g(x()),.5-h+0))
+print("Sin(pi+q) --> ", Sin(pi+q))
qsin=QuantSpec('qsin','zv-sin(beta)')
assert str(qsin.eval()) == 'zv-sin(beta)'
-print "\n\nDemos for local scope evaluation and **:\n"
-print "q=Var('xv+1','qv')"
-print "x=Var('3','xv')"
+print("\n\nDemos for local scope evaluation and **:\n")
+print("q=Var('xv+1','qv')")
+print("x=Var('3','xv')")
q=Var('xv+1','qv')
x=Var('3','xv')
sc1 = str(q.eval()) == '4'
-print "q.eval() == 4? ", sc1
+print("q.eval() == 4? ", sc1)
assert sc1
-print "a=x/q"
+print("a=x/q")
a=x/q
sc2 = str(a) == 'xv/qv'
-print "a == xv/qv? ", sc2
+print("a == xv/qv? ", sc2)
assert sc2
sc3 = str(a.eval())=='0.75'
-print "a.eval() == 0.75? ", sc3
+print("a.eval() == 0.75? ", sc3)
assert sc3
sc4 = str(a.eval(xv=5))=='5/qv'
-print "a.eval(xv=5) == 5/q? ", sc4
+print("a.eval(xv=5) == 5/q? ", sc4)
assert sc4
sc5 = (str(a.eval(xv=5,qv=q())),'0.83333333333333337')
assert_approx_equal(*sc5)
-print "assert_approx_equal(%s,%s)" % sc5
+print("assert_approx_equal(%s,%s)" % sc5)
sc6 = (str(a.eval({'xv': 10, 'qv': q()})),'0.90909090909090906')
-print "assert_approx_equal(%s,%s)" % sc6
+print("assert_approx_equal(%s,%s)" % sc6)
assert_approx_equal(*sc6)
-print "qs=QuantSpec('qsv','xsv+1')"
-print "xs=QuantSpec('xsv','3')"
+print("qs=QuantSpec('qsv','xsv+1')")
+print("xs=QuantSpec('xsv','3')")
qs=QuantSpec('qsv','xsv+1')
xs=QuantSpec('xsv','3')
qse = qs.eval()
qt1 = str(qse) == '4'
-print "qs.eval() == 4? ", qt1
+print("qs.eval() == 4? ", qt1)
assert qt1
assert qse.tonumeric() == 4
-print "asq = xs/qs"
+print("asq = xs/qs")
asq=xs/qs
qt2 = str(asq) == '3/(xsv+1)'
-print "asq == 3/(xsv+1)? ", qt2
+print("asq == 3/(xsv+1)? ", qt2)
assert qt2
qt3 = str(asq.eval()) == '0.75'
-print "as.evRefactoringTool: Refactored ./PyDSTool/tests/Symbolic_Diff_test.py
al() == 0.75? ", qt3
+print("as.eval() == 0.75? ", qt3)
assert qt3
ps = asq**xs
-print "ps = as**xs"
+print("ps = as**xs")
qt4 = str(ps) == 'Pow(3/(xsv+1),3)'
-print "ps == Pow(3/(xsv+1),3)? ", qt4
+print("ps == Pow(3/(xsv+1),3)? ", qt4)
assert qt4
qt5 = str(ps.eval()) == str(0.75**3)
-print "ps.eval() == 0.421875? ", qt5
+print("ps.eval() == 0.421875? ", qt5)
assert qt5
-print "sq=QuantSpec('sv','sin(xsv)')"
-print "s2q=QuantSpec('s2v','Sin(xv)')"
+print("sq=QuantSpec('sv','sin(xsv)')")
+print("s2q=QuantSpec('s2v','Sin(xv)')")
sq=QuantSpec('sv','sin(xsv)')
s2q=QuantSpec('s2v','Sin(xv)')
-print "sq.eval() --> ", sq.eval()
-print "s2q.eval() --> ", s2q.eval()
+print("sq.eval() --> ", sq.eval())
+print("s2q.eval() --> ", s2q.eval())
assert sq.eval().tonumeric() == s2q.eval().tonumeric()
assert sq[:] == ['sin','(','xsv',')']
-print "\n\nDemos for multiple quantity definitions:\n"
+print("\n\nDemos for multiple quantity definitions:\n")
mp=QuantSpec('p','a + 3*z[4*i-2]')
m=Var(mp, 'z[i,2,5]', specType='RHSfuncSpec')
v=Var('3*z[i-1]+z4-i', 'z[i,1,5]', specType='RHSfuncSpec')
-print "mp=QuantSpec('p','a + 3*z[4*i-2]')"
-print "m=Var(mp, 'z[i,2,5]', specType='RHSfuncSpec')"
-print "v=Var('3*z[i-1]+z4-i', 'z[i,1,5]', specType='RHSfuncSpec')"
-print "v[3] -->", v[3]
+print("mp=QuantSpec('p','a + 3*z[4*i-2]')")
+print("m=Var(mp, 'z[i,2,5]', specType='RHSfuncSpec')")
+print("v=Var('3*z[i-1]+z4-i', 'z[i,1,5]', specType='RHSfuncSpec')")
+print("v[3] -->", v[3])
assert str(v[3])=='z3'
-print "v.freeSymbols -->", v.freeSymbols
+print("v.freeSymbols -->", v.freeSymbols)
assert v.freeSymbols == ['z0']
-print "\nModelSpec a already contains 'z0', which was defined as part of"
-print "a multiple quantity definition, so check that attempting to add"
-print "v to a results in an error ..."
+print("\nModelSpec a already contains 'z0', which was defined as part of")
+print("a multiple quantity definition, so check that attempting to add")
+print("v to a results in an error ...")
try:
a.add(v)
- print "v was successfully added -- test failed"
+ print("v was successfully added -- test failed")
except:
- print "v was rejected - test passed"
-print "\nTest of eval method, e.g. on a function f(s,t)..."
-print "f.eval(s='1', t='t_val') -->", f.eval(s='1', t='t_val')
-print "f.eval(s=1, t='t_val', p=0.5) -->", f.eval(s=1, t='t_val', p=0.5)
-print "\nTesting convertPowers():"
+ print("v was rejected - test passed")
+print("\nTest of eval method, e.g. on a function f(s,t)...")
+print("f.eval(s='1', t='t_val') -->", f.eval(s='1', t='t_val'))
+print("f.eval(s=1, t='t_val', p=0.5) -->", f.eval(s=1, t='t_val', p=0.5))
+print("\nTesting convertPowers():")
cp_tests = ["phi1dot^m3", "1+phi1dot^m3*s",
"phi1dot**m3", "1+phi1dot**m3*s",
"sin(x^3)**4", "(2/3)^2.5", "3^cos(x)-pi",
"3^(cos(x)-pi)", "2^(sin(y**p))"]
for spec in cp_tests:
- print spec, " --> ", convertPowers(spec)
+ print(spec, " --> ", convertPowers(spec))
qc=QuantSpec('t', "a+coot+b/'coot'")
@@ -326,13 +326,13 @@
coot=QuantSpec('coot', "1.05")
assert str(qc.eval()) == 'a+1.05+b/"coot"'
-print "\nTest of function calling with argument names that clash with"
-print "bound names inside the function."
+print("\nTest of function calling with argument names that clash with")
+print("bound names inside the function.")
x0=Var('x0')
x1=Var('x1')
x2=Var('x2')
F=Fun([x0*x2,x0*5,x2**0.5], [x0,x1,x2], 'F')
-print "F=Fun([x0*x2,x0*5,x2**0.5], [x0,x1,x2], 'F')"
-print "F(3,2,Sin(x0))) = [3*Sin(x0),15,Pow(Sin(x0),0.5)] ..."
-print " ... even though x0 is a bound name inside definition of F"
+print("F=Fun([x0*x2,x0*5,x2**0.5], [x0,x1,x2], 'F')")
+print("F(3,2,Sin(x0))) = [3*Sin(x0),15,Pow(Sin(x0),0.5)] ...")
+print(" ... even though x0 is a bound name inside definition of F")
assert str(F(3,2,Sin(x0)))=='[3*Sin(x0),15,Pow(Sin(x0),0.5)]'
--- ./PyDSTool/tests/Symbolic_Diff_test.py (original)
+++ ./PyDSTool/tests/Symbolic_Diff_test.py (refactored)
@@ -11,7 +11,7 @@
assert DiffStr('x-(4*x*y)/(1+x*x)','x') == \
'1-4*(y)/(1+x*x)+(4*x*y)*2*x*pow((1+x*x),-2)'
-print "Showing the variety of ways that symbolic Diff() can be used:"
+print("Showing the variety of ways that symbolic Diff() can be used:")
f1 = '[-3*x**2+2*(x+y),-y/2]'
f2 = ['-3*x**2+2*(x+y)','-y/2']
@@ -21,26 +21,26 @@
f4 = ['-3*x**2.+2*(x+y)','-y/2.']
xx = QuantSpec('dummy','x')
-print "The following strings should all be identical"
-print Diff(f1,'x')
-print Diff(f2,'x')
-print Diff(f3,'x')
-print Diff(f1,x)
-print Diff(f2,x)
-print Diff(f3,x)
-print Diff(f3,xx)
-print "\n"
-print Diff(f1, ['x','y'])
-print Diff(f1, [x,y])
-print Diff(f1, [xx,y])
-print Diff(f2, ['x','y'])
-print Diff(f2, [x,y])
-print Diff(f3, ['x','y'])
-print Diff(f3, [x,y])
-
-print "--------------------------\n"
-
-print "Now some more complex tests..."
+print("The following strings should all be identical")
+print(Diff(f1,'x'))
+print(Diff(f2,'x'))
+print(Diff(f3,'x'))
+print(Diff(f1,x))
+print(Diff(f2,x))
+print(Diff(f3,x))
+print(Diff(f3,xx))
+print("\n")
+print(Diff(f1, ['x','y']))
+print(Diff(f1, [x,y]))
+print(Diff(f1, [xx,y]))
+print(Diff(f2, ['x','y']))
+print(Diff(f2, [x,y]))
+print(Diff(f3, ['x','y']))
+print(Diff(f3, [x,y]))
+
+print("--------------------------\n")
+
+print("Now some more complex tests...")
t=Var('t')
s=Var('s')
@@ -49,47 +49,47 @@
p=Par('3.','p')
f = Fun(QuantSpec('f', str(2.0+s-10*(t**2)+Exp(p))), ['s','t'])
f_0=Fun(QuantSpec('f_0', str(Diff(f(s,t),t))), ['t'])
-print 2*f.eval(s=3,t=t)
-print Diff('-10*Pow(t,2)','t')
-print Diff(2*f.eval(s=3,t=t), t)
-print Diff(3+t*f.eval(s=3,t=t),t)
-print Diff(3+t*f(s,t),t).eval(s=3,t=1,p=p)
-print Diff(3+t*f(s,t),t).eval(s=3,t=1,p=p())
+print(2*f.eval(s=3,t=t))
+print(Diff('-10*Pow(t,2)','t'))
+print(Diff(2*f.eval(s=3,t=t), t))
+print(Diff(3+t*f.eval(s=3,t=t),t))
+print(Diff(3+t*f(s,t),t).eval(s=3,t=1,p=p))
+print(Diff(3+t*f(s,t),t).eval(s=3,t=1,p=p()))
assert Diff(str(f(s,t)),'t') == Diff(f(s,t),t)
q1=Diff(f(s,t),t)
q2=Diff(str(f(s,t)),t)
assert q1 == q2
q1.difference(q2)
-print "\n"
-print Diff(f(t,s),t)
-print Diff(2*f(3,t*5), t)
+print("\n")
+print(Diff(f(t,s),t))
+print(Diff(2*f(3,t*5), t))
assert str(Diff(2*f(3,t*5), t)) != str(0)
assert f(s,t) != f(t,s)
-print f(s,t).eval()
+print(f(s,t).eval())
q=f(s,t)
-print q.eval()
-
-print Diff('g(s)',s)
-print Diff('g(s)',s).eval()
+print(q.eval())
+
+print(Diff('g(s)',s))
+print(Diff('g(s)',s).eval())
dg_dt=Fun(QuantSpec('g_0', '2-Sin(t/2)'),['t'])
assert str(Diff('g(t)',t).eval()) != 'g_0(t)'
-print "\n\n"
-print Diff('g(s)',s)
-print Diff('g(s)',s).eval()
+print("\n\n")
+print(Diff('g(s)',s))
+print(Diff('g(s)',s).eval())
g=Fun('',[t],'g') # declare empty function
assert str(g(t)) == 'g(t)'
-print Diff(g(s),s).eval()
+print(Diff(g(s),s).eval())
assert eval(str(Diff('pow(1,2)*t','t'))) == 1
assert eval(str(Diff(Pow(1,2)*t,t))) == 1
assert str(Diff(Sin(Pow(t,1)),t)) == 'Cos(t)'
q=QuantSpec('q','-0+3+pow(g(x)*h(y,x),1)*1')
-print Diff(q,'x')
+print(Diff(q,'x'))
assert str(Diff(q,'x')) == '(g_0(x)*h(y,x)+g(x)*h_1(y,x))'
# BROKEN in this version (need to move to SymPy)
#print Diff(q,'x').eval()
@@ -99,8 +99,8 @@
p1=Var('p1')
pv=Var([p0,p1], 'p')
-print pv()
-print pv.eval()
+print(pv())
+print(pv.eval())
u=Var('Pi/(2*Sin(Pi*t/2))','u')
assert u.eval(t=1).tonumeric() == pi/2
@@ -155,23 +155,23 @@
#------------------
-print "\nSymbolic vector tests"
+print("\nSymbolic vector tests")
q0=Var(p0+3,'q0')
q1=Var(Diff(1+Sin(Pow(p0,3)+q0),p0),'q1')
qv=Var([q0,q1], 'q')
-print qv()
-print qv.eval()
+print(qv())
+print(qv.eval())
v=Var('v')
w=Var('w')
f=Var([-3*Pow((2*v+1),3)+2*(w+v),-w/2], 'f')
df = Diff(f, [v,w])
-print df
+print(df)
dfe = df.eval(v=3,w=10).tonumeric()
-print dfe
+print(dfe)
assert isinstance(dfe, ndarray)
assert isinstance(df.fromvector(), list)
@@ -202,37 +202,37 @@
f1 = Fun([-3*x**3+2*(x+y),-y/2], [x,y], 'f1')
f2 = ['-3*x**3+2*(x+y)','-y/2']
f3 = [-3*x**3.+2*(x+y),-y/2.]
-print "\n\nVector-valued function f(x,y) =", f1
-print "The function string can be passed to Diff in various ways..."
-prRefactoringTool: Refactored ./PyDSTool/tests/SLIP_plot.py
RefactoringTool: Refactored ./PyDSTool/tests/SLIP_2D_pdc.py
int str(f1)
-print str(f2)
-print str(f3)
-print "\nThe following outputs are for Diff(f,'x') for each of these forms"
-print "They should all be the same (except for some may contain decimal points)"
+print("\n\nVector-valued function f(x,y) =", f1)
+print("The function string can be passed to Diff in various ways...")
+print(str(f1))
+print(str(f2))
+print(str(f3))
+print("\nThe following outputs are for Diff(f,'x') for each of these forms")
+print("They should all be the same (except for some may contain decimal points)")
f4 = [-3*Pow((2*x+1),3)+2*(x+y),-y/2]
xx = QuantSpec('dummy','x')
f5=Var([-3*Pow((2*x+1),3)+2*(x+y),-y/2], 'f5')
assert Diff(f1,x) == Diff(f1,'x')
-print Diff(f1,x)
-print Diff(f3,x)
-print Diff(f3,xx)
-print Diff(f4,x)
-print Diff(f4,xx)
-print "\nExamples of Jacobian Diff(f, [x,y])..."
+print(Diff(f1,x))
+print(Diff(f3,x))
+print(Diff(f3,xx))
+print(Diff(f4,x))
+print(Diff(f4,xx))
+print("\nExamples of Jacobian Diff(f, [x,y])...")
assert Diff(f1, [x,y]) == Diff(f1, ['x','y']) == Diff(f1(x,y), [x,y])
-print Diff(f2, ['x','y'])
-print Diff(f3, ['x','y'])
-print Diff(f1, [xx,y])
-print Diff(f1, [xx,'y'])
-print Diff(f2, [x,y])
-print Diff(f3, [x,y]), "\n"
-print Diff(f4, [x,y])
+print(Diff(f2, ['x','y']))
+print(Diff(f3, ['x','y']))
+print(Diff(f1, [xx,y]))
+print(Diff(f1, [xx,'y']))
+print(Diff(f2, [x,y]))
+print(Diff(f3, [x,y]), "\n")
+print(Diff(f4, [x,y]))
df5 = Diff(f5, [x,y])
-print df5
-print df5.eval(x=3,y=10).tonumeric()
-print df5.eval(x=3,y=10).fromvector(0)
-print df5.fromvector(0)
+print(df5)
+print(df5.eval(x=3,y=10).tonumeric())
+print(df5.eval(x=3,y=10).fromvector(0))
+print(df5.fromvector(0))
assert isinstance(df5.fromvector(), list)
a = df5.fromvector(0).eval(x=3,y=10).tonumeric()
b = df5.eval(x=3,y=10).tonumeric()[0]
@@ -240,8 +240,8 @@
# --
-print "\nExamples of differentiation using nested functions"
-print " - this functionality is built in to Symbolic.prepJacobian"
+print("\nExamples of differentiation using nested functions")
+print(" - this functionality is built in to Symbolic.prepJacobian")
func_ma_spec = (['p', 'v'], '0.32*(v+54)/(1-exp(-p*(v+54)/4))')
ma = Fun(func_ma_spec[1], func_ma_spec[0], 'ma')
ma_1 = Fun(Diff(ma, 'v'), ['v'], 'ma_1')
--- ./PyDSTool/tests/SLIP_plot.py (original)
+++ ./PyDSTool/tests/SLIP_plot.py (refactored)
@@ -56,5 +56,5 @@
z3 = pt2('z')
if verboselevel > 0:
delta = math.asin(z3)
- print "|delta - beta| =", abs(delta - beta)
+ print("|delta - beta| =", abs(delta - beta))
plot([y2,y3],[z2,z3],'r-',linewidth=3)
--- ./PyDSTool/tests/SLIP_2D_pdc.py (original)
+++ ./PyDSTool/tests/SLIP_2D_pdc.py (refactored)
@@ -28,9 +28,9 @@
info(ics, "Initial conditions")
# Choose makeSLIP2D_Dopri or makeSLIP2D_Vode as alternatives...
-print "Beware that Radau has problems with this model on Mac OS X and maybe linux too..."
-print "If you get a bus error then please inform me of what your setup is."
-print "Then try re-running by changing the integrator to Dopri (see line below this in script)"
+print("Beware that Radau has problems with this model on Mac OS X and maybe linux too...")
+print("If you get a bus error then please inform me of what your setup is.")
+print("Then try re-running by changing the integrator to Dopri (see line below this in script)")
SLIP = makeSLIP2D_Radau(pars)
SLIP.set(verboselevel=0)
@@ -39,14 +39,14 @@
# residual fn for searching in beta
def residual_fn_beta(x):
ics['incontact'] = 0
- print "Trying beta =", x[0]
+ print("Trying beta =", x[0])
try:
SLIP.compute(pars={'beta': x[0]}, force=True,
trajname='par_est', tdata=[0, 12],
ics=ics)
except PyDSTool_ExistError:
# beta chosen such that no eligible generators found
- print " ... arbitrarily setting cost to be 1000"
+ print(" ... arbitrarily setting cost to be 1000")
return 1000
# time of touchdown and liftoff
RefactoringTool: Refactored ./PyDSTool/tests/SLIP_2D_maps.py
evs = SLIP.getTrajEventTimes('par_est')
@@ -58,13 +58,13 @@
if LOev < TDev:
LOev = evs['liftoff'][2]
z3 = SLIP('par_est',LOev,'z')
- print "z3=",z3
+ print("z3=",z3)
delta = math.asin(z3)
- print "delta =",delta
+ print("delta =",delta)
# Dpsi = pi-beta-delta
# target Dpsi = pi-2*beta, i.e. beta=delta
cost = (beta-delta)**2
- print "cost =", cost
+ print("cost =", cost)
else:
raise RuntimeError("Not enough events found")
return cost
@@ -84,7 +84,7 @@
ics=ics)
except PyDSTool_ExistError:
# ydot chosen such that no eligible generators found
- print " ... arbitrarily setting cost to be 1000"
+ print(" ... arbitrarily setting cost to be 1000")
return 1000
# time of touchdown and liftoff
evs = SLIP.getTrajEventTimes('par_est')
@@ -102,21 +102,21 @@
# Dpsi = pi-beta-delta
# target Dpsi = pi-2*beta, i.e. beta=delta
cost = (beta-delta)**2
- print "cost =", cost
+ print("cost =", cost)
else:
- print evs
- print "Found %i TD events, %i LO events"%(numTDs, numLOs)
+ print(evs)
+ print("Found %i TD events, %i LO events"%(numTDs, numLOs))
raise RuntimeError("Not enough events found")
return cost
Dpsi_tol = 1e-3
-print "Finding periodic gait by varying initial y velocity,"
-print "to tolerance in Dpsi of", Dpsi_tol, "\n"
+print("Finding periodic gait by varying initial y velocity,")
+print("to tolerance in Dpsi of", Dpsi_tol, "\n")
# use optimizer with boundary constraints
ydot_opt = optimize.fminbound(residual_fn_ydot, 0.5, 0.75, xtol=Dpsi_tol)
ydot_opt_known = 0.666463229031
-print "ydot for periodic gait = ", ydot_opt
+print("ydot for periodic gait = ", ydot_opt)
assert abs(ydot_opt-ydot_opt_known)<Dpsi_tol, "Optimal ydot not found accurately"
# ---- Compute periodic trajectory
@@ -125,7 +125,7 @@
icdict_pdc['ydot'] = ydot_opt
icdict_pdc['incontact'] = 0
-print "Computing trajectory...\n"
+print("Computing trajectory...\n")
start = clock()
SLIP.compute(trajname='pdc',
tdata=[0, 12],
@@ -133,9 +133,9 @@
verboselevel=1) # optional
assert allclose(SLIP.trajectories['pdc'].indepdomain.get(), [0, 12], 1e-8), "Independent domain not correct"
assert allclose(SLIP('pdc', 12, 'y'), 8.18, 1e-2), "Hybrid model computation has a problem"
-print '... finished in %.3f seconds.\n' % (clock()-start)
+print('... finished in %.3f seconds.\n' % (clock()-start))
-print 'Plotting periodic trajectory'
+print('Plotting periodic trajectory')
SLIP_plot(SLIP, 'pdc', 'plane')
show()
--- ./PyDSTool/tests/SLIP_2D_maps.py (original)
+++ ./PyDSTool/tests/SLIP_2D_maps.py (refactored)
@@ -24,7 +24,7 @@
y_ic = cos(beta)
info(pars, "Parameter values")
icdict = {'y': y_ic, 'z': z_ic, 'ydot': 0.8, 'zdot': .3, 'incontact': 0}
-print "\n"
+print("\n")
info(icdict, "Initial conditions")
@@ -39,7 +39,7 @@
# extract single point from pointset using [0] reference
res = SLIP_map.getTrajEvents('pdc', 'liftoff')[0]
res['incontact'] = 0 # make eligible for new i.c.
- return res[icdict.keys()]
+ return res[list(icdict.keys())]
# Find fixed point of gait map parameterized by beta,
@@ -54,7 +54,7 @@
x1 = pdc_map(x0)
except:
# no liftoff event so probably a failed trajectory
- print "Problem at x0 =", x0
+ print("Problem at x0 =", x0)
return Point({'zdot': 1e6})
return x1['zdot']-x0['zdot'] # Point
@@ -69,13 +69,13 @@
icdict_pert = copy(icdict)
icpt = Point({'coorddict': icdict_pert})
-print "\nFinding fixed point of periodic map as a function of beta"
+print("\nFinding fixed point of periodic map as a function of beta")
# Equally efficient alternatives to shoot for f.p. solution
beta_pdc = minpack.fsolve(fp_beta_fsolve, beta, args=(icpt,), xtol=1e-4)
##beta_pdc = minpack.newton(fp_beta_newton, beta, args=(icpt,), tol=1e-4)
beta_pdc_knownRefactoringTool: No changes to ./PyDSTool/tests/SLIP_2D.py
RefactoringTool: Refactored ./PyDSTool/tests/PySCes_import_test.py
RefactoringTool: Refactored ./PyDSTool/tests/PyCont_vanDerPol.py
= 1.21482619378
-print "beta_pdc = ", beta_pdc
+print("beta_pdc = ", beta_pdc)
assert abs(beta_pdc-beta_pdc_known)<1e-4, "beta_pdc was not found accurately"
# update i.c. for new beta
@@ -83,16 +83,16 @@
icdict_pert['y'] = math.cos(beta_pdc)
icdict_maps = copy(icdict_pert)
icpt = Point({'coorddict': icdict_maps})
-print "\nCalculating approximation to periodic maps"
+print("\nCalculating approximation to periodic maps")
SLIP_map.set(pars={'beta': beta_pdc})
states = [icpt]
for i in range(5):
states.append(pdc_map(states[-1]))
-pdcgaittraj = pointsToPointset(states, 'n', range(len(states)))
+pdcgaittraj = pointsToPointset(states, 'n', list(range(len(states))))
-print "\nCalculating approximation to periodic trajectory"
+print("\nCalculating approximation to periodic trajectory")
pars['beta'] = beta_pdc
SLIP = makeSLIP2D_Vode(pars, dt=0.005)
SLIP.compute(trajname='pdc',
@@ -100,7 +100,7 @@
ics=icdict_pert,
verboselevel=0)
-print 'Plotting periodic trajectory (event dots from application of map)'
+print('Plotting periodic trajectory (event dots from application of map)')
SLIP_plot(SLIP, 'pdc', 'plane')
# Plot successive (y,z) events points overlayed
nmax = pdcgaittraj.indepvararray[-1]
@@ -127,22 +127,22 @@
-print "Jacobian DP as a function of z, ydot, zdot (y contributes an e'val = 1)"
+print("Jacobian DP as a function of z, ydot, zdot (y contributes an e'val = 1)")
DP = diff2(pdc_map, icpt, axes=['z','ydot','zdot'],
vars=['z','ydot','zdot'], eps=0.01)
-print "DP(fp) =\n",DP
-print "|DP(fp)| =", det(DP)
+print("DP(fp) =\n",DP)
+print("|DP(fp)| =", det(DP))
evals = eigvals(DP)
-print "\nDP's eigenvalues are ",evals
-print "Max eigenvalue magnitude = ", max(abs(evals))
+print("\nDP's eigenvalues are ",evals)
+print("Max eigenvalue magnitude = ", max(abs(evals)))
# verify beta = delta using the geometry
tTD = SLIP.getTrajEventTimes('pdc')['touchdown'][0] # time at first touchdown
sTD = SLIP('pdc',tTD) # system state at t=TD
delta=math.atan(-sTD('ydot')/sTD('zdot')) # angle of velocity vector from horizontal
theta_qv=beta_pdc-delta
-print "Geometry shows that beta = delta, as theta_qv = beta-delta ..."
-print "theta_qv =", theta_qv
+print("Geometry shows that beta = delta, as theta_qv = beta-delta ...")
+print("theta_qv =", theta_qv)
assert abs(theta_qv-0.0028)<1e-4, "theta_qv not found accurately"
# Check against Eq. (14) in ref (P. Holmes et al)
@@ -153,6 +153,6 @@
assert abs(vmag_LOtheory - vmag_LO) < 1e-6, "vmag value doesn't match prediction"
-print "Using Eq. (14), difference in velocity magnitudes v_LO given by"
-print "simulation vs. conservation of energy =", vmag_LOtheory - vmag_LO
+print("Using Eq. (14), difference in velocity magnitudes v_LO given by")
+print("simulation vs. conservation of energy =", vmag_LOtheory - vmag_LO)
show()
--- ./PyDSTool/tests/PySCes_import_test.py (original)
+++ ./PyDSTool/tests/PySCes_import_test.py (refactored)
@@ -6,7 +6,7 @@
from PyDSTool import *
from PyDSTool.Toolbox.PySCes_SBML import *
-print "Modify the path variable to indicate where your PySCes models are..."
+print("Modify the path variable to indicate where your PySCes models are...")
path = '/pysces/pscmodels/'
#fname = 'pysces_test_linear1.psc'
fname = 'pysces_test_branch1.psc'
--- ./PyDSTool/tests/PyCont_vanDerPol.py (original)
+++ ./PyDSTool/tests/PyCont_vanDerPol.py (refactored)
@@ -11,7 +11,7 @@
import sys
vdp_filename = 'vanderPol.dat'
-print "At end of testing you can delete the temp file", vdp_filename
+print("At end of testing you can delete the temp file", vdp_filename)
def integrate(DS, t1=200, name='traj'):
DS.set(tdata=[0, t1])
@@ -224,7 +224,7 @@
DS = C.gensys
DS.pars['a'] = pt['a']
- if ((not C._userdata.has_key('sgn')) or C._userdata.sgn == -1):
+ if (('sgn' not in C._userdata) or C._userdata.sgn == -1):
x1 = {'x': -1.0, 'y': pars['y1']}
else:
x1 = {'x': DS.pars['a'], 'y': pars['y1']}
@@ -234,7 +234,7 @@
try:
tx1b = DS.compute('x1b', dRefactoringTool: Refactored ./PyDSTool/tests/PyCont_hybrid_osc.py
RefactoringTool: Refactored ./PyDSTool/tests/PyCont_SaddleNode.py
irn='b', ics=x1)
except PyDSTool_ExistError:
- print 'Lost canard!\n'
+ print('Lost canard!\n')
C._userdata.problem = True
return array([0], float)
x1b = DS.getEvents()['event_x_a'][0].toarray()
@@ -259,7 +259,7 @@
px1b = tx1b.sample(dt=0.01)
plt.plot(px1f['x'], px1f['y'])
plt.plot(px1b['x'], px1b['y'])
- raw_input()
+ input()
plt.close()
F = array([x1f[1]-x1b[1]], float)
@@ -271,7 +271,7 @@
if meas is None and solution measure nm2 or max if specified."""
if meas is None:
for pt in PyCont[name].sol:
- if 'UD' in pt.labels and pt.labels['UD']['data'].has_key('cycle'):
+ if 'UD' in pt.labels and 'cycle' in pt.labels['UD']['data']:
cycle = pt.labels['UD']['data'].cycle
plt.plot(cycle['x'], cycle['y'], '-b')
else:
@@ -280,7 +280,7 @@
ind = []
if meas == 'nm2':
for i, pt in enumerate(PyCont[name].sol):
- if 'UD' in pt.labels and pt.labels['UD']['data'].has_key('cycle'):
+ if 'UD' in pt.labels and 'cycle' in pt.labels['UD']['data']:
cycle = pt.labels['UD']['data'].cycle
dt = (cycle['t'][1:]-cycle['t'][0:-1])/(cycle['t'][-1]-cycle['t'][0])
solmeas.append(sqrt(0.5*(sum(dt*(cycle['x'][1:]*cycle['x'][1:] + \
@@ -288,7 +288,7 @@
ind.append(i)
elif meas == 'max':
for i, pt in enumerate(PyCont[name].sol):
- if 'UD' in pt.labels and pt.labels['UD']['data'].has_key('cycle'):
+ if 'UD' in pt.labels and 'cycle' in pt.labels['UD']['data']:
solmeas.append(max(abs(pt.labels['UD']['data'].cycle['x'])))
ind.append(i)
@@ -303,7 +303,7 @@
# Compute limit cycle
cycle = find_cycle(DS, disp=False)
-print "Finding limit cycle using AUTO"
+print("Finding limit cycle using AUTO")
C = ContClass(DS)
continuation(C, cycle=cycle, compute=True, disp=False)
@@ -315,7 +315,7 @@
plt.xlim([-2.5, 2.5])
plt.ylim([-1, 1])
-print "Continuing limit cycle"
+print("Continuing limit cycle")
continuation(C, cycle=None, compute=False, disp=False)
DS.set(tdata=[0, 400])
@@ -328,20 +328,20 @@
C['UD1'].gensys.eventstruct['event_x_a'].activeFlag = True
C['UD1'].gensys.eventstruct['event_x_a'].termFlag = True
-print 'UD1: Integrating backward...'
+print('UD1: Integrating backward...')
try:
C['UD1'].backward()
except:
exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
- print "Error: ", exceptionType, ": message:", exceptionValue
-print 'done!\n\n'
-print 'UD1: Integrating forward...'
+ print("Error: ", exceptionType, ": message:", exceptionValue)
+print('done!\n\n')
+print('UD1: Integrating forward...')
try:
C['UD1'].forward()
except:
exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
- print "Error: ", exceptionType, ": message:", exceptionValue
-print 'done!\n\n'
+ print("Error: ", exceptionType, ": message:", exceptionValue)
+print('done!\n\n')
## Temp removed UD2 calculation (broken)
@@ -367,5 +367,5 @@
plot_manifold()
plot_cycles(C, 'UD1')
#plot_cycles(C, 'UD2')
-print "At end of testing you can delete the temp file", vdp_filename
+print("At end of testing you can delete the temp file", vdp_filename)
show()
--- ./PyDSTool/tests/PyCont_hybrid_osc.py (original)
+++ ./PyDSTool/tests/PyCont_hybrid_osc.py (refactored)
@@ -37,7 +37,7 @@
try:
F = get_cycle(DS)
except PyDSTool_ExistError:
- print 'Problem computing orbit'
+ print('Problem computing orbit')
C._userdata.problem = True
return array([0], float)
else:
@@ -60,7 +60,7 @@
PCargs.initpoint = {'gl': PyCont.gensys.query('pars')['gl']}
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
PyCont['UD1'].forward()
PyCont['UD1'].backward()
--- ./PyDSTool/tests/PyCont_SaddleNode.py (original)
+++ ./PyDSTool/tests/PyCont_SaddleNodRefactoringTool: Refactored ./PyDSTool/tests/PyCont_PredPrey.py
RefactoringTool: Refactored ./PyDSTool/tests/PyCont_NewLorenz.py
RefactoringTool: Refactored ./PyDSTool/tests/PyCont_MorrisLecar_TypeII.py
RefactoringTool: Refactored ./PyDSTool/tests/PyCont_MorrisLecar_TypeI.py
RefactoringTool: Refactored ./PyDSTool/tests/PyCont_Lorenz.py
e.py (refactored)
@@ -35,10 +35,10 @@
PCargs.Corrector = 'Natural'
PyCont.newCurve(PCargs)
-print 'Computing equilibrium curve...'
+print('Computing equilibrium curve...')
start = clock()
PyCont['EQ1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Plot
PyCont.display(('r','x'), stability=True, linewidth=0.5)
--- ./PyDSTool/tests/PyCont_PredPrey.py (original)
+++ ./PyDSTool/tests/PyCont_PredPrey.py (refactored)
@@ -45,10 +45,10 @@
PCargs.verbosity = 2
PC.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PC['EQ1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs.name = 'HO1'
PCargs.type = 'H-C2'
@@ -59,10 +59,10 @@
PCargs.LocBifPoints = ['ZH']
PC.newCurve(PCargs)
-print 'Computing Hopf curve...'
+print('Computing Hopf curve...')
start = clock()
PC['HO1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs = args(name = 'FO1', type = 'LP-C')
PCargs.initpoint = 'HO1:ZH1'
@@ -72,15 +72,15 @@
PCargs.LocBifPoints = 'all'
PC.newCurve(PCargs)
-print 'Computing fold curve (forward)...'
+print('Computing fold curve (forward)...')
start = clock()
PC['FO1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
-print 'Computing fold curve (backward)...'
+print('Computing fold curve (backward)...')
start = clock()
PC['FO1'].backward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Plot
PC.display(('k','D'))
--- ./PyDSTool/tests/PyCont_NewLorenz.py (original)
+++ ./PyDSTool/tests/PyCont_NewLorenz.py (refactored)
@@ -34,10 +34,10 @@
PCargs.verbosity = 2
PyCont.newCurve(PCargs)
-print 'Computing equilibrium curve...'
+print('Computing equilibrium curve...')
start = clock()
PyCont['EQ1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Hopf curve
PCargs = args(name='HO1', type='H-C2')
@@ -47,10 +47,10 @@
PyCont.newCurve(PCargs)
-print 'Computing hopf curve...'
+print('Computing hopf curve...')
start = clock()
PyCont['HO1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Plot
PyCont.display(('F','x'))
--- ./PyDSTool/tests/PyCont_MorrisLecar_TypeII.py (original)
+++ ./PyDSTool/tests/PyCont_MorrisLecar_TypeII.py (refactored)
@@ -52,10 +52,10 @@
PCargs.SaveEigen = True
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PyCont['EQ1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs.name = 'LC1'
PCargs.type = 'LC-C'
@@ -70,10 +70,10 @@
PCargs.SaveEigen = True
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PyCont['LC1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Plot
PyCont.display(('Iapp','v'),stability=True)
--- ./PyDSTool/tests/PyCont_MorrisLecar_TypeI.py (original)
+++ ./PyDSTool/tests/PyCont_MorrisLecar_TypeI.py (refactored)
@@ -52,10 +52,10 @@
PCargs.SaveEigen = True
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PyCont['EQ1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs.name = 'LC1'
PCargs.type = 'LC-C'
@@ -70,10 +70,10 @@
PCargs.SaveEigen = True
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PyCont['LC1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Plot
PyCont.display(('Iapp','v'),stability=True)
--- ./PyDSTool/tests/PyCont_Lorenz.py (original)
+++ ./PyDSTool/tests/PyCont_Lorenz.py (refactored)
@@ -54,12 +54,12 @@RefactoringTool: Refactored ./PyDSTool/tests/PyCont_Logistic.py
RefactoringTool: Refactored ./PyDSTool/tests/PyCont_LevelCurve.py
PCargs.SaveJacobian = True
PyCont.newCurve(PCargs)
-print "Beginning computation of curve in backward and then forward direction..."
+print("Beginning computation of curve in backward and then forward direction...")
start = clock()
PyCont['LC1'].backward()
PyCont['LC1'].update({'MaxNumPoints': 90, 'NumSPOut': 90})
PyCont['LC1'].forward()
-print "\nComputation complete in %.3f seconds.\n" % (clock()-start)
+print("\nComputation complete in %.3f seconds.\n" % (clock()-start))
# Plot
PyCont['LC1'].cleanLabels()
--- ./PyDSTool/tests/PyCont_Logistic.py (original)
+++ ./PyDSTool/tests/PyCont_Logistic.py (refactored)
@@ -36,10 +36,10 @@
PCargs.SPOut = {'r': [0.1919191, 1.5353535]}
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PyCont['FP1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
s = PyCont['FP1'].sol
assert len(s.bylabel('SP-r-0')) == 1
@@ -52,10 +52,10 @@
PCargs.LocBifPoints = ['PD', 'B']
PyCont.newCurve(PCargs)
-print 'Computing second branch...'
+print('Computing second branch...')
start = clock()
PyCont['FP2'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs.name = 'FP3'
PCargs.initpoint = 'FP2:PD1'
@@ -65,12 +65,12 @@
PCargs.period = 2
PyCont.newCurve(PCargs)
-print 'Computing 2-cycle branch...'
+print('Computing 2-cycle branch...')
start = clock()
PyCont['FP3'].forward()
PyCont['FP3'].backward()
PyCont['FP3'].cleanLabels()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs.name='FP4'
PCargs.initpoint = 'FP3:PD1'
@@ -78,24 +78,24 @@
PCargs.period = 4
PyCont.newCurve(PCargs)
-print 'Computing 1st 4-cycle branch...'
+print('Computing 1st 4-cycle branch...')
start = clock()
PyCont['FP4'].forward()
PyCont['FP4'].backward()
PyCont['FP4'].cleanLabels()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs.name = 'FP5'
PCargs.initpoint = 'FP3:PD2'
PCargs.initdirec = PyCont['FP3'].getSpecialPoint('PD2').labels['PD']['data'].branch
PyCont.newCurve(PCargs)
-print 'Computing 2nd 4-cycle branch...'
+print('Computing 2nd 4-cycle branch...')
start = clock()
PyCont['FP5'].forward()
PyCont['FP5'].backward()
PyCont['FP5'].cleanLabels()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Plot
PyCont.display(stability=True)
--- ./PyDSTool/tests/PyCont_LevelCurve.py (original)
+++ ./PyDSTool/tests/PyCont_LevelCurve.py (refactored)
@@ -49,23 +49,23 @@
sol = P['test'].sol
-print "There were %i points computed" % len(sol)
+print("There were %i points computed" % len(sol))
# solution points:
-print sol
+print(sol)
-print "\nLabels for each point in sol pointset give diagnostic information about"
-print "first derivative of the point along the curve ('V' entry) and the arc "
-print "length parameter shows distance along the curve so far ('ds' entry)."
+print("\nLabels for each point in sol pointset give diagnostic information about")
+print("first derivative of the point along the curve ('V' entry) and the arc ")
+print("length parameter shows distance along the curve so far ('ds' entry).")
-print "\nVelocity around curve is always 1, e.g. look at 100th point"
-print "norm(Point(sol[100].labels['EP']['data'].V)) =", \
- norm(Point(sol[100].labels['EP']['data'].V))
+print("\nVelocity around curve is always 1, e.g. look at 100th point")
+print("norm(Point(sol[100].labels['EP']['data'].V)) =", \
+ norm(Point(sol[100].labels['EP']['data'].V)))
-print "... at which we have travelled distance ds =", \
- sol[100].labels['EP']['data'].ds
+print("... at which we have travelled distance ds =", \
+ sol[100].labels['EP']['data'].ds)
-print "\nThis distance is equal to 100 * the max step size (0.01) which PyCont"
-print "deemed sufficient for the desired accuracy."
+print("\nThis distance is equal to 100 * the max step sizRefactoringTool: Refactored ./PyDSTool/tests/PyCont_LPNeuron.py
RefactoringTool: Refactored ./PyDSTool/tests/PyCont_Hopfield.py
RefactoringTool: Refactored ./PyDSTool/tests/PyCont_HindmarshRose.py
RefactoringTool: Refactored ./PyDSTool/tests/PyCont_Hamiltonian.py
e (0.01) which PyCont")
+print("deemed sufficient for the desired accuracy.")
# easy way to plot the result
P.display(curves=['test'], coords=('x','y'))
--- ./PyDSTool/tests/PyCont_LPNeuron.py (original)
+++ ./PyDSTool/tests/PyCont_LPNeuron.py (refactored)
@@ -116,10 +116,10 @@
PCargs.verbosity = 2
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PyCont['EQ1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PyCont['EQ1'].display(('Iext','v'), figure='new')
PyCont.plot.toggleAll('off', bytype='P')
@@ -138,10 +138,10 @@
PCargs.TestTol = 1e-8
PyCont.newCurve(PCargs)
-print 'Computing limit-cycle curve...'
+print('Computing limit-cycle curve...')
start = clock()
PyCont['LC1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PyCont['LC1'].display(('Iext','v'), stability=True)
--- ./PyDSTool/tests/PyCont_Hopfield.py (original)
+++ ./PyDSTool/tests/PyCont_Hopfield.py (refactored)
@@ -39,10 +39,10 @@
testDS = Generator.Vode_ODEsystem(DSargs)
-print 'Integrating...'
+print('Integrating...')
start = clock()
testtraj = testDS.compute('testDS')
-print ' ... finished in %.3f seconds.\n' % (clock()-start)
+print(' ... finished in %.3f seconds.\n' % (clock()-start))
if 0:
plotData=testtraj.sample(dt=0.1)
@@ -67,10 +67,10 @@
PCargs.MaxTestIters = 200
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PyCont['EQ1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
if 0:
PyCont.display(('alpha','m'),stability=True)
@@ -83,11 +83,11 @@
PCargs.StopAtPoints = ['B']
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PyCont['FO1'].forward()
PyCont['FO1'].backward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PyCont['FO1'].display(('theta','alpha'),stability=True)
show()
--- ./PyDSTool/tests/PyCont_HindmarshRose.py (original)
+++ ./PyDSTool/tests/PyCont_HindmarshRose.py (refactored)
@@ -41,11 +41,11 @@
PCargs.verbosity = 2
HR_fast.newCurve(PCargs)
- print 'Computing curve...'
+ print('Computing curve...')
start = clock()
HR_fast['EQ1'].forward()
HR_fast['EQ1'].backward()
- print 'done in %.3f seconds!' % (clock()-start)
+ print('done in %.3f seconds!' % (clock()-start))
PCargs.name = 'LC1'
PCargs.type = 'LC-C'
@@ -63,10 +63,10 @@
PCargs.SaveEigen = True
HR_fast.newCurve(PCargs)
- print 'Computing LC-C from H1...'
+ print('Computing LC-C from H1...')
start = clock()
HR_fast['LC1'].forward()
- print 'done in %.3f seconds!' % (clock()-start)
+ print('done in %.3f seconds!' % (clock()-start))
def plot_fast_subsystem(HR_fast):
HR_fast['EQ1'].display(figure='new', coords=('z', 'x'), stability=True)
@@ -122,11 +122,11 @@
HR.newCurve(PCargs)
if EQ:
- print 'Computing curve...'
+ print('Computing curve...')
start = clock()
HR['EQ1'].forward()
HR['EQ1'].backward()
- print 'done in %.3f seconds!' % (clock()-start)
+ print('done in %.3f seconds!' % (clock()-start))
PCargs.name = 'LC1'
PCargs.type = 'LC-C'
@@ -150,10 +150,10 @@
HR.newCurve(PCargs)
if LC:
- print 'Computing LC-C from H1...'
+ print('Computing LC-C from H1...')
start = clock()
HR['LC1'].forward()
- print 'done in %.3f seconds!' % (clock()-start)
+ print('done in %.3f seconds!' % (clock()-start))
def create_HR_cycle(HR, t1=3000):
DS = HR.gensys
--- ./PyDSTool/tests/PyCont_Hamiltonian.py (original)
+++ ./PyDSTool/tests/PyCont_Hamiltonian.py (refactored)
@@ -35,19 +35,19 @@
PCargs.verbosity = 2
PyCont.newCurve(PCargs)
-print 'Computing equilibrium curve...'
+print('Computing equilibrium curve...')
start = clock()
PyCont['ERefactoringTool: Refactored ./PyDSTool/tests/PyCont_DiscPredPrey.py
RefactoringTool: Refactored ./PyDSTool/tests/PyCont_Catalytic_demo.py
Q1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs.initpoint = {'x': 1, 'y': 0}
PCargs.name = 'EQ2'
PyCont.newCurve(PCargs)
-print 'Computing equilibrium curve...'
+print('Computing equilibrium curve...')
start = clock()
PyCont['EQ2'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs.name = 'LC1'
PCargs.type = 'LC-C'
@@ -60,19 +60,19 @@
PCargs.SaveEigen = False
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PyCont['LC1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs.name = 'LC2'
PCargs.initpoint = 'EQ2:H1'
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PyCont['LC2'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Plot
PyCont.display(curves=['EQ1', 'EQ2'], coords=('x','y'),stability=True)
--- ./PyDSTool/tests/PyCont_DiscPredPrey.py (original)
+++ ./PyDSTool/tests/PyCont_DiscPredPrey.py (refactored)
@@ -33,10 +33,10 @@
PCargs.verbosity = 2
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PyCont['FP1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs = args(name='FP2', type='FP-C')
PCargs.freepars = ['p1']
@@ -47,13 +47,13 @@
PCargs.verbosity = 2
PyCont.newCurve(PCargs)
-print 'Computing second branch...'
+print('Computing second branch...')
start = clock()
PyCont['FP2'].forward()
PyCont['FP2'].update(args(MaxNumPoints=10))
PyCont['FP2'].backward()
PyCont['FP2'].cleanLabels()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs.name = 'FP3'
PCargs.initpoint = 'FP2:BP2'
@@ -61,12 +61,12 @@
PCargs.MaxNumPoints = 50
PyCont.newCurve(PCargs)
-print 'Computing third branch...'
+print('Computing third branch...')
start = clock()
PyCont['FP3'].forward()
PyCont['FP3'].backward()
PyCont['FP3'].cleanLabels()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs.name = 'FP4'
PCargs.initpoint = 'FP2:PD1'
@@ -75,12 +75,12 @@
PCargs.MaxNumPoints = 100
PyCont.newCurve(PCargs)
-print 'Computing third branch...'
+print('Computing third branch...')
start = clock()
PyCont['FP4'].forward()
PyCont['FP4'].backward()
PyCont['FP4'].cleanLabels()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Plot
PyCont.display(('p1','u1'))
--- ./PyDSTool/tests/PyCont_Catalytic_demo.py (original)
+++ ./PyDSTool/tests/PyCont_Catalytic_demo.py (refactored)
@@ -29,9 +29,9 @@
PyCont = ContClass(testDS)
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+exec(str)
str = """
PCargs = args(name='EQ1', type='EP-C')
@@ -45,68 +45,68 @@
PyCont['EQ1'].forward()
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-print 'Computing curve...'
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+print('Computing curve...')
+exec(str)
str = """
PyCont['EQ1'].info()
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+exec(str)
str = """
X = PyCont['EQ1'].getSpecialPoint('LP1')
print X
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+exec(str)
str = """
print X.labels['LP']['data'].a
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+exec(str)
str = """
PyCont['EQ1'].display(axes=(1,2,1))
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-exec str
+print('\n' + c*d(RefactoringTool: Refactored ./PyDSTool/tests/PyCont_Catalytic.py
RefactoringTool: Refactored ./PyDSTool/tests/PyCont_Brusselator.py
str) + str + c*d(str))
+dummy = input()
+exec(str)
show()
str = """
PyCont['EQ1'].display(('q2','x'), axes=(1,2,2))
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+exec(str)
str = """
PyCont.plot.info()
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+exec(str)
str = """
PyCont.info()
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+exec(str)
str = """
PCargs = args(name='HO1', type='H-C2')
@@ -120,19 +120,19 @@
PyCont['HO1'].forward()
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-print 'Computing curve...'
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+print('Computing curve...')
+exec(str)
str = """
PyCont.plot.clearall()
PyCont.display(('q2','x'))
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+exec(str)
str = """
PCargs = args(name='FO1', type='LP-C')
@@ -145,45 +145,45 @@
PyCont['FO1'].forward()
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-print 'Computing curve...'
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+print('Computing curve...')
+exec(str)
str = """
PyCont.plot.clearall()
PyCont.display(('q2','x'))
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+exec(str)
str = """
PyCont['FO1'].backward()
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-print 'Computing curve...'
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+print('Computing curve...')
+exec(str)
str = """
PyCont.plot.fig1.axes1.FO1.delete()
PyCont['FO1'].display(('q2','x'))
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+exec(str)
str = """
PyCont.plot.toggleLabels('off')
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+exec(str)
str = """
PyCont.plot.toggleLabels('on')
@@ -192,9 +192,9 @@
PyCont.plot.fig1.axes1.HO1.toggleCurve('off')
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-exec str
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+exec(str)
str = """
PyCont.computeEigen()
@@ -202,10 +202,10 @@
PyCont.plot.fig2.toggleAll('off', bytype='P')
"""
-print '\n' + c*d(str) + str + c*d(str)
-dummy = raw_input()
-exec str
-
-print '\n'
-
-dummy = raw_input()
+print('\n' + c*d(str) + str + c*d(str))
+dummy = input()
+exec(str)
+
+print('\n')
+
+dummy = input()
--- ./PyDSTool/tests/PyCont_Catalytic.py (original)
+++ ./PyDSTool/tests/PyCont_Catalytic.py (refactored)
@@ -37,10 +37,10 @@
PCargs.SaveEigen = True
PyCont.newCurve(PCargs)
-print 'Computing equilibrium curve...'
+print('Computing equilibrium curve...')
start = clock()
PyCont['EQ1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Hopf curve
PCargs.name = 'HO1'
@@ -53,10 +53,10 @@
PyCont.newCurve(PCargs)
-print 'Computing hopf curve...'
+print('Computing hopf curve...')
start = clock()
PyCont['HO1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Fold curve
PCargs.name = 'FO1'
@@ -68,10 +68,10 @@
PyCont.newCurve(PCargs)
-print 'Computing fold curve...'
+print('Computing fold curve...')
start = clock()
PyCont['FO1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Plot
PyCont.display(('q2','x'), axes=(3,1,1))
--- ./PyDSTool/tests/PyCont_Brusselator.py (original)
+++ ./PyDSTool/tests/PyCont_Brusselator.py (refactored)
@@ -42,10 +42,10 @@
PCargs.SaveEigen = TRefactoringTool: Refactored ./PyDSTool/tests/PyCont_ABReaction.py
RefactoringTool: Refactored ./PyDSTool/tests/PyCont_ABCReaction.py
RefactoringTool: Refactored ./PyDSTool/tests/PointInfo_test.py
RefactoringTool: Refactored ./PyDSTool/tests/NineML_import_test.py
RefactoringTool: Refactored ./PyDSTool/tests/MultiCompartments2.py
rue
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PyCont['EQ1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Plot
PyCont['EQ1'].display(('lambda','X1'), stability=True)
--- ./PyDSTool/tests/PyCont_ABReaction.py (original)
+++ ./PyDSTool/tests/PyCont_ABReaction.py (refactored)
@@ -39,10 +39,10 @@
PCargs.verbosity = 2
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PyCont['EQ1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs.name = 'LC1'
PCargs.type = 'LC-C'
@@ -57,10 +57,10 @@
PCargs.SaveEigen = True
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PyCont['LC1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
PCargs.name = 'FO1'
PCargs.type = 'LP-C'
@@ -73,10 +73,10 @@
PCargs.verbosity = 2
PyCont.newCurve(PCargs)
-print 'Computing Fold curve...'
+print('Computing Fold curve...')
start = clock()
PyCont['FO1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Plot
PyCont['EQ1'].display(stability=True, axes=(1,2,1))
--- ./PyDSTool/tests/PyCont_ABCReaction.py (original)
+++ ./PyDSTool/tests/PyCont_ABCReaction.py (refactored)
@@ -34,10 +34,10 @@
PCargs.SaveEigen = True
PyCont.newCurve(PCargs)
-print 'Computing curve...'
+print('Computing curve...')
start = clock()
PyCont['EQ1'].forward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Hopf Curve -- Curiously screws up further out on curve. Will take a closer look later .....
PCargs = args(name='HO1', type='H-C2')
@@ -48,10 +48,10 @@
PCargs.verbosity = 2
PyCont.newCurve(PCargs)
-print 'Computing Hopf curve...'
+print('Computing Hopf curve...')
start = clock()
PyCont['HO1'].backward()
-print 'done in %.3f seconds!' % (clock()-start)
+print('done in %.3f seconds!' % (clock()-start))
# Plot
PyCont.display(('p1','u1'), stability=True)
--- ./PyDSTool/tests/PointInfo_test.py (original)
+++ ./PyDSTool/tests/PointInfo_test.py (refactored)
@@ -6,7 +6,7 @@
from PyDSTool import *
from PyDSTool.parseUtils import symbolMapClass
-print "Tests on Pointset labelling class: PointInfo"
+print("Tests on Pointset labelling class: PointInfo")
sm = symbolMapClass({'a': 'A'})
@@ -16,7 +16,7 @@
p['a'] = (5, {'bif': 'h'})
p[1] = ('b', {'bif': 'c'})
-assert p['a'].keys() == [3,5]
+assert list(p['a'].keys()) == [3,5]
sorted = p.sortByIndex()
assert [s[0] for s in sorted] == [1,3,5]
assert p.getIndices() == [1,3,5]
@@ -24,7 +24,7 @@
p.update(3, 'c', {'foo': 'bar'})
p.update(3, 'h')
-assert p[3].keys() == ['a','h','c']
+assert list(p[3].keys()) == ['a','h','c']
try:
p[-1]
--- ./PyDSTool/tests/NineML_import_test.py (original)
+++ ./PyDSTool/tests/NineML_import_test.py (refactored)
@@ -133,7 +133,7 @@
plt.title('Hodgkin-Huxley membrane potential')
ev_info = pts.labels.by_label['Event:spikeoutput']
- for ev_ix, ev_tdata in ev_info.items():
+ for ev_ix, ev_tdata in list(ev_info.items()):
plt.plot(ev_tdata['t'], pts[ev_ix]['V'], 'ko')
plt.xlabel('t')
--- ./PyDSTool/tests/MultiCompartments2.py (original)
+++ ./PyDSTool/tests/MultiCompartments2.py (refactored)
@@ -60,13 +60,13 @@
####### User demonstration stuff
-print "*** Example of hierarchical referencing to components, etc."
-print "Na vrev Par object is given by >>> net['cell2.soma.Na.vrev'] = \n ", \
- repr(net['cell2.soma.Na.vrev'])
-print "which is equivalent to >>> net.components['cell2'].components['soma'].components['Na'].pars['vrev']"
-print "Na vrev value is given by >>> net['cell2.soma1.Na.vrev']() = \n ", \
- net['cell2.soma.Na.vrev']()
-print "Could delete this Par in place using >>> del net['cell2.soma.Na.vrev'] (not done here!)"
+print("*** Example of hierRefactoringTool: No changes to ./PyDSTool/tests/MultiCompartments.py
RefactoringTool: Refactored ./PyDSTool/tests/ModelSpec_test.py
RefactoringTool: Refactored ./PyDSTool/tests/ML_adjointPRC.py
RefactoringTool: Refactored ./PyDSTool/tests/IF_squarespike_model.py
archical referencing to components, etc.")
+print("Na vrev Par object is given by >>> net['cell2.soma.Na.vrev'] = \n ", \
+ repr(net['cell2.soma.Na.vrev']))
+print("which is equivalent to >>> net.components['cell2'].components['soma'].components['Na'].pars['vrev']")
+print("Na vrev value is given by >>> net['cell2.soma1.Na.vrev']() = \n ", \
+ net['cell2.soma.Na.vrev']())
+print("Could delete this Par in place using >>> del net['cell2.soma.Na.vrev'] (not done here!)")
--- ./PyDSTool/tests/ModelSpec_test.py (original)
+++ ./PyDSTool/tests/ModelSpec_test.py (refactored)
@@ -20,7 +20,7 @@
# -------------------------------------------------------------------------
-print "ModelSpec and neural computation toolbox tests..."
+print("ModelSpec and neural computation toolbox tests...")
def make_noise_signal(dt, t_end, mean, stddev, num_cells, seed=None):
"""Helper function: Gaussian white noise at sample rate = dt for 1 or more cells,
@@ -251,4 +251,4 @@
v2line = plt.plot(v_dat['t'], v_dat['cell2.V'])
plt.show()
-print " ... passed"
+print(" ... passed")
--- ./PyDSTool/tests/ML_adjointPRC.py (original)
+++ ./PyDSTool/tests/ML_adjointPRC.py (refactored)
@@ -49,7 +49,7 @@
# ------------------------------------------------------------
-print '-------- Test: PRC on Morris-Lecar system'
+print('-------- Test: PRC on Morris-Lecar system')
par_args = {'gca': 4, 'gk': 8, 'gl': 2,
'vca': 120, 'vk': -80, 'vl': -60,
'v1': -1.2, 'v2': 18, 'v3': 4, 'v4': 17.4,
@@ -65,11 +65,11 @@
'term': False}, ['v'],
targetlang='c')
-print "Making ML neuron"
+print("Making ML neuron")
ML = makeMLneuron('ML_PRCtest', 0.01, par_args, ic_args, [thresh_ev])
ML.set(tdata=[0, 500])
-print "Computing long orbit to converge to limit cycle"
+print("Computing long orbit to converge to limit cycle")
MLtraj = ML.compute('test')
evt=ML.getEventTimes()['thresh_ev']
MLpts = MLtraj.sample()
@@ -93,6 +93,6 @@
plot(po['t'],po['v'])
show()
-print "Calling adjoint PRC calculator"
+print("Calling adjoint PRC calculator")
PRCdata = adjointPRC(ML, po, 'v', 'I', numIntervals=200, numCollocation=5,
spike_est=50, doPlot=True, saveData=False, verbosity=1)
--- ./PyDSTool/tests/IF_squarespike_model.py (original)
+++ ./PyDSTool/tests/IF_squarespike_model.py (refactored)
@@ -99,7 +99,7 @@
if __name__=='__main__':
# need the __main__ to use above functions as imports for other
# scripts without running this part
- print '-------- IF model test 1'
+ print('-------- IF model test 1')
par_args_linear = {'Iapp': 1.3, 'gl': 0.1, 'vl': -67,
'threshval': -65, 'C': 1}
@@ -109,21 +109,21 @@
icdict = {'v': -80, 'excited': 0}
start = clock()
- print 'Computing trajectory...'
+ print('Computing trajectory...')
IFmodel.compute(trajname='onespike',
tdata=[0, 60],
ics=icdict,
verboselevel=0)
- print '\n... finished in %.3f seconds.\n' % (clock()-start)
+ print('\n... finished in %.3f seconds.\n' % (clock()-start))
IFmodel.set(pars={'Iapp': 1.0, 'threshval': -60})
- print 'Recomputing trajectory with new params...'
+ print('Recomputing trajectory with new params...')
IFmodel.compute(trajname='twospike',
tdata=[0, 60],
ics=icdict)
- print 'Preparing plot'
+ print('Preparing plot')
plotData = IFmodel.sample('onespike', dt=0.05)
plotData2 = IFmodel.sample('twospike', ['v', 'testaux'], 0.05)
plt.ylabel('v, testaux')
@@ -132,26 +132,26 @@
vline2 = plt.plot(plotData2['t'], plotData2['v'])
aline = plt.plot(plotData['t'], plotData['testaux'])
- print "\nLast point of hybrid trajectory: "
- print "IFmodel.getEndPoint('onespike') -->\n", \
- IFmodel.getEndPoint('onespike')
+ print("\nLast point of hybrid trajectory: ")
+ print("IFmodel.getEndPoint('onespikRefactoringTool: Refactored ./PyDSTool/tests/IF_model_test.py
RefactoringTool: Refactored ./PyDSTool/tests/IF_delaynet_syn.py
e') -->\n", \
+ IFmodel.getEndPoint('onespike'))
- print "\nFirst point of hybrid trajectory: "
- print "IFmodel.getEndPoint('onespike', 0) -->\n", \
- IFmodel.getEndPoint('onespike', 0)
+ print("\nFirst point of hybrid trajectory: ")
+ print("IFmodel.getEndPoint('onespike', 0) -->\n", \
+ IFmodel.getEndPoint('onespike', 0))
- print "Testing IF hybrid model as mapping ..."
+ print("Testing IF hybrid model as mapping ...")
num_parts = len(IFmodel.getTrajTimePartitions('twospike'))
#eventvals = IFmodel('onespike', range(0, num_parts+1), asmap=True)
- eventvals = IFmodel('twospike', range(0, num_parts+1), asmap=True)
+ eventvals = IFmodel('twospike', list(range(0, num_parts+1)), asmap=True)
for i in range(0,num_parts+1):
- print "(v, t) at event(%i) = (%.4f, %.4f)" % (i, eventvals(i)('v'),
- eventvals(i)('t'))
- print "\nAlternative access to explicit event info using " + \
- "getTrajEvents(trajname) method:\n"
+ print("(v, t) at event(%i) = (%.4f, %.4f)" % (i, eventvals(i)('v'),
+ eventvals(i)('t')))
+ print("\nAlternative access to explicit event info using " + \
+ "getTrajEvents(trajname) method:\n")
evs = IFmodel.getTrajEvents('twospike')
evtimes = IFmodel.getTrajEventTimes('onespike')
- print evs
+ print(evs)
assert len(evs['threshold']) == 2, "Problem with hybrid events"
assert len(evtimes['threshold']) == 4, "Problem with hybrid events"
assert allclose(evtimes['threshold'][3], 54.009, 1e-3), \
@@ -159,6 +159,6 @@
assert allclose(evs['threshold'][1]['v'], -60, 1e-3), \
"Problem with hybrid events"
- print "\nDepending on your platform and matplotlib configuration you may need"
- print " to execute the plt.show() command to see the plots"
+ print("\nDepending on your platform and matplotlib configuration you may need")
+ print(" to execute the plt.show() command to see the plots")
# plt.show()
--- ./PyDSTool/tests/IF_model_test.py (original)
+++ ./PyDSTool/tests/IF_model_test.py (refactored)
@@ -18,7 +18,7 @@
# ---------------------------------------------------------------------------
-print '-------- Model test'
+print('-------- Model test')
all_model_names = ['leak', 'spike']
# 'excited' is an internal variable of the model, and is used to
@@ -76,18 +76,18 @@
IFmodel = Model.HybridModel({'name': 'IF_fit', 'modelInfo': modelInfoDict})
-print "Computing trajectory...\n"
+print("Computing trajectory...\n")
start = clock()
IFmodel.compute(trajname='onespike', tdata=[0,30], ics=ics, verboselevel=2, force=True)
-print '... finished in %.3f seconds.\n' % (clock()-start)
+print('... finished in %.3f seconds.\n' % (clock()-start))
-print 'Preparing plot to show non-identity mapping of epoch state transitions'
+print('Preparing plot to show non-identity mapping of epoch state transitions')
plotData = IFmodel.sample('onespike', ['V'], 0.02)
plt.ylabel('V')
plt.xlabel('t')
vline = plt.plot(plotData['t'], plotData['V'])
-print "\n\nInformation about Model's components:\n"
+print("\n\nInformation about Model's components:\n")
info(IFmodel.query('submodels'))
plt.show()
--- ./PyDSTool/tests/IF_delaynet_syn.py (original)
+++ ./PyDSTool/tests/IF_delaynet_syn.py (refactored)
@@ -158,9 +158,9 @@
# -------------------------------------------------------------------------
-print '-------- IF network test with delayed pulse coupling'
-
-print "Building coupled IF model\n"
+print('-------- IF network test with delayed pulse coupling')
+
+print("Building coupled IF model\n")
delay = Par('6', 'delay')
vreset = Par('-90', 'Vreset')
@@ -194,7 +194,7 @@
# -------------------------------------------------------------------------
-print "Computing trajectory...\n"
+print("Computing trajectory...\n")
icdict = {'IF1.V': -76, 'IF2.V': -66, 'IF1.excited': 0, 'IF2.excited': 0,
'IF1.syn_IF2_IF1.s': 0, 'IF2.syn_IF1_IF2.s': 0}
sRefactoringTool: Refactored ./PyDSTool/tests/IF_delaynet.py
RefactoringTool: Refactored ./PyDSTool/tests/HH_model_testbounds.py
RefactoringTool: Refactored ./PyDSTool/tests/HH_model_Cintegrator_testbounds.py
tart = clock()
@@ -202,11 +202,11 @@
tdata=[0, 1000],
ics=icdict,
verboselevel=0)
-print '... finished in %.3f seconds.\n' % (clock()-start)
-
-# -------------------------------------------------------------------------
-
-print "Testing synch orbits"
+print('... finished in %.3f seconds.\n' % (clock()-start))
+
+# -------------------------------------------------------------------------
+
+print("Testing synch orbits")
icdict['IF1.V'] = icdict['IF2.V']
IFmodel.compute(trajname='synch_test', tdata=[0,30], ics=icdict)
assert IFmodel.getTrajEventTimes('synch_test')['IF1_thresh'][-1] - \
--- ./PyDSTool/tests/IF_delaynet.py (original)
+++ ./PyDSTool/tests/IF_delaynet.py (refactored)
@@ -108,9 +108,9 @@
# -------------------------------------------------------------------------
-print '-------- IF network test with delayed pulse coupling'
+print('-------- IF network test with delayed pulse coupling')
-print "Building coupled IF model\n"
+print("Building coupled IF model\n")
delay = Par('9', 'delay')
vreset = Par('-90', 'Vreset')
@@ -142,7 +142,7 @@
# -------------------------------------------------------------------------
-print "Computing trajectory...\n"
+print("Computing trajectory...\n")
icdict = {'IF1.V': -75, 'IF2.V': -85}
def test():
IFmodel.compute(trajname='test',
@@ -151,7 +151,7 @@
verboselevel=0)
start = clock()
test()
-print '... finished in %.3f seconds.\n' % (clock()-start)
+print('... finished in %.3f seconds.\n' % (clock()-start))
# -------------------------------------------------------------------------
--- ./PyDSTool/tests/HH_model_testbounds.py (original)
+++ ./PyDSTool/tests/HH_model_testbounds.py (refactored)
@@ -56,14 +56,14 @@
if __name__=='__main__':
- print '-------- Test: Hodgkin-Huxley system'
+ print('-------- Test: Hodgkin-Huxley system')
par_args = {'gna': 100, 'gk': 80, 'gl': 0.1,
'vna': 50, 'vk': -100, 'vl': -67,
'I': 1.75, 'C': 1.0}
ic_args = {'v':-70.0, 'm': 0, 'h': 1, 'n': 0}
# test single terminal event first
- print "Testing bounds terminal event and its sampling"
+ print("Testing bounds terminal event and its sampling")
HH = makeHHneuron('HHtest_bdev', par_args, ic_args, [],
enforce_bds=True)
@@ -74,19 +74,19 @@
assert trajdata['v_bd1'][0]==50
assert trajdata['v_bd0'][0]==-90
assert len(HH.getEventTimes()['v_domlo']) > 0
- print "Voltage hit low domain bound defined by event v_domlo:"
- print HH.getEventTimes()['v_domlo']
+ print("Voltage hit low domain bound defined by event v_domlo:")
+ print(HH.getEventTimes()['v_domlo'])
- print 'Testing continued integration, having now set voltage domain to be [-100,20]'
+ print('Testing continued integration, having now set voltage domain to be [-100,20]')
HH.set(xdomain={'v':[-100,20]}, tdata=[HHtraj.indepdomain[1],50])
HHtraj2 = HH.compute('test_cont', 'c')
assert len(HH.getEventTimes()['v_domhi']) > 0
- print "Sampled this data up until the event v_domhi:"
- print HH.getEventTimes()['v_domhi']
+ print("Sampled this data up until the event v_domhi:")
+ print(HH.getEventTimes()['v_domhi'])
- print "Plotting continued orbit..."
+ print("Plotting continued orbit...")
plotData = HHtraj2.sample(dt=0.1)
- evt=HH.getEventTimes().values()[0]
+ evt=list(HH.getEventTimes().values())[0]
yaxislabelstr = 'v'
plt.ylabel(yaxislabelstr)
plt.xlabel('t')
--- ./PyDSTool/tests/HH_model_Cintegrator_testbounds.py (original)
+++ ./PyDSTool/tests/HH_model_Cintegrator_testbounds.py (refactored)
@@ -58,14 +58,14 @@
if __name__=='__main__':
- print '-------- Test: Hodgkin-Huxley system'
+ print('-------- Test: Hodgkin-Huxley system')
par_args = {'gna': 100, 'gk': 80, 'gl': 0.1,
'vna': 50, 'vk': -100, 'vl': -67,
'I': 1.75, 'C': 1.0}
ic_args = {'v':-70.0, 'm': 0, 'h': 1, 'n': 0}
# test single terminal evenRefactoringTool: Refactored ./PyDSTool/tests/HH_model_Cintegrator.py
RefactoringTool: Refactored ./PyDSTool/tests/HH_model.py
t first
- print "Testing bounds terminal event and its sampling"
+ print("Testing bounds terminal event and its sampling")
bd_event = Events.makeZeroCrossEvent('v-getbound("v",1)', 1,
{'name': 'bd_ev',
@@ -82,11 +82,11 @@
assert trajdata['v_bd1'][0]==50
assert trajdata['v_bd0'][0]==-100
- print 'Testing continued integration from t=25, having now set'
- print 'voltage domain to be [-100,20]'
+ print('Testing continued integration from t=25, having now set')
+ print('voltage domain to be [-100,20]')
HH.set(xdomain={'v':[-100,20]}, tdata=[0,50])
HHtraj2 = HH.compute('test_cont', 'c')
- print "Sampled this data up until the event", HH.getEventTimes(), ":"
+ print("Sampled this data up until the event", HH.getEventTimes(), ":")
plotData = HHtraj2.sample(dt=0.1)
evt=HH.getEventTimes()['bd_ev']
--- ./PyDSTool/tests/HH_model_Cintegrator.py (original)
+++ ./PyDSTool/tests/HH_model_Cintegrator.py (refactored)
@@ -55,14 +55,14 @@
# ------------------------------------------------------------
-print '-------- Test: Hodgkin-Huxley system'
+print('-------- Test: Hodgkin-Huxley system')
par_args = {'gna': 100, 'gk': 80, 'gl': 0.1,
'vna': 50, 'vk': -100, 'vl': -67,
'I': 1.75, 'C': 1.0}
ic_args = {'v':-70.0, 'm': 0, 'h': 1, 'n': 0}
# test single terminal event first
-print "Testing single terminal event and its sampling"
+print("Testing single terminal event and its sampling")
thresh_ev = Events.makeZeroCrossEvent('v', 1,
{'name': 'thresh_ev',
@@ -79,15 +79,15 @@
nobuild=True)
# test inclusion of other libraries in C file (not used in this example!)
HH_term.makeLib(include=['limits.h'])
-print "Successfully tested inclusion of additional C libraries into vector"
-print "field definition code."
+print("Successfully tested inclusion of additional C libraries into vector")
+print("field definition code.")
HH_term.set(tdata=[0, 25])
start = clock()
HHtraj_term = HH_term.compute('test_term')
-print 'Computed trajectory in %.3f seconds.\n' % (clock()-start)
+print('Computed trajectory in %.3f seconds.\n' % (clock()-start))
trajdata = HHtraj_term.sample(dt=1.0)
-print "Sampled this data at dt=1.0 up to the event", HH_term.getEventTimes(), ":"
-print trajdata['v'], "\n"
+print("Sampled this data at dt=1.0 up to the event", HH_term.getEventTimes(), ":")
+print(trajdata['v'], "\n")
# HH is a "Generator" object (an ODE in this case)
# (Generator is the new name for the DynamicalSystem class, because some
@@ -96,23 +96,23 @@
HH = makeHHneuron('HH_model_test', par_args, ic_args, [thresh_ev])
HH.set(tdata=[0, 50])
-print 'Integrating...'
+print('Integrating...')
start = clock()
HHtraj = HH.compute('test')
-print ' ... finished in %.3f seconds.\n' % (clock()-start)
+print(' ... finished in %.3f seconds.\n' % (clock()-start))
plotData = HHtraj.sample(dt=0.1)
evt=HH.getEventTimes()['thresh_ev']
-print 'Saving Model and Trajectory...'
+print('Saving Model and Trajectory...')
saveObjects([HH, HHtraj], 'temp_HH_Cintegrator.pkl', True)
-print 'Testing continued integration'
+print('Testing continued integration')
new_t0 = HHtraj.indepdomain[1]
HH.set(tdata=[new_t0,new_t0+20])
HHtraj2 = HH.compute('test_cont', 'c')
-print "Non-terminal events found:", HH.getEvents()
+print("Non-terminal events found:", HH.getEvents())
-print 'Preparing plot'
+print('Preparing plot')
plotData2 = HHtraj2.sample(dt=0.1)
evt2=HH.getEventTimes()['thresh_ev']
yaxislabelstr = 'v'
--- ./PyDSTool/tests/HH_model.py (original)
+++ ./PyDSTool/tests/HH_model.py (refactored)
@@ -62,14 +62,14 @@
if __name__=='__main__':
# need the __main__ to use above functions as imports without running this part
- print '-------- Test: Hodgkin-Huxley system'
+ print('-------- Test: Hodgkin-Huxley system')
par_args = {'gna': 100, 'gk': 80, 'gl': 0.1,
'vna': 50, 'vk': -100, 'vl': -67,
'Iapp': 1.75, 'C': 1.0}
ic_args RefactoringTool: Refactored ./PyDSTool/tests/HH_loaded_Cintegrator.py
RefactoringTool: Refactored ./PyDSTool/tests/HH_loaded.py
RefactoringTool: Refactored ./PyDSTool/tests/HH_adjointPRC.py
= {'v':-70.0, 'm': 0, 'h': 1, 'n': 0}
# test single terminal event first
- print "Testing single terminal event and its sampling"
+ print("Testing single terminal event and its sampling")
thresh_ev = Events.makePythonStateZeroCrossEvent('v', 0, 1,
{'name': 'thresh_ev',
@@ -88,10 +88,10 @@
HH_term.set(tdata=[0, 25])
start = clock()
HHtraj_term = HH_term.compute('test_term')
- print 'Computed trajectory in %.3f seconds.\n' % (clock()-start)
+ print('Computed trajectory in %.3f seconds.\n' % (clock()-start))
trajdata = HHtraj_term.sample(dt=1.0, precise=True)
- print "sampled this data up until the event", HH_term.getEventTimes(), ":"
- print trajdata['v'], "\n"
+ print("sampled this data up until the event", HH_term.getEventTimes(), ":")
+ print(trajdata['v'], "\n")
HH = makeHHneuron('HHtest', par_args, ic_args, [thresh_ev])
@@ -109,33 +109,33 @@
# equations, are not dynamical systems!)
HH.set(tdata=[0, 6.797])
- print 'Integrating...'
+ print('Integrating...')
start = clock()
HHtraj = HH.compute('test')
- print ' ... finished in %.3f seconds.\n' % (clock()-start)
+ print(' ... finished in %.3f seconds.\n' % (clock()-start))
evt = HH.getEventTimes()['thresh_ev']
evt_same = HH.getEventTimes('thresh_ev')
assert evt == [] == evt_same
- print 'Saving Model and Trajectory...'
+ print('Saving Model and Trajectory...')
saveObjects([HH, HHtraj], 'temp_HH.pkl', True)
# try a longer run
- print "Trying a longer run"
+ print("Trying a longer run")
HH.set(tdata=[0, 40])
HHtraj2 = HH.compute('test_long')
evts=HH.getEvents()
HH.set(tdata=[40, 60])
HHtraj3 = HH.compute('test_long_c','c')
- print "In 50ms, found the following events:"
+ print("In 50ms, found the following events:")
evts_c=HH.getEvents()
all_evts = copy(evts)
- for k, a in evts_c.items():
+ for k, a in list(evts_c.items()):
if k in evts and a is not None:
all_evts[k].append(a)
else:
all_evts[k] = a
- print all_evts
+ print(all_evts)
assert len(all_evts['thresh_ev']) == 4, "Problem with ODE events"
assert allclose(all_evts['thresh_ev']['t'][3], 56.218, 1e-3), "Problem with ODE events"
@@ -147,8 +147,8 @@
# pick out first event
evt = evts['thresh_ev']['t'][0]
plt.plot(evt, HHtraj(evt, 'v'), 'ro')
- print "Showing longer trajectory with +10mV offset, using the syntax"
- print ">>> plotData2['v'] += 10"
+ print("Showing longer trajectory with +10mV offset, using the syntax")
+ print(">>> plotData2['v'] += 10")
plotData2 = HHtraj2.sample()
plotData3 = HHtraj3.sample()
plotData2['v'] += 10 # could have plotted plotData2['v']+10
--- ./PyDSTool/tests/HH_loaded_Cintegrator.py (original)
+++ ./PyDSTool/tests/HH_loaded_Cintegrator.py (refactored)
@@ -7,7 +7,7 @@
try:
objs = loadObjects('temp_HH_Cintegrator.pkl')
except:
- print "Only run after test 'HH_model_Cintegrator.py'"
+ print("Only run after test 'HH_model_Cintegrator.py'")
raise
HH = objs[0]
HHtraj1 = objs[1]
--- ./PyDSTool/tests/HH_loaded.py (original)
+++ ./PyDSTool/tests/HH_loaded.py (refactored)
@@ -6,7 +6,7 @@
try:
objs = loadObjects('temp_HH.pkl')
except:
- print "Only run after test 'HH_model.py'"
+ print("Only run after test 'HH_model.py'")
raise
HH = objs[0]
HHtraj1 = objs[1]
--- ./PyDSTool/tests/HH_adjointPRC.py (original)
+++ ./PyDSTool/tests/HH_adjointPRC.py (refactored)
@@ -60,7 +60,7 @@
# ------------------------------------------------------------
-print '-------- Test: PRC on Hodgkin-Huxley system'
+print('-------- Test: PRC on Hodgkin-Huxley system')
par_args = {'gna': 120, 'gk': 36, 'gl': 0.3,
'vna': 115, 'vk': -12, 'vl': 10.559,
'T': 6.3, 'I': 12, 'C': 1.0}
@@ -76,12 +76,12 @@
'term': False}, ['v'],
targetlang='c')
-print "Making RefactoringTool: Refactored ./PyDSTool/tests/HH_DSSRTtest.py
HH neuron"
+print("Making HH neuron")
HH = makeHHneuron('HH_PRCtest', 0.01, par_args, ic_args, [thresh_ev],
special=linspace(0,100,100/0.001))
HH.set(tdata=[0, 100])
-print "Computing long orbit to converge to limit cycle"
+print("Computing long orbit to converge to limit cycle")
HHtraj = HH.compute('test')
evt=HH.getEventTimes()['thresh_ev']
HHpts = HHtraj.sample()
@@ -105,6 +105,6 @@
plot(po['t'],po['v'])
show()
-print "Calling adjoint PRC calculator"
+print("Calling adjoint PRC calculator")
PRCdata = adjointPRC(HH, po, 'v', 'I', numIntervals=300, numCollocation=5,
spike_est=10, doPlot=True, saveData=False, verbosity=1)
--- ./PyDSTool/tests/HH_DSSRTtest.py (original)
+++ ./PyDSTool/tests/HH_DSSRTtest.py (refactored)
@@ -49,7 +49,7 @@
'tau_h', 'inf_h']
if aux_vars is not None:
DSargs['varspecs'].update(aux_vars)
- DSargs['auxvars'].extend(aux_vars.keys())
+ DSargs['auxvars'].extend(list(aux_vars.keys()))
DSargs['pars'] = par_args
DSargs['fnspecs'] = auxdict
DSargs['xdomain'] = {'v': [-130, 70], 'm': [0,1], 'h': [0,1], 'n': [0,1]}
@@ -68,13 +68,13 @@
peak_ev = Events.makeZeroCrossEvent(vfn_str, -1,
{'name': 'peak_ev',
'eventtol': 1e-5,
- 'term': False}, ['v','m','n','h'], par_args.keys(),
+ 'term': False}, ['v','m','n','h'], list(par_args.keys()),
fnspecs={'Itot': auxdict['Itot']},
targetlang=targetlang)
trough_ev = Events.makeZeroCrossEvent(vfn_str, 1,
{'name': 'trough_ev',
'eventtol': 1e-5,
- 'term': False}, ['v','m','n','h'], par_args.keys(),
+ 'term': False}, ['v','m','n','h'], list(par_args.keys()),
fnspecs={'Itot': auxdict['Itot']},
targetlang=targetlang)
DSargs['events'] = [peak_ev, trough_ev]
@@ -124,7 +124,7 @@
Dargs.infs = {}
Dargs.psis = {}
-for var in ics.keys():
+for var in list(ics.keys()):
Dargs.taus[var] = 'tau_%s' % var
Dargs.infs[var] = 'inf_%s' % var
Dargs.psis[var] = None
@@ -168,7 +168,7 @@
plt.plot(ts, cycle['v'])
plt.plot(ts, cycle['inf_v'])
plt.title('v(t) and v_inf(t) for one approximate period')
-print "Graph shows **approximate** period of tonic spiking =", t1-t0
+print("Graph shows **approximate** period of tonic spiking =", t1-t0)
for ep in epochs:
ep.info()
@@ -185,9 +185,9 @@
def make_evs(evdefs, pars, evtol, targetlang):
extra_evs = []
- for evname, evargs in evdefs.items():
- all_pars = pars.keys()
- all_pars.extend(remain(evargs.pars, pars.keys()))
+ for evname, evargs in list(evdefs.items()):
+ all_pars = list(pars.keys())
+ all_pars.extend(remain(evargs.pars, list(pars.keys())))
extra_evs.append(makeZeroCrossEvent(evargs.defn, evargs.dirn,
{'name': evname,
'eventtol': evtol, 'term': True},
@@ -221,7 +221,7 @@
# and whether epoch conditions are met throughout the trajectory.
#
# Acquire underlying Generator from target model interface
- gen = target.model.registry.values()[0]
+ gen = list(target.model.registry.values())[0]
ptsFS = target.test_traj.sample()
# pick up or create DSSRT assistant object for this regime
@@ -311,9 +311,9 @@
# diagnostics
if test1 and (not test3 or not test2):
- print "Time scale tests failed"
- print "Fast:", epoch_reg.fast, self.pars.fast
- print "Slow:", epoch_reg.slow, self.pars.slow
+ print("Time scale tests failed")
+ print("Fast:", epoch_reg.fast, self.pars.fast)
+ print("Slow:", epoch_reg.slow, self.pars.slow)
return test1 and test2 and test3
@@ -483,7 +483,7 @@
plt.title('Original (B) and hybrRefactoringTool: Refactored ./PyDSTool/tests/Dopri_backwards_test.py
RefactoringTool: No changes to ./PyDSTool/tests/DAE_example.py
RefactoringTool: Refactored ./PyDSTool/tests/CIN.py
id (G) model voltage vs. t')
## Bifurcation-like diagram, to compare at different parameter values
-print "\nComparing bifurcations of spiking onset"
+print("\nComparing bifurcations of spiking onset")
bifpar = 'Iapp'
bifpar_range = concatenate((linspace(0.2, 0.4, 7), linspace(0.5, 3, 18)))
@@ -505,19 +505,19 @@
return 0
# Compute long runs (100 ms) to approximate a settled periodic orbit
-print "\nOriginal model",
+print("\nOriginal model", end=' ')
sys.stdout.flush()
for bpval in bifpar_range:
- print ".",
+ print(".", end=' ')
sys.stdout.flush()
HH.set(pars={bifpar: bpval}, tdata=[0,100])
traj = HH.compute('orig_bif')
period_data_orig.append(find_period(traj))
-print "\nHybrid model",
+print("\nHybrid model", end=' ')
sys.stdout.flush()
for i, bpval in enumerate(bifpar_range):
- print ".",
+ print(".", end=' ')
sys.stdout.flush()
hybrid_HH.set(pars={bifpar: bpval})
hybrid_HH.compute('hyb_bif', tdata=[0,100], ics=ics, verboselevel=0,
@@ -527,6 +527,6 @@
plt.figure()
plt.plot(bifpar_range, period_data_hyb, 'ko')
plt.plot(bifpar_range, period_data_orig, 'kx')
-print "\nDepending on your platform and matplotlib configuration you may need"
-print " to execute the plt.show() command to see the plots"
+print("\nDepending on your platform and matplotlib configuration you may need")
+print(" to execute the plt.show() command to see the plots")
# plt.show()
--- ./PyDSTool/tests/Dopri_backwards_test.py (original)
+++ ./PyDSTool/tests/Dopri_backwards_test.py (refactored)
@@ -21,7 +21,7 @@
ode = Generator.Dopri_ODEsystem(DSargs)
ode.set(tdata=[0, 10])
trajf = ode.compute('testf')
-print "======================"
+print("======================")
DSargsB = args()
DSargsB.varspecs = {'x': 'k*x'}
DSargsB.pars = {'k': .1}
@@ -34,7 +34,7 @@
odeb.set(tdata=[-10, 0])
trajb = odeb.compute('testb', 'b')
-print 'Preparing plot (curves should align to be a single smooth curve)'
+print('Preparing plot (curves should align to be a single smooth curve)')
plotDataf = trajf.sample(dt=0.1)
plotDatab = trajb.sample(dt=0.1)
--- ./PyDSTool/tests/CIN.py (original)
+++ ./PyDSTool/tests/CIN.py (refactored)
@@ -24,17 +24,17 @@
# test of inherited sub-components
c=MNcell('c')
-print "Inherited compatible sub-components of an MN cell are:"
+print("Inherited compatible sub-components of an MN cell are:")
allcompats = [className(csub) for csub in c._allSubcomponentTypes]
-print allcompats, "\n"
+print(allcompats, "\n")
assert allcompats==['channel', 'Par', 'Var', 'Input', 'Fun', 'Component']
def gaussianICs(varnames, mu, sigma):
- return dict(zip(varnames, [random.gauss(mu, sigma) for v in varnames]))
+ return dict(list(zip(varnames, [random.gauss(mu, sigma) for v in varnames])))
def uniformICs(varnames, a, b):
- return dict(zip(varnames, [random.uniform(a, b) for v in varnames]))
+ return dict(list(zip(varnames, [random.uniform(a, b) for v in varnames])))
defICs_soma = {
@@ -47,7 +47,7 @@
def defaultICs(cell):
defICs = defICs_soma[type(cell)]
ics = {}
- for k, v in defICs.iteritems():
+ for k, v in defICs.items():
ics[cell.name+'.'+k] = v
return ics
@@ -66,13 +66,13 @@
noauxs = True
auxwarning_part="Building model with auxiliary variables"
if noauxs:
- print "Not "+auxwarning_part.lower()
+ print("Not "+auxwarning_part.lower())
else:
- print auxwarning_part
+ print(auxwarning_part)
targetGen = 'Dopri_ODEsystem'
-print "Target integrator is "+targetGen
-print "------------------------------------"
+print("Target integrator is "+targetGen)
+print("------------------------------------")
# measure time to build model
t0 = clock()
@@ -165,7 +165,7 @@
HHnet = makePointNeuronNetwork('HHnet', [RGNcell1, MNcell1, synRGN_MN])
t1=clock()
-print "Compiled network specification in %f seconds"%(t1-t0)
+print("Compiled network specification in %f seconds"%(t1-t0))
## uncomment for easy interactive reference at prompt
#flatspec = HHnet.flattenSpec()
@@ -188,8 +188,8 @@
CB.set(ics=ic_args_net,RefactoringTool: Refactored ./PyDSTool/scipy_ode.py
checklevel=0)
t1=clock()
-print "Instantiated model for target ODE solver %s in %f seconds"%(targetGen,
- t1-t0)
+print("Instantiated model for target ODE solver %s in %f seconds"%(targetGen,
+ t1-t0))
def getTraj(dt_plot=0.25, tend=1000):
# dt_plot only controls resolution of plot data, not integration
@@ -199,16 +199,16 @@
return CB.sample('test')#, dt=dt_plot)
-print "\nParameters defined: check using who(Par)"
+print("\nParameters defined: check using who(Par)")
who(Par)
-print "\nCells defined: check using who(soma, deepSearch=True)"
+print("\nCells defined: check using who(soma, deepSearch=True)")
who(soma, deepSearch=True)
# try out conversion of expression to a function of the free names
RGNtaun_fun = expr2fun(RGNtaun, theta_n=-52, k_n=-5, taun_bar=10)
-print "\nRGNtaun_fun is a Python function created from the ModelSpecs using expr2fun()"
-print "RGNtaun_fun(-10.) =", RGNtaun_fun(-10.)
+print("\nRGNtaun_fun is a Python function created from the ModelSpecs using expr2fun()")
+print("RGNtaun_fun(-10.) =", RGNtaun_fun(-10.))
# --------------------------------------------------------------------
@@ -243,26 +243,26 @@
# --------------------------------------------------------------------
-print "\n\nComputing trajectory and getting plot data..."
+print("\n\nComputing trajectory and getting plot data...")
t0=clock()
v_dat = getTraj()
t1=clock()
-print "... finished in %f seconds\n"%(t1-t0)
+print("... finished in %f seconds\n"%(t1-t0))
#plotActivation(MNtaun, [-100,30], [MNtheta_n, MNk_n, MNtaun_bar])
plotVoltages(v_dat)
plt.figure()
-print "Plotting synaptic facilitation variable, sRM.d ..."
+print("Plotting synaptic facilitation variable, sRM.d ...")
plot(v_dat['t'], v_dat['sRM.d'])
-print "Setting other terminal events ..."
+print("Setting other terminal events ...")
CB.setDSEventActive(target='HHnet', eventTarget='RGNcell1_K_n_stat_dec_evt',
flagVal=True)
CB.setDSEventTerm(target='HHnet', eventTarget='RGNcell1_K_n_stat_dec_evt',
flagVal=True)
CB.compute(trajname='test2', tdata=[0,300])
-print "Computed additional trajectory."
+print("Computed additional trajectory.")
###### Other useful operations with CIN
--- ./PyDSTool/scipy_ode.py (original)
+++ ./PyDSTool/scipy_ode.py (refactored)
@@ -151,7 +151,7 @@
def set_initial_value(self,y,t=0.0):
"""Set initial conditions y(t) = y."""
- if type(y) in [types.IntType,types.FloatType]:
+ if type(y) in [int,float]:
y = [y]
n_prev = len(self.y)
self.y = asarray(y,'d')
@@ -165,8 +165,8 @@
"""Set integrator by name."""
integrator = find_integrator(name)
if integrator is None:
- print 'No integrator name match with %s or is not available.'\
- %(`name`)
+ print('No integrator name match with %s or is not available.'\
+ %(repr(name)))
else:
self._integrator = integrator(**integrator_params)
if not len(self.y):
@@ -233,18 +233,17 @@
Return 2-tuple (y1,t1) where y1 is the result and t=t1
defines the stoppage coordinate of the result.
"""
- raise NotImplementedError,\
- 'all integrators must define run(f,jac,t0,t1,y0,f_params,jac_params)'
+ raise NotImplementedError('all integrators must define run(f,jac,t0,t1,y0,f_params,jac_params)')
def step(self,f,jac,y0,t0,t1,f_params,jac_params):
"""Make one integration step and return (y1,t1)."""
- raise NotImplementedError,'%s does not support step() method' %\
- (self.__class__.__name__)
+ raise NotImplementedError('%s does not support step() method' %\
+ (self.__class__.__name__))
def run_relax(self,f,jac,y0,t0,t1,f_params,jac_params):
"""Integrate from t=t0 to t>=t1 and return (y1,t)."""
- raise NotImplementedERefactoringTool: Refactored ./PyDSTool/parseUtils.py
rror,'%s does not support run_relax() method' %\
- (self.__class__.__name__)
+ raise NotImplementedError('%s does not support run_relax() method' %\
+ (self.__class__.__name__))
#XXX: __str__ method for getting visual state of the integrator
@@ -252,7 +251,7 @@
try:
import scipy.integrate.vode as _vode
except ImportError:
- print sys.exc_value
+ print(sys.exc_info()[1])
_vode = None
runner = getattr(_vode,'dvode',None)
@@ -282,7 +281,7 @@
if re.match(method,r'adams',re.I): self.meth = 1
elif re.match(method,r'bdf',re.I): self.meth = 2
- else: raise ValueError,'Unknown integration method %s'%(method)
+ else: raise ValueError('Unknown integration method %s'%(method))
self.with_jacobian = with_jacobian
self.rtol = rtol
self.atol = atol
@@ -336,7 +335,7 @@
elif mf in [24,25]:
lrw = 22 + 11*n + (3*self.ml+2*self.mu)*n
else:
- raise ValueError,'Unexpected mf=%s'%(mf)
+ raise ValueError('Unexpected mf=%s'%(mf))
if miter in [0,3]:
liw = 30
else:
@@ -357,7 +356,7 @@
def run(self,*args):
y1,t,istate = self.runner(*(args[:5]+tuple(self.call_args)+args[5:]))
if istate <0:
- print 'vode:',self.messages.get(istate,'Unexpected istate=%s'%istate)
+ print('vode:',self.messages.get(istate,'Unexpected istate=%s'%istate))
self.success = 0
else:
self.call_args[3] = 2 # upgrade istate from 1 to 2
@@ -389,7 +388,7 @@
while ode_runner.successful() and ode_runner.t < 50:
y1 = ode_runner.integrate(ode_runner.t+2)
- print ode_runner.t,y1[:3]
+ print(ode_runner.t,y1[:3])
def test2(f, jac):
# Stiff problem. Requires analytic Jacobian.
@@ -399,11 +398,11 @@
method='bdf',
)
r.set_initial_value([1,0,0])
- print 'At t=%s y=%s'%(r.t,r.y)
+ print('At t=%s y=%s'%(r.t,r.y))
tout = 0.4
for i in range(12):
r.integrate(tout)
- print 'At t=%s y=%s'%(r.t,r.y)
+ print('At t=%s y=%s'%(r.t,r.y))
tout *= 10
@@ -425,9 +424,8 @@
if __name__ == "__main__":
- print 'Integrators available:',\
- ', '.join(map(lambda c:c.__name__,
- IntegratorBase.integrator_classes))
+ print('Integrators available:',\
+ ', '.join([c.__name__ for c in IntegratorBase.integrator_classes]))
test1(f1)
test2(f2, jac)
--- ./PyDSTool/parseUtils.py (original)
+++ ./PyDSTool/parseUtils.py (refactored)
@@ -8,9 +8,9 @@
"""
# IMPORTS
-from __future__ import division
-from errors import *
-from common import *
+
+from .errors import *
+from .common import *
import re
import math, random
from numpy import alltrue, sometrue
@@ -80,10 +80,8 @@
'exp2', 'radian', 'cosdg', 'sindg', 'tandg', 'cotdg',
'log1p', 'expm1', 'cosm1', 'round']
protected_specialfns = ['special_'+s for s in specialfns]
-protected_mathnames = filter(lambda s: not s.startswith('__'), \
- dir(math))
-protected_randomnames = filter(lambda s: not s.startswith('_'), \
- dir(random)) # yes, just single _
+protected_mathnames = [s for s in dir(math) if not s.startswith('__')]
+protected_randomnames = [s for s in dir(random) if not s.startswith('_')] # yes, just single _
# We add internal default auxiliary function names for use by
# functional specifications.
builtin_auxnames = ['globalindepvar', 'initcond', 'heav', 'if',
@@ -152,7 +150,7 @@
name_chars_RE = re.compile('\w')
alphanumeric_chars_RE = re.compile('[a-zA-Z0-9]') # without the '_'
alphabet_chars_RE = re.compile('[a-zA-Z]')
-num_chars = map(lambda i: str(i), range(10))
+num_chars = [str(i) for i in range(10)]
if DO_POW:
POW_STR = 'pow(%s,%s)'
@@ -180,7 +178,7 @@
# and Robert Clewley.
syms=token.tok_name
-for s in symbol.sym_name.keys():
+for s in list(symbol.sym_name.keys()):
syms[s]=symbol.sym_name[s]
@@ -295,8 +293,8 @@
# so ignore
return t
except:
- print t
- print ast2string(t)
+ print(t)
+ print(ast2string(t))
raise
elif t[0] == 'xor_expr' and t[2][0]=='CIRCUMFLEX':
# ^ syntax has complex binding rules in python parser's AST!
@@ -419,7 +417,7 @@
def sym2name(t):
if type(t) is parser.ASTType: return sym2name(t.tolist())
if not isinstance(t, list): return t
- return [syms[t[0]]]+map(sym2name,t[1:])
+ return [syms[t[0]]]+list(map(sym2name,t[1:]))
def string2ast(t):
return sym2name(ast2shortlist(parser.expr(t)))
@@ -928,7 +926,7 @@
# not copyable, so no need to worry
res = arg
try:
- for k, v in arg.iteritems():
+ for k, v in arg.items():
new_k = self.__call__(k)
new_v = self.__call__(v)
res[new_k] = new_v
@@ -1004,26 +1002,25 @@
return self.lookupDict.__contains__(symbol)
def keys(self):
- return self.lookupDict.keys()
+ return list(self.lookupDict.keys())
def values(self):
- return self.lookupDict.values()
+ return list(self.lookupDict.values())
def items(self):
- return self.lookupDict.items()
+ return list(self.lookupDict.items())
def iterkeys(self):
- return self.lookupDict.iterkeys()
+ return iter(self.lookupDict.keys())
def itervalues(self):
- return self.lookupDict.itervalues()
+ return iter(self.lookupDict.values())
def iteritems(self):
- return self.lookupDict.iteritems()
+ return iter(self.lookupDict.items())
def inverse(self):
- return symbolMapClass(dict(map(lambda (k,v): (v,k),
- self.lookupDict.iteritems())))
+ return symbolMapClass(dict([(k_v[1],k_v[0]) for k_v in iter(self.lookupDict.items())]))
def update(self, amap):
try:
@@ -1079,7 +1076,7 @@
def __call__(self, parserObj=None):
if parserObj is None:
# return all auxiliary functions known
- return self.auxnames.values()
+ return list(self.auxnames.values())
else:
try:
return [self.auxnames[parserObj]]
@@ -1088,7 +1085,7 @@
def removeAuxFn(self, auxfnName):
flagdelete = None
- for k, v in self.auxnames.iteritems():
+ for k, v in self.auxnames.items():
if v == auxfnName:
flagdelete = k
break
@@ -1129,7 +1126,7 @@
if type(specStr) is str:
self.specStr = specStr
else:
- print "Found type", type(specStr), ": ", specStr
+ print("Found type", type(specStr), ": ", specStr)
raise TypeError("specStr must be a string")
self.treatMultiRefs = treatMultiRefs
# record init options in case want to reset
@@ -1335,7 +1332,7 @@
## raise ValueError('Symbol ^ is not allowed. '
## 'Please use the pow() call')
## else:
- print "Problem with string '%s'"%specstr
+ print("Problem with string '%s'"%specstr)
raise ValueError('Symbol %s is illegal. '%stemp)
elif stemp == '[':
# self.treatMultiRefs == False and '[' in specialtokens
@@ -1484,7 +1481,7 @@
if s == 'for':
# check next char is '('
if specstr[scount] != '(':
- print "Next char found:", specstr[scount]
+ print("Next char found:", specstr[scount])
raise ValueError("Invalid 'for' macro syntax")RefactoringTool: Refactored ./PyDSTool/matplotlib_import.py
# find next ')' (for statement should contain no
# braces itself)
@@ -1502,9 +1499,9 @@
temp.tokenized[2] == temp.tokenized[4] == ',',
temp.tokenized[5] in ['+','*']]
if not alltrue(macrotests):
- print "specstr was: ", specstr
- print "tokens: ", temp.tokenized
- print "test results: ", macrotests
+ print("specstr was: ", specstr)
+ print("tokens: ", temp.tokenized)
+ print("test results: ", macrotests)
raise ValueError("Invalid sub-clause in "
"'for' macro")
# start next parsing iteration after the ')'
@@ -1765,7 +1762,7 @@
return tuple(themap(target))
elif hasattr(target, 'iteritems'):
o = {}
- for k, v in target.iteritems():
+ for k, v in target.items():
o[themap(k)] = v
return o
elif isinstance(target, str):
@@ -1929,7 +1926,7 @@
else:
splitdone = True
except:
- print "Error in matrix specification"
+ print("Error in matrix specification")
raise
return specdict
@@ -2029,7 +2026,7 @@
def makeParList(objlist, prefix=''):
"""wrap objlist into a comma separated string of str(objects)"""
- parlist = ', '.join(map(lambda i: prefix+str(i), objlist))
+ parlist = ', '.join([prefix+str(i) for i in objlist])
return parlist
@@ -2050,7 +2047,7 @@
# find callfn in source
findposlist = [source[currpos:].find(callfn+'(')]
try:
- findpos = min(filter(lambda x:x>=0,findposlist))+currpos
+ findpos = min([x for x in findposlist if x>=0])+currpos
except ValueError:
done = True
if not done:
@@ -2247,7 +2244,7 @@
sub_source = source[startbrace+1:endbrace]
embedded_calls = [sub_source.find(fname+'(') for fname in callfns]
try:
- subpositions = filter(lambda x:x>0, embedded_calls)
+ subpositions = [x for x in embedded_calls if x>0]
if subpositions == []:
filtered_sub_source = sub_source
new_d = {}
@@ -2270,7 +2267,7 @@
output += source[currpos:]
if dummies != {}:
new_dummies = dummies.copy()
- for k, v in dummies.items():
+ for k, v in list(dummies.items()):
new_v, new_d = replaceCallsWithDummies(v, callfns,
used_dummies, notFirst=True)
new_dummies[k] = new_v
@@ -2317,7 +2314,7 @@
# remove so that findpos except clause doesn't get confused
findposlist_candidates.remove(candidate_pos)
try:
- findpos = min(filter(lambda x:x>=0,findposlist))+currpos
+ findpos = min([x for x in findposlist if x>=0])+currpos
except ValueError:
# findposlist is empty
done = True
@@ -2338,7 +2335,7 @@
sub_source = source[startbrace+1:endbrace]
embedded_calls = [sub_source.find(fname+'(') for fname in callfns]
try:
- subpositions = filter(lambda x:x>0,embedded_calls)
+ subpositions = [x for x in embedded_calls if x>0]
if subpositions == []:
filtered_sub_source = sub_source
else:
--- ./PyDSTool/matplotlib_import.py (original)
+++ ./PyDSTool/matplotlib_import.py (refactored)
@@ -14,7 +14,7 @@
else:
import matplotlib.pyplot as plt
from matplotlib.pyplot import *
-except RuntimeError, err:
+except RuntimeError as err:
if str(err) == 'could not open display':
failed=True
else:
@@ -26,18 +26,18 @@
# DummyRefactoringTool: Refactored ./PyDSTool/integrator.py
RefactoringTool: Refactored ./PyDSTool/fixedpickle.py
plot overrides for PyDSTool when matplotlib fails to import
def plot(*args, **kw):
- print "Warning: plot does not work!"
+ print("Warning: plot does not work!")
def save_fig(fignum, fname, formats=[]):
- print "Warning: plot does not work!"
+ print("Warning: plot does not work!")
- print "Warning: matplotlib failed to import properly and so is not"
- print " providing a graphing interface"
+ print("Warning: matplotlib failed to import properly and so is not")
+ print(" providing a graphing interface")
plt = None # will cause an error if someone tries to access in order to plot
else:
import os
- from Trajectory import Trajectory
- from common import _num_types
+ from .Trajectory import Trajectory
+ from .common import _num_types
# Convenient shorthand to permit singleton numeric types and Trajectories
# in the plot arguments without first converting them to lists or arrays.
--- ./PyDSTool/integrator.py (original)
+++ ./PyDSTool/integrator.py (refactored)
@@ -2,9 +2,9 @@
Erik Sherwood, September 2006
"""
-from errors import PyDSTool_InitError as InitError
-from errors import PyDSTool_ClearError as ClearError
-from common import _all_int, _real_types, \
+from .errors import PyDSTool_InitError as InitError
+from .errors import PyDSTool_ClearError as ClearError
+from .common import _all_int, _real_types, \
verify_intbool, verify_pos, verify_nonneg, verify_values
from numpy import isinf, Inf
import operator
@@ -110,7 +110,7 @@
verify_nonneg('nExtInputs', nExtInputs, _all_int)
verify_nonneg('extraSpace', extraSpace, _all_int)
except:
- print sys.exc_info()[0], sys.exc_info()[1]
+ print(sys.exc_info()[0], sys.exc_info()[1])
raise InitError('Integrator initialization failed!')
@@ -366,7 +366,7 @@
if orientation > 0:
for y in range(len(extInputTimes[x])-1):
if extInputTimes[x][y] >= extInputTimes[x][y+1]:
- print x, y, extInputTimes[x][y],extInputTimes[x][y+1]
+ print(x, y, extInputTimes[x][y],extInputTimes[x][y+1])
raise ValueError("extInputTimes must be ordered consistently")
@@ -442,7 +442,7 @@
if not isinstance(ic, list):
raise TypeError("ic must be list")
if len(ic) != self.phaseDim:
- print "IC length %i didn't match phaseDim %i"%(len(ic), self.phaseDim), ic
+ print("IC length %i didn't match phaseDim %i"%(len(ic), self.phaseDim), ic)
raise ValueError('ic must have length equal to phaseDim')
for x in ic:
if not isinstance(x, _real_types):
--- ./PyDSTool/fixedpickle.py (original)
+++ ./PyDSTool/fixedpickle.py (refactored)
@@ -30,8 +30,8 @@
__version__ = "$Revision: 1.156 $" # Code version
from types import *
-from copy_reg import dispatch_table
-from copy_reg import _extension_registry, _inverted_registry, _extension_cache
+from copyreg import dispatch_table
+from copyreg import _extension_registry, _inverted_registry, _extension_cache
import marshal
import sys
import struct
@@ -199,7 +199,7 @@
"""
if protocol is not None and bin is not None:
- raise ValueError, "can't specify both 'protocol' and 'bin'"
+ raise ValueError("can't specify both 'protocol' and 'bin'")
if bin is not None:
warnings.warn("The 'bin' argument to Pickler() is deprecated",
PendingDeprecationWarning)
@@ -264,7 +264,7 @@
else:
return LONG_BINPUT + pack("<i", i)
- return PUT + `i` + '\n'
+ return PUT + repr(i) + '\n'
# Return a GET (BINGET, LONG_BINGET) opcode string, with argument i.
def get(self, i, pack=struct.pack):
@@ -274,7 +274,7 @@
else:
return LONG_BINGET + pack("<i", i)
- return GET + `i` + '\n'
+ return GET + repr(i) + '\n'
def save(self, obj):
# Check for persistent id (defined by a subclass)
@@ -317,7 +317,7 @@
try:
rv = reduce(self.proto)
except:
- print "Problem with ", obj
+ print("Problem with ", obj)
raise
else:
reduce = getattr(obj, "__reduce__", None)
@@ -477,7 +477,7 @@
self.write(BININT + pack("<i", obj))
return
# Text pickle, or int too big to fit in signed 4-byte format.
- self.write(INT + `obj` + '\n')
+ self.write(INT + repr(obj) + '\n')
dispatch[IntType] = save_int
def save_long(self, obj, pack=struct.pack):
@@ -489,14 +489,14 @@
else:
self.write(LONG4 + pack("<i", n) + bytes)
return
- self.write(LONG + `obj` + '\n')
+ self.write(LONG + repr(obj) + '\n')
dispatch[LongType] = save_long
def save_float(self, obj, pack=struct.pack):
if self.bin:
self.write(BINFLOAT + pack('>d', obj))
else:
- self.write(FLOAT + `obj` + '\n')
+ self.write(FLOAT + repr(obj) + '\n')
dispatch[FloatType] = save_float
def save_string(self, obj, pack=struct.pack):
@@ -507,7 +507,7 @@
else:
self.write(BINSTRING + pack("<i", n) + obj)
else:
- self.write(STRING + `obj` + '\n')
+ self.write(STRING + repr(obj) + '\n')
self.memoize(obj)
dispatch[StringType] = save_string
@@ -526,28 +526,28 @@
if StringType == UnicodeType:
# This is true for Jython
def save_string(self, obj, pack=struct.pack):
- unicode = obj.isunicode()
+ str = obj.isunicode()
if self.bin:
- if unicode:
+ if str:
obj = obj.encode("utf-8")
l = len(obj)
- if l < 256 and not unicode:
+ if l < 256 and not str:
self.write(SHORT_BINSTRING + chr(l) + obj)
else:
s = pack("<i", l)
- if unicode:
+ if str:
self.write(BINUNICODE + s + obj)
else:
self.write(BINSTRING + s + obj)
else:
- if unicode:
+ if str:
obj = obj.replace("\\", "\\u005c")
obj = obj.replace("\n", "\\u000a")
obj = obj.encode('raw-unicode-escape')
self.write(UNICODE + obj + '\n')
else:
- self.write(STRING + `obj` + '\n')
+ self.write(STRING + repr(obj) + '\n')
self.memoize(obj)
dispatch[StringType] = save_string
@@ -638,12 +638,12 @@
write(APPEND)
return
- r = xrange(self._BATCHSIZE)
+ r = range(self._BATCHSIZE)
while items is not None:
tmp = []
for i in r:
try:
- x = items.next()
+ x = next(items)
tmp.append(x)
except StopIteration:
items = None
@@ -668,7 +668,7 @@
write(MARK + DICT)
self.memoize(obj)
- self._batch_setitems(obj.iteritems())
+ self._batch_setitems(iter(obj.items()))
dispatch[DictionaryType] = save_dict
if not PyStringMap is None:
@@ -686,12 +686,12 @@
write(SETITEM)
return
- r = xrange(self._BATCHSIZE)
+ r = range(self._BATCHSIZE)
while items is not None:
tmp = []
for i in r:
try:
- tmp.append(items.next())
+ tmp.append(next(items))
except StopIteration:
items = None
break
@@ -833,7 +833,7 @@
if func in classmap:
return classmap[func]
- for name, module in sys.modules.items():
+ for name, module in list(sys.modules.items()):
if module is None:
continue # skip dummy package entries
if name != '__main__' and getattr(module, funcname, None) is func:
@@ -878,7 +878,7 @@
while 1:
key = read(1)
dispatch[key](self)
- except _Stop, stopinst:
+ except _Stop as stopinst:
return stopinst.value
# Return largest index k such that self.stack[k] is self.mark.
@@ -905,7 +905,7 @@
def load_proto(self):
proto = ord(self.read(1))
if not 0 <= proto <= 2:
- raise ValueError, "unsupported pickle protocol: %d" % proto
+ raise ValueError("unsupported pickle protocol: %d" % proto)
dispatch[PROTO] = load_proto
def load_persid(self):
@@ -940,7 +940,7 @@
try:
val = int(data)
except ValueError:
- val = long(data)
+ val = int(data)
self.append(val)
dispatch[INT] = load_int
@@ -957,7 +957,7 @@
dispatch[BININT2] = load_binint2
def load_long(self):
- self.append(long(self.readline()[:-1], 0))
+ self.append(int(self.readline()[:-1], 0))
dispatch[LONG] = load_long
def load_long1(self):
@@ -985,7 +985,7 @@
elif s in ["NAN","1.#QNAN","QNAN","1.#IND","IND","-1.#IND"]:
f = -((1e300*1e300)/(1e300*1e300))
else:
- raise ValueError, "Don't know what to do with "+`s`
+ raise ValueError("Don't know what to do with "+repr(s))
self.append(f)
dispatch[FLOAT] = load_float
@@ -998,11 +998,11 @@
for q in "\"'": # double or single quote
if rep.startswith(q):
if not rep.endswith(q):
- raise ValueError, "insecure string pickle"
+ raise ValueError("insecure string pickle")
rep = rep[len(q):-len(q)]
break
else:
- raise ValueError, "insecure string pickle"
+ raise ValueError("insecure string pickle")
self.append(rep.decode("string-escape"))
dispatch[STRING] = load_string
@@ -1012,12 +1012,12 @@
dispatch[BINSTRING] = load_binstring
def load_unicode(self):
- self.append(unicode(self.readline()[:-1],'raw-unicode-escape'))
+ self.append(str(self.readline()[:-1],'raw-unicode-escape'))
dispatch[UNICODE] = load_unicode
def load_binunicode(self):
len = mloads('i' + self.read(4))
- self.append(unicode(self.read(len),'utf-8'))
+ self.append(str(self.read(len),'utf-8'))
dispatch[BINUNICODE] = load_binunicode
def load_short_binstring(self):
@@ -1093,9 +1093,9 @@
if not instantiated:
try:
value = klass(*args)
- except TypeError, err:
- raise TypeError, "in constructor for %s: %s" % (
- klass.__name__, str(err)), sys.exc_info()[2]
+ except TypeError as err:
+ raise TypeError("in constructor for %s: %s" % (
+ klass.__name__, str(err))).with_traceback(sys.exc_info()[2])
self.append(value)
def load_inst(self):
@@ -1194,12 +1194,12 @@
def load_binget(self):
i = ord(self.read(1))
- self.append(self.memo[`i`])
+ self.append(self.memo[repr(i)])
dispatch[BINGET] = load_binget
def load_long_binget(self):
i = mloads('i' + self.read(4))
- self.append(self.memo[`i`])
+ self.append(self.memo[repr(i)])
dispatch[LONG_BINGET] = load_long_binget
def load_put(self):
@@ -1208,12 +1208,12 @@
def load_binput(self):
i = ord(self.read(1))
- self.memo[`i`] = self.stack[-1]
+ self.memo[repr(i)] = self.stack[-1]
dispatch[BINPUT] = load_binput
def load_long_binput(self):
i = mloads('i' + self.read(4))
- self.memo[`i`] = self.stack[-1]
+ self.mRefactoringTool: No changes to ./PyDSTool/errors.py
RefactoringTool: Refactored ./PyDSTool/conf.py
RefactoringTool: Refactored ./PyDSTool/common.py
emo[repr(i)] = self.stack[-1]
dispatch[LONG_BINPUT] = load_long_binput
def load_append(self):
@@ -1273,10 +1273,10 @@
# .update() business, and always uses
# PyObject_SetItem(inst.__dict__, key, value) in a
# loop over state.items().
- for k, v in state.items():
+ for k, v in list(state.items()):
setattr(inst, k, v)
if slotstate:
- for k, v in slotstate.items():
+ for k, v in list(slotstate.items()):
setattr(inst, k, v)
dispatch[BUILD] = load_build
@@ -1345,7 +1345,7 @@
# Extend to a full byte.
nibbles += 1
nbits = nibbles * 4
- x += 1L << nbits
+ x += 1 << nbits
assert x > 0
ashex = hex(x)
njunkchars = 2 + ashex.endswith('L')
@@ -1385,19 +1385,19 @@
nbytes = len(data)
if nbytes == 0:
- return 0L
+ return 0
ashex = _binascii.hexlify(data[::-1])
- n = long(ashex, 16) # quadratic time before Python 2.3; linear now
+ n = int(ashex, 16) # quadratic time before Python 2.3; linear now
if data[-1] >= '\x80':
- n -= 1L << (nbytes * 8)
+ n -= 1 << (nbytes * 8)
return n
# Shorthands
try:
- from cStringIO import StringIO
+ from io import StringIO
except ImportError:
- from StringIO import StringIO
+ from io import StringIO
def dump(obj, file, protocol=None, bin=None):
Pickler(file, protocol, bin).dump(obj)
--- ./PyDSTool/conf.py (original)
+++ ./PyDSTool/conf.py (refactored)
@@ -40,8 +40,8 @@
master_doc = 'index'
# General information about the project.
-project = u'PyDSTool'
-copyright = u'2010, Robert Clewley'
+project = 'PyDSTool'
+copyright = '2010, Robert Clewley'
# The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the
@@ -178,8 +178,8 @@
# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
- ('index', 'PyDSTool.tex', u'PyDSTool Documentation',
- u'Robert Clewley', 'manual'),
+ ('index', 'PyDSTool.tex', 'PyDSTool Documentation',
+ 'Robert Clewley', 'manual'),
]
# The name of an image file (relative to this directory) to place at the top of
@@ -211,6 +211,6 @@
# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
- ('index', 'pydstool', u'PyDSTool Documentation',
- [u'Robert Clewley'], 1)
+ ('index', 'pydstool', 'PyDSTool Documentation',
+ ['Robert Clewley'], 1)
]
--- ./PyDSTool/common.py (original)
+++ ./PyDSTool/common.py (refactored)
@@ -4,7 +4,7 @@
Robert Clewley, September 2005.
"""
-from errors import *
+from .errors import *
import sys, types
import numpy as npy
@@ -42,9 +42,9 @@
import os
if os.name == 'nt':
# slow object copying for you guys
- import fixedpickle as pickle
+ from . import fixedpickle as pickle
else:
- import cPickle as pickle
+ import pickle as pickle
# ----------------------------------------------------------------------------
### EXPORTS
@@ -410,7 +410,7 @@
# removed offset=0 from arg list
if len(self.__dict__) > 0:
res = "%s ("%attributeTitle
- for k, v in self.__dict__.iteritems():
+ for k, v in self.__dict__.items():
try:
istr = v._infostr(verbose-1) #, offset+2)
except AttributeError:
@@ -427,27 +427,27 @@
return self._infostr()
def info(self):
- print self._infostr()
+ print(self._infostr())
__str__ = __repr__
def values(self):
- return self.__dict__.values()
+ return list(self.__dict__.values())
def keys(self):
- return self.__dict__.keys()
+ return list(self.__dict__.keys())
def items(self):
- return self.__dict__.items()
+ return list(self.__dict__.items())
def itervalues(self):
- return self.__dict__.itervalues()
+ return iter(self.__dict__.values())
def iterkeys(self):
- return self.__dict__.iterkeys()
+ return iter(self.__dict__.keys())
def iteritems(self):
- return self.__dict__.iteritems()
+ return iter(self.__dict__.items())
def __getitem__(self, k):
return self.__dict__[k]
@@ -468,7 +468,7 @@
return self.__dict__.get(k, d)
def has_key(self, k):
- return self.__dict__.has_key(k)
+ return k in self.__dict__
def pop(self, k, d=None):
return self.__dict__.pop(k, d)
@@ -593,7 +593,7 @@
def clearWarnings(self):
self.warnings = []
- for obj in self.propagate_dict.values():
+ for obj in list(self.propagate_dict.values()):
try:
obj.diagnostics.clearWarnings()
except AttributeError:
@@ -605,7 +605,7 @@
def showWarnings(self):
if len(self.warnings)>0:
- print self.getWarnings()
+ print(self.getWarnings())
def getWarnings(self):
if len(self.warnings)>0:
@@ -640,7 +640,7 @@
def clearErrors(self):
self.errors = []
- for obj in self.propagate_dict.values():
+ for obj in list(self.propagate_dict.values()):
try:
obj.diagnostics.clearErrors()
except AttributeError:
@@ -652,7 +652,7 @@
def showErrors(self):
if len(self.errors)>0:
- print self.getErrors()
+ print(self.getErrors())
def getErrors(self):
if len(self.errors)>0:
@@ -696,7 +696,7 @@
or *not* containing the specified keys if option neg=True."""
out_d = {}
if neg:
- out_keys = remain(d.keys(), keys)
+ out_keys = remain(list(d.keys()), keys)
else:
out_keys = keys
for k in out_keys:
@@ -713,7 +713,7 @@
retstr = ''
if d != {}:
if order == []:
- order = d.keys()
+ order = list(d.keys())
for key in order:
itemlist = d[key]
for strlist in itemlist:
@@ -735,10 +735,10 @@
if var.is_continuous_valued():
out_varnames.append(varname)
out_vars.append(var)
- return dict(zip(out_varnames, out_vars))
- else:
- return dict(zip(sortedDictKeys(vardict), [copy(v) for v in \
- sortedDictValues(vardict)]))
+ return dict(list(zip(out_varnames, out_vars)))
+ else:
+ return dict(list(zip(sortedDictKeys(vardict), [copy(v) for v in \
+ sortedDictValues(vardict)])))
def insertInOrder(sourcelist, inslist, return_ixs=False, abseps=0):
@@ -832,9 +832,9 @@
for x, y in zip(a1,a2):
o.append(max(x,y))
except TypeError:
- print "Problem with type of arguments in arraymax:"
- print "Received a1 =", a1
- print " a2 =", a2
+ print("Problem with type of arguments in arraymax:")
+ print("Received a1 =", a1)
+ print(" a2 =", a2)
raise
return array(o,t)
@@ -978,7 +978,7 @@
if vars is None:
if x0type == 'array':
dim = len(x0)
- vars = range(dim)
+ vars = list(range(dim))
elif x0type == 'num':
dim = 1
vars = [0]
@@ -1007,8 +1007,8 @@
if sfx0[0] == 0:
raise TypeError("Invalid function return type")
except AssertionError:
- print "fx0 shape is", sfx0
- print fx0
+ print("fx0 shape is", sfx0)
+ print(fx0)
raise ValueError("Function should return an N-vector or N x 1 matrix,"
" but it returned a matrix with shape %s" % str(sfx0))
if isinstance(fx0, _float_types):
@@ -1029,7 +1029,7 @@
if axes is None:
if x0type in ['array', 'num']:
try:
- axes = range(sfx0[0])
+ axes = list(range(sfx0[0]))
except IndexError:
# then singleton (scalar) was returned
axes = [0]
@@ -1061,8 +1061,8 @@
else:
# Point
x0a = x0[vars].toarray()
- dx = dict(zip(vars,
- eps*(abs(x0a) + array(x0a==zeros(dim),'float64'))))
+ dx = dict(list(zip(vars,
+ eps*(abs(x0a) + array(x0a==zeros(dim),'float64')))))
try:
dim_mat = len(axes)
except TypeError:
@@ -1163,7 +1163,7 @@
try:
x0 = x0.astype(float)
except:
- print "Found type:", x0.dtype.type
+ print("Found type:", x0.dtype.type)
raise TypeError("Only real-valued arrays valid")
elif isinstance(x0, _real_types):
x0type = 'num'
@@ -1181,7 +1181,7 @@
if vars is None:
if x0type == 'array':
dim = len(x0)
- vars = range(dim)
+ vars = list(range(dim))
elif x0type == 'num':
dim = 1
vars = [0]
@@ -1221,8 +1221,8 @@
else:
raise TypeError("Invalid function return type")
except AssertionError:
- print "fx0 shape is", sfx0
- print fx0
+ print("fx0 shape is", sfx0)
+ print(fx0)
raise ValueError("Function should return an N-vector or N x 1 matrix,"
" but it returned a matrix with shape %s" % str(sfx0))
else:
@@ -1234,7 +1234,7 @@
if axes is None:
if x0type in ['array', 'num']:
try:
- axes = range(sfx0[0])
+ axes = list(range(sfx0[0]))
except IndexError:
# then singleton (scalar) was returned
axes = [0]
@@ -1268,8 +1268,8 @@
else:
# Point
x0a = x0[vars].toarray()
- dx = dict(zip(vars,
- eps*(abs(x0a) + array(x0a==zeros(dim),'float64'))))
+ dx = dict(list(zip(vars,
+ eps*(abs(x0a) + array(x0a==zeros(dim),'float64')))))
assert dir==1 or dir==-1, "Direction code must be -1 or 1"
try:
@@ -1544,9 +1544,9 @@
try:
code = compile(fstr, 'test', 'exec')
except:
- print " Cannot make unique function because of a syntax (or other) error " \
- "in supplied code:\n"
- print fstr
+ print(" Cannot make unique function because of a syntax (or other) error " \
+ "in supplied code:\n")
+ print(fstr)
raise
bracepos = fstr.index("(")
if idstr is None:
@@ -1589,7 +1589,7 @@
"""Convert occurrences of types / classes,
to pretty-printable strings."""
try:
- if type(x) in [types.InstanceType, types.TypeType]:
+ if type(x) in [types.InstanceType, type]:
return className(x, True)
elif isinstance(x, list):
# search through any iterable parts (that aren't strings)
@@ -1611,7 +1611,7 @@
elif isinstance(x, dict):
rx = "{"
if len(x)>0:
- for k, o in x.iteritems():
+ for k, o in x.items():
rx += object2str(k, digits) + ": " + object2str(o, digits) + ", "
return rx[:-2]+"}"
else:
@@ -1754,7 +1754,7 @@
# returns the mapping from the entries in an array or list to their indices
def makeArrayIxMap(a):
- return dict(zip(a, range(len(a))))
+ return dict(list(zip(a, list(range(len(a))))))
# invert an index mapping or other form of mapping
@@ -1766,12 +1766,12 @@
returned."""
if isinstance(themap, dict):
try:
- return dict(map(lambda (k,v): (v,k), themap.iteritems()))
+ return dict([(k_v[1],k_v[0]) for k_v in iter(themap.items())])
except TypeError:
# e.g., list objects are unhashable
# try it the slow way for this case
result = {}
- for k, v in themap.iteritems():
+ for k, v in themap.items():
if isinstance(v, (list,tuple)):
for val in v:
result[val] = k
@@ -1780,10 +1780,10 @@
return result
elif isinstance(themap, (list,tuple)):
# input domain is the position index
- return dict(zip(themap, range(len(themap))))
+ return dict(list(zip(themap, list(range(len(themap))))))
elif isinstance(themap, ndarray):
# input domain is the position index
- return dict(zip(themap.tolist(), range(len(themap))))
+ return dict(list(zip(themap.tolist(), list(range(len(themap))))))
elif hasattr(themap, 'inverse'):
# symbolMapClass type
return themap.inverse()
@@ -1867,13 +1867,13 @@
added filtering of keys.
"""
if onlykeys is None:
- keys = d.keys()
- else:
- keys = intersect(d.keys(), onlykeys)
+ keys = list(d.keys())
+ else:
+ keys = intersect(list(d.keys()), onlykeys)
keys.sort()
if reverse:
keys.reverse()
- return map(d.get, keys)
+ return list(map(d.get, keys))
def sortedDictKeys(d, onlykeys=None, reverse=False):
"""Return sorted list of keys from a dictionary.
@@ -1881,9 +1881,9 @@
Adapted from original function by Alex Martelli:
added filtering of keys."""
if onlykeys is None:
- keys = d.keys()
- else:
- keys = intersect(d.keys(), onlykeys)
+ keys = list(d.keys())
+ else:
+ keys = intersect(list(d.keys()), onlykeys)
keys.sort()
if reverse:
keys.reverse()
@@ -1895,9 +1895,9 @@
Adapted from an original function by Duncan Booth.
"""
if onlykeys is None:
- onlykeys = d.keys()
+ onlykeys = list(d.keys())
if byvalue:
- i = [(val, key) for (key, val) in d.items() if key in onlykeys]
+ i = [(val, key) for (key, val) in list(d.items()) if key in onlykeys]
i.sort()
if reverse:
i.reverse()
@@ -1905,7 +1905,7 @@
rkeys = [key for (val, key) in i]
else:
# by key
- i = [(key, val) for (key, val) in d.items() if key in onlykeys]
+ i = [(key, val) for (key, val) in list(d.items()) if key in onlykeys]
i.sort()
if reverse:
i.reverse()
@@ -1918,7 +1918,7 @@
sorted by value (default) or key.
Adapted from an original function by Duncan Booth.
"""
- return zip(*sortedDictLists(d, byvalue, onlykeys, reverse))
+ return list(zip(*sortedDictLists(d, byvalue, onlykeys, reverse)))
# ----------------------------------------------------------------------
@@ -1926,12 +1926,12 @@
# find intersection of two lists, sequences, etc.
def intersect(a, b):
- return filter(lambda e : e in b, a)
+ return [e for e in a if e in b]
# find remainder of two lists, sequences, etc., after intersection
def remain(a, b):
- return filter(lambda e : e not in b, a)
+ return [e for e in a if e not in b]
# ----------------------------------------------------------------------
@@ -2344,7 +2344,7 @@
self.vector_valued = False
self.yi = self.yi[:,npy.newaxis]
elif len(self.yi.shape)>2:
- raise ValueError, "y coordinates must be either scalars or vectors"
+ raise ValueError("y coordinates must be either scalars or vectors")
else:
self.vector_valued = True
@@ -2352,19 +2352,19 @@
self.n = n
nn, r = self.yi.shape
if nn!=n:
- raise ValueError, "%d x values provided and %d y values; must be equal" % (n, nn)
+ raise ValueError("%d x values provided and %d y values; must be equal" % (n, nn))
self.r = r
c = npy.zeros((n+1,r))
c[0] = yi[0]
Vk = npy.zeros((n,r))
- for k in xrange(1,n):
+ for k in range(1,n):
s = 0
while s<=k and xi[k-s]==xi[k]:
s += 1
s -= 1
Vk[0] = yi[k]/float(spy.factorial(s))
- for i in xrange(k-s):
+ for i in range(k-s):
assert xi[i]!=xi[k]
if s==0:
Vk[i+1] = (c[i]-Vk[i])/(xi[i]-xi[k])
@@ -2399,7 +2399,7 @@
pi = 1
p = npy.zeros((m,self.r))
p += self.c[0,npy.newaxis,:]
- for k in xrange(1,n):
+ for k in range(1,n):
w = x - self.xi[k-1]
pi = w*pi
p = p + npy.multiply.outer(pi,self.c[k])
@@ -2465,7 +2465,7 @@
p = npy.zeros((m,self.r))
p += self.c[0,npy.newaxis,:]
- for k in xrange(1,n):
+ for k in range(1,n):
w[k-1] = x - self.xi[k-1]
pi[k] = w[k-1]*pi[k-1]
p += npy.multiply.outer(pi[k],self.c[k])
@@ -2473,8 +2473,8 @@
cn = npy.zeros((max(der,n+1),m,r))
cn[:n+1,...] += self.c[:n+1,npy.newaxis,:]
cn[0] = p
- for k in xrange(1,n):
- for i in xrange(1,n-k+1):
+ for k in range(1,n):
+ for i in range(1,n-k+1):
pi[i] = w[k+i-1]*pi[i-1]+pi[i]
cn[k] = cn[k]+pi[i,:,npy.newaxis]*cn[k+i]
cn[k]*=factorial(k)
@@ -2554,11 +2554,11 @@
self.n = len(xi)
self.xi = npy.asarray(xi)
if yi is not None and len(yi)!=len(self.xi):
- raise ValueError, "yi dimensions do not match xi dimensions"
+ raise ValueError("yi dimensions do not match xi dimensions")
self.set_yi(yi)
self.wi = npy.zeros(self.n)
self.wi[0] = 1
- for j in xrange(1,self.n):
+ for j in range(1,self.n):
self.wi[:j]*=(self.xi[j]-self.xi[:j])
self.wi[j] = npy.multiply.reduce(self.xi[:j]-self.xi[j])
self.wi**=-1
@@ -2585,13 +2585,13 @@
self.vector_valued = False
yi = yi[:,npy.newaxis]
elif len(yi.shape)>2:
- raise ValueError, "y coordinates must be either scalars or vectors"
+ raise ValueError("y coordinates must be either scalars or vectors")
else:
self.vector_valued = True
n, r = yi.shape
if n!=len(self.xi):
- raise ValueError, "yi dimensions do not match xi dimensions"
+ raise ValueError("yi dimensions do not match xi dimensions")
self.yi = yi
self.r = r
@@ -2614,23 +2614,23 @@
"""
if yi is not None:
if self.yi is None:
- raise ValueError, "No previous yi value to update!"
+ raise ValueError("No previous yi value to update!")
yi = npy.asarray(yi)
if len(yi.shape)==1:
if self.vector_valued:
- raise ValueError, "Cannot extend dimension %d y vectors with scalars" % self.r
+ raise ValueError("Cannot extend dimension %d y vectors with scalars" % self.r)
yi = yi[:,npy.newaxis]
elif len(yi.shape)>2:
- raise ValueError, "y coordinates must be either scalars or vectors"
+ raise ValueError("y coordinates must be either scalars or vectors")
else:
n, r = yi.shape
if r!=self.r:
- raise ValueError, "Cannot extend dimension %d y vectors with dimension %d y vectors" % (self.r, r)
+ raise ValueError("Cannot extend dimension %d y vectors with dimension %d y vectors" % (self.r, r))
self.yi = npy.vstack((self.yi,yi))
else:
if self.yi is not None:
- raise ValueError, "No update to yi provided!"
+ raise ValueError("No update to yi provided!")
old_n = self.n
self.xi = npy.concatenate((self.xi,xi))
self.n = len(self.xi)
@@ -2638,7 +2638,7 @@
old_wi = self.wi
self.wi = npy.zeros(self.n)
self.wi[:old_n] = old_wi
- for j in xrange(old_n,self.n):
+ for j in range(old_n,self.n):
self.wi[:j]*=(self.xi[j]-self.xi[:j])
self.wi[j] = npy.multiply.reduce(self.xi[:j]-self.xi[j])
self.wi**=-1
@@ -2733,7 +2733,7 @@
self.vector_valued = False
self.r = 1
else:
- raise ValueError, "Each derivative must be a vector, not a higher-rank array"
+ raise ValueError("Each derivative must be a vector, not a higher-rank array")
self.xi = [xi[0]]
self.yi = [yi0]
@@ -2760,7 +2760,7 @@
n2 = min(n-n1,len(y2))
n1 = min(n-n2,len(y1))
if n1+n2!=n:
- raise ValueError, "Point %g has %d derivatives, point %g has %d derivatives, but order %d requested" % (x1, len(y1), x2, len(y2), order)
+ raise ValueError("Point %g has %d derivatives, point %g has %d derivatives, but order %d requested" % (x1, len(y1), x2, len(y2), order))
assert n1<=len(y1)
assert n2<=len(y2)
@@ -2793,15 +2793,15 @@
yi = npy.asarray(yi)
if self.vector_valued:
if (len(yi.shape)!=2 or yi.shape[1]!=self.r):
- raise ValueError, "Each derivative must be a vector of length %d" % self.r
+ raise ValueError("Each derivative must be a vector of length %d" % self.r)
else:
if len(yi.shape)!=1:
- raise ValueError, "Each derivative must be a scalar"
+ raise ValueError("Each derivative must be a scalar")
if self.direction is None:
self.direction = npy.sign(xi-self.xi[-1])
elif (xi-self.xi[-1])*self.direction < 0:
- raise ValueError, "x coordinates must be in the %d direction: %s" % (self.direction, self.xi)
+ raise ValueError("x coordinates must be in the %d direction: %s" % (self.direction, self.xi))
self.xi.append(xi)
self.yi.append(yi)
@@ -2839,7 +2839,7 @@
None indicates that it should be deduced from the first two xi
"""
- for i in xrange(len(xi)):
+ for i in range(len(xi)):
if orders is None or npy.isscalar(orders):
self.append(xi[i],yi[i],orders)
else:
@@ -2867,7 +2867,7 @@
y = npy.zeros((m,self.r))
else:
y = npy.zeros(m)
- for i in xrange(self.n-1):
+ for i in range(self.n-1):
c = pos==i
y[c] = self.polynomials[i](x[c])
return y
@@ -2920,7 +2920,7 @@
y = npy.zeros((der,m,self.r))
else:
y = npy.zeros((der,m))
- for i in xrange(self.n-1):
+ for i in range(self.n-1):
c = pos==i
y[:,c] = self.polynomials[i].derivatives(x[c],der=der)
return y
@@ -3019,9 +3019,9 @@
if constraint is None:
if self.verbose:
def res_fn(p):
- print "\n",p
+ print("\n",p)
r = self.fn(xs, *p) - ys
- print "Residual = %f"%norm(r*weight)
+ print("Residual = %f"%norm(r*weight))
return r*weight
else:
def res_fn(p):
@@ -3030,9 +3030,9 @@
else:
if self.verbose:
def res_fn(p):
- print "\n",p
+ print("\n",p)
r = npy.concatenate((constraint(*p), (self.fn(xs, *p) - ys)*weight))
- print "Residual = %f"%norm(r)
+ print("Residual = %f"%norm(r))
return r
else:
def res_fn(p):
@@ -3046,10 +3046,10 @@
gtol = self.algpars.gtol,
maxfev = self.algpars.maxfev)
except:
- print "Error at parameters", pars_ic
+ print("Error at parameters", pars_ic)
raise
if self.verbose:
- print "Result: ", res
+ print("Result: ", res)
return res
def fit(self, xs, ys, pars_ic=None, opts=None):
@@ -3502,7 +3502,7 @@
value indicates whether a message was issue.
RefactoringTool: Refactored ./PyDSTool/__init__.py
"""
if self.ge(level):
- print >>self.fileo, s
+ print(s, file=self.fileo)
return True
return False
@@ -3512,7 +3512,7 @@
value indicates whether a message was issued
"""
if self.ge('error'):
- print >>self.erro, s
+ print(s, file=self.erro)
return True
return False
--- ./PyDSTool/__init__.py (original)
+++ ./PyDSTool/__init__.py (refactored)
@@ -83,31 +83,31 @@
import types, time
# PyDSTool imports
-from Events import *
-from Interval import *
-from Points import *
-from Variable import *
-from Trajectory import *
-from FuncSpec import *
+from .Events import *
+from .Interval import *
+from .Points import *
+from .Variable import *
+from .Trajectory import *
+from .FuncSpec import *
# \begin{hacksRus}
-import Generator as GenModule
-from Generator import Generator as Generator_
-from Generator import *
+from . import Generator as GenModule
+from .Generator import Generator as Generator_
+from .Generator import *
Generator = GenModule
-import Model as ModelModule
-from Model import Model as Model_
-from Model import *
+from . import Model as ModelModule
+from .Model import Model as Model_
+from .Model import *
Model = ModelModule
# \end{hacksRus}
-from ModelConstructor import *
-from Toolbox.ParamEst import ParamEst
-from Toolbox.ModelEst import ModelEst
-from MProject import *
-from Symbolic import *
-from ModelSpec import *
-from parseUtils import auxfnDBclass, protected_allnames, protected_auxnamesDB, \
+from .ModelConstructor import *
+from .Toolbox.ParamEst import ParamEst
+from .Toolbox.ModelEst import ModelEst
+from .MProject import *
+from .Symbolic import *
+from .ModelSpec import *
+from .parseUtils import auxfnDBclass, protected_allnames, protected_auxnamesDB, \
convertPowers
-from PyCont import *
+from .PyCont import *
import numpy
import numpy as npy # alternate
# import scipy already done at top
@@ -125,13 +125,13 @@
# note that the names with leading underscores will not be exported by
# "from PyDSTool import *"
# diff overwrites numpy diff
-from common import Verbose, Continuous, Discrete, targetLangs, _seq_types, \
+from .common import Verbose, Continuous, Discrete, targetLangs, _seq_types, \
_num_types, _int_types, _float_types, _complex_types, \
_real_types, _all_numpy_int, _all_numpy_float, \
_all_numpy_complex, _all_int, _all_float, _all_complex, \
LargestInt32, diff, diff2
from scipy import who as scipy_who
-from utils import *
+from .utils import *
# ------ Check Python version compatibility
@@ -215,8 +215,8 @@
# typelist_actual = [typelist]
#else:
# raise TypeError("Invalid PyDSTool object types passed")
- for objname, obj in objdict.iteritems():
- if type(obj) not in [type, types.ClassType, types.ModuleType]:
+ for objname, obj in objdict.items():
+ if type(obj) not in [type, type, types.ModuleType]:
if compareClassAndBases(obj, typelist_actual):
if isinstance(obj, QuantSpec) and objname in protected_allnames:
# don't display internally-created QuantSpecs (i.e. all
@@ -230,29 +230,29 @@
objdict_out[objname] = obj
elif isinstance(obj, dict):
if any([compareClassAndBases(x, typelist_actual) \
- for x in obj.values()]):
+ for x in list(obj.values())]):
objdict_out[objname] = obj
if returnlevel == 1:
# silent mode -- just return the objects
- return objdict_out.values()
+ return list(objdict_out.values())
elif returnlevel == 2:
# silent mode -- return the objects mapped by their names
return objdict_out
else:
- for objname, obj in objdict_out.iteritems():
+ for objname, obj in objdict_out.items():
# make appropriate separation between output itemRefactoringTool: Refactored ./PyDSTool/Variable.py
s
if verboselevel > 0:
- print "\n"*(verboselevel-1)
+ print("\n"*(verboselevel-1))
if hasattr(obj, '_infostr') and not isinstance(obj, type):
try:
- print objname + ": " + obj._infostr(verboselevel)
+ print(objname + ": " + obj._infostr(verboselevel))
except:
- print "Problem with: ", objname, className(obj), \
- obj.info
+ print("Problem with: ", objname, className(obj), \
+ obj.info)
raise
else:
- print objname + " (Class " + className(obj) + ")" \
- + (verboselevel > 0)*":"
+ print(objname + " (Class " + className(obj) + ")" \
+ + (verboselevel > 0)*":")
if verboselevel > 0:
info(obj, objname, recurseDepthLimit=verboselevel-1)
@@ -271,10 +271,10 @@
objlist.append(objnamelist)
saveObjects(objlist, sessionName+'.'+__session_ext, force)
if not silent:
- print "Important!"
- print "If you used any user-defined classes for ModelSpec, these need to "
- print "be recreated by running their definition scripts when you restore "
- print "the session. saveSession only saves class _instances_."
+ print("Important!")
+ print("If you used any user-defined classes for ModelSpec, these need to ")
+ print("be recreated by running their definition scripts when you restore ")
+ print("the session. saveSession only saves class _instances_.")
#Symbolic.saveDiffs(sessionName+'.'+__symbolic_ext)
@@ -289,11 +289,11 @@
try:
loadlist = loadObjects(sessionName)
except:
- print "Problem loading session " + sessionName
+ print("Problem loading session " + sessionName)
raise
numobjs = len(loadlist) - 1 # last entry is obj name list
if len(loadlist) <= 0:
- raise ValueError, "Session was empty!"
+ raise ValueError("Session was empty!")
objnamelist = loadlist[-1]
objlist = loadlist[:-1]
frame = sys._getframe().f_back
@@ -303,11 +303,11 @@
nspace = frame.f_globals
# bind the original session names for the objects to the objects
try:
- for i in xrange(numobjs):
+ for i in range(numobjs):
nspace[objnamelist[i]] = objlist[i]
except:
- print "Problem recreating objects"
- print "Debug info: ", len(objnamelist), len(objlist), numobjs
+ print("Problem recreating objects")
+ print("Debug info: ", len(objnamelist), len(objlist), numobjs)
raise
# load any symbolic derivatives previously auto-saved
#symbolic.loadDiffs(sessionName+'.'+__symbolic_ext)
@@ -331,7 +331,7 @@
objdict = who(returnlevel=2, _localCall=True, deepSearch=deep)
frame = sys._getframe().f_back
nspace = frame.f_globals
- for objname, obj in objdict.iteritems():
+ for objname, obj in objdict.items():
if objname not in ['nameResolver', 'protected_auxnamesDB'] and \
(not isinstance(obj, ndarray) or delall==2):
# don't delete those types of global objects
--- ./PyDSTool/Variable.py (original)
+++ ./PyDSTool/Variable.py (refactored)
@@ -6,12 +6,12 @@
# ----------------------------------------------------------------------------
# PyDSTool imports
-from utils import *
-from common import *
-from errors import *
-from Points import *
-from Interval import *
-from FuncSpec import ImpFuncSpec
+from .utils import *
+from .common import *
+from .errors import *
+from .Points import *
+from .Interval import *
+from .FuncSpec import ImpFuncSpec
from numpy import Inf, NaN, isfinite, sometrue, alltrue, any, all, \
array, float64, int32, ndarray, asarray
@@ -238,9 +238,9 @@
# user-defined auxiliary functions
# (built-ins are provided explicitly)
try:
- exec fninfo[0] in globals()
+ exec(fninfo[0], globals())
except:
- print 'Error in supplied auxiliary function code'
+ print('Error in supplied auxiliary function code')
raise
self._funcreg[fninfo[1]] = ('Variable', fninfo[0])
setattr(Variable, fninfo[1], eval(fninfo[1]))
@@ -248,9 +248,9 @@
fninfo_spec = funcspec.spec
if not hasattr(Variable, fninfo_spec[1]):
try:
- exec fninfo_spec[0] in globals()
+ exec(fninfo_spec[0], globals())
except:
- print 'Error in supplied functional specification code'
+ print('Error in supplied functional specification code')
raise
self._funcreg[fninfo_spec[1]] = ('Variable', fninfo_spec[0])
setattr(Variable, fninfo_spec[1], eval(fninfo_spec[1]))
@@ -259,9 +259,9 @@
fninfo_auxspec = funcspec.auxspec
if not hasattr(Variable, fninfo_auxspec[1]):
try:
- exec fninfo_auxspec[0] in globals()
+ exec(fninfo_auxspec[0], globals())
except:
- print 'Error in supplied auxiliary variable code'
+ print('Error in supplied auxiliary variable code')
raise
self._funcreg[fninfo_auxspec[1]] = ('Variable', fninfo_auxspec[0])
setattr(Variable, fninfo_auxspec[1], eval(fninfo_auxspec[1]))
@@ -303,9 +303,9 @@
solmethod=funcspec.algparams['solvemethod'],
standalone=False)"""
try:
- exec impfn_str in this_scope
+ exec(impfn_str, this_scope)
except:
- print 'Error in supplied implicit function code'
+ print('Error in supplied implicit function code')
raise
# record special reference to the implicit fn,
# as its a method of Variable (for delete method).
@@ -396,7 +396,7 @@
self.coordtype,
extent(output.pts.coordarray[0]),
abseps=abseps)
- elif type(output) in [types.InstanceType, types.TypeType] \
+ elif type(output) in [types.InstanceType, type] \
or isinstance(output, (OutputFn, interpclass)):
if hasattr(output, 'types'):
deptype = output.types[0]
@@ -448,9 +448,9 @@
raise ValueError('funcspec missing in setOutput')
# Add the specific mapping functions for Ex/ImplicitFnGen objects
try:
- exec outputdata[1] in globals()
+ exec(outputdata[1], globals())
except:
- print 'Internal Error in _mapspecfn code'
+ print('Internal Error in _mapspecfn code')
raise
has_op = hasattr(self, 'output')
# have to define this function in here because use of lambda
@@ -467,14 +467,14 @@
except ValueError:
self.initialconditions = {self.coordname: NaN}
except TypeError:
- print "Debugging info: self.output = ", self.output
+ print("Debugging info: self.output = ", self.output)
raise
else:
self.initialconditions = ics
self._vectorizable = False
self._refvars = refvars
self.defined = True
- elif type(outputdata) in [types.InstanceType, types.TypeType] \
+ elif type(outputdata) in [types.InstanceType, type] \
or isinstance(outputdata, (OutputFn, interpclass)):
# Variable generated by callable object that generates values over
# mesh points that it holds, e.g. by interpolation
@@ -548,13 +548,13 @@
# enumerated discrete domains
assert len(indepdomain) == 1, "Independent variable " \
"dictionary must have only 1 entry"
- d = indepdomain.values()[0]
+ d = list(indepdomain.values())[0]
assert all(isfinite(d)), "Independent variable values must be" \
" finite"
if self.trajirange:
assert self.trajirange[0] in d
assert self.trajirange[1] in d
- self.indepvarname = indepdomain.keys()[0]
+ self.indepvarname = list(indepdomain.keys())[0]
if isinstance(d, (list, tuple)):
if self.coordtype is not None:
self.indepdomain = array(d, self.coordtype)
@@ -578,7 +578,7 @@
"Independent variable values must be increasing"
self.indepvartype = self.indepdomain.dtype.type
else:
- print "Independent variable argument domain was:", indepdomain
+ print("Independent variable argument domain was:", indepdomain)
raise TypeError("Invalid type for independent variable "
"domain")
@@ -626,13 +626,13 @@
elif isinstance(depdomain, dict):
assert len(depdomain) == 1, \
"Depend variables dictionary must have only 1 entry"
- d = depdomain.values()[0]
+ d = list(depdomain.values())[0]
if self.trajdrange:
assert self.trajdrange[0] in d
assert self.trajdrange[1] in d
## Assume d is in increasing order
assert all(isfinite(d)), "Values must be finite"
- self.coordname = depdomain.keys()[0]
+ self.coordname = list(depdomain.keys())[0]
if isinstance(d, (list, tuple)):
if self.coordtype is not None:
self.depdomain = array(d, self.coordtype)
@@ -651,7 +651,7 @@
"domain")
self.coordtype = self.depdomain.dtype.type
else:
- print "Dependent variable domain argument was:", depdomain
+ print("Dependent variable domain argument was:", depdomain)
raise TypeError("Invalid type for dependent variable domain")
if isinstance(self.output, Pointset):
assert self.coordname == self.output.coordnames[0], \
@@ -727,7 +727,7 @@
vectorizable = True
try:
indepvar_ok = indepvar in idep
- except PyDSTool_UncertainValueError, errinfo:
+ except PyDSTool_UncertainValueError as errinfo:
# adjust for rounding error so that interpolator
# does not barf on out-of-range values
if indepvar < idep[0]:
@@ -757,7 +757,7 @@
else:
depvar = [self.output(ival) for ival in indepvar]
depvar_ok = True
- except PyDSTool_BoundsError, errinfo:
+ except PyDSTool_BoundsError as errinfo:
depvar_ok = False
# Now check that all computed values were in depdomain
if depvar_ok:
@@ -774,7 +774,7 @@
# interval, array and index indeps
try:
contresult = d in self.depdomain
- except PyDSTool_UncertainValueError, errinfo:
+ except PyDSTool_UncertainValueError as errinfo:
contresult = True
if checklevel == 2:
# find which indepvar was the cause of
@@ -809,7 +809,7 @@
dv = depvar
try:
depvar_ok = dv in RefactoringTool: Refactored ./PyDSTool/Trajectory.py
self.depdomain
- except PyDSTool_UncertainValueError, errinfo:
+ except PyDSTool_UncertainValueError as errinfo:
if checklevel == 2:
self.diagnostics.warnings.append((indepvar, errinfo.varval))
if not isfinite(dv):
@@ -846,7 +846,7 @@
else:
vectorizable = True
indepvar_ok = indepvar in self.indepdomain
- except TypeError, e:
+ except TypeError as e:
raise TypeError('Something messed up with the Variable '
'initialization: '+str(e))
else:
@@ -865,13 +865,13 @@
depvar = [self.output(ival) for ival in indepvar]
depvar_ok = all([d in self.depdomain for d in \
depvar])
- except PyDSTool_BoundsError, e:
+ except PyDSTool_BoundsError as e:
raise ValueError("Cannot compute a return value for "
"this independent variable value: "
+ str(e))
except PyDSTool_TypeError:
if not self.defined:
- print "Variable '%s' not fully defined."%self.name
+ print("Variable '%s' not fully defined."%self.name)
return None
else:
raise
@@ -934,7 +934,7 @@
def info(self, verboselevel=1):
- print self._infostr(verboselevel)
+ print(self._infostr(verboselevel))
def __copy__(self):
@@ -958,7 +958,7 @@
# function that's not in the global namespace (so pickle fails
# to find it)
del d['output']
- for fname, finfo in self._funcreg.iteritems():
+ for fname, finfo in self._funcreg.items():
if finfo[0] == 'self':
try:
del d[fname]
@@ -977,7 +977,7 @@
self.indepvartype = _num_name2type[self.indepvartype]
self.coordtype = _num_name2type[self.coordtype]
# reinstate dynamic methods / functions
- for fname, finfo in self._funcreg.iteritems():
+ for fname, finfo in self._funcreg.items():
if finfo[0] == 'self' and not hasattr(eval(finfo[0]), fname):
# avoids special entry for 'outputdata'
setattr(eval(finfo[0]), fname, finfo[1])
@@ -1010,7 +1010,7 @@
# to avoid crowding namespace
## if hasattr(self, 'output'):
## del self.output
- for fname, finfo in self._funcreg.iteritems():
+ for fname, finfo in self._funcreg.items():
# Treat special cases first
if finfo[0] is None:
# don't want to eval(None) below
@@ -1018,7 +1018,7 @@
elif fname == '_impfn':
exec_str = 'del Variable.' + finfo[0]
try:
- exec exec_str
+ exec(exec_str)
except AttributeError:
# Uncertain why the name appears multiple times for their
# to be multiple attempts to delete it (which of course
@@ -1035,7 +1035,7 @@
elif hasattr(eval(finfo[0]), fname):
exec_str = 'del '+ finfo[0] + '.' + fname
try:
- exec exec_str
+ exec(exec_str)
except RuntimeError:
# sometimes get these when objects improperly delted
# and new objects with the same name created
--- ./PyDSTool/Trajectory.py (original)
+++ ./PyDSTool/Trajectory.py (refactored)
@@ -6,14 +6,14 @@
# ----------------------------------------------------------------------------
# PyDSTool imports
-from Variable import *
-from Interval import *
-from Points import *
-from utils import *
-from common import *
-from common import _num_types
-from parseUtils import *
-from errors import *
+from .Variable import *
+from .Interval import *
+from .Points import *
+from .utils import *
+from .common import *
+from .common import _num_types
+from .parseUtils import *
+from .errors import *
# Other imports
from numpy import array, arange, float64, int32, concatenate, zeros, shape, \
@@ -53,11 +53,11 @@
vars = numeric_to_vars(vals, coordnames, indepvar, indepvarname,
indepdomain, all_types_float, discrete)
if event_times is not None:
- return Trajectory(trajname, vars.values(),
+ return Trajectory(trajname, list(vars.values()),
parameterized=indepvar is not None,
eventTimes=event_times, events=event_vals)
else:
- return Trajectory(trajname, vars.values(),
+ return Trajectory(trajname, list(vars.values()),
parameterized=indepvar is not None)
def convert_ptlabel_events(pts, return_vals_dict=False):
@@ -78,7 +78,7 @@
ixlist = []
ix_dict = pts.labels.by_label['Event:'+l]
# don't use tdict in labels in case indepvararray has been re-scaled
- for ix in ix_dict.keys():
+ for ix in list(ix_dict.keys()):
ts.append(pts.indepvararray[ix])
ixlist.append(ix)
ts.sort()
@@ -102,9 +102,9 @@
events found in the pointset and place them in the resulting Trajectory.
"""
if events is not None:
- all_ev_names = events.keys()
+ all_ev_names = list(events.keys())
ev_times, ev_vals = convert_ptlabel_events(pts, True)
- unused_keys = remain(all_ev_names, ev_times.keys())
+ unused_keys = remain(all_ev_names, list(ev_times.keys()))
for k in unused_keys:
ev_times[k] = []
ev_vals[k] = None
@@ -280,7 +280,7 @@
eventTimes = {}
# if events was provided then fill in with that -- most
# commonly used by Generators that only pass events object
- for evname, evpts in self.events.iteritems():
+ for evname, evpts in self.events.items():
if evpts is None:
eventTimes[evname] = []
else:
@@ -326,7 +326,7 @@
"""Truncate trajectory according to a last coordinate specified by idx
argument, provided trajectory is defined by an underlying mesh."""
t_vals = None
- for vname, v in self.variables.iteritems():
+ for vname, v in self.variables.items():
# vmesh is an array with two rows, the first = indep var, the second = dep var
vmesh = v.underlyingMesh()
if vmesh is not None:
@@ -386,7 +386,7 @@
else:
test_names = copy.copy(self.coordnames)
if remain(coords, test_names) != []:
- print "Valid coordinate names:", self.coordnames
+ print("Valid coordinate names:", self.coordnames)
raise ValueError("Invalid coordinate names passed")
elif any([isinstance(c, str) for c in coords]):
raise TypeError("Cannot mix string and numeric values in "
@@ -422,15 +422,15 @@
for v in [self.variables[vn] for vn in coordlist]]
except:
if checklevel > 1:
- print "\nProblem calling with coords:", coordlist
- print "Indepdendent variable values:", indepvals
- print "Containment:", self.indepdomain.contains(t)
+ print("\nProblem calling with coords:", coordlist)
+ print("Indepdendent variable values:", indepvals)
+ print("Containment:", self.indepdomain.contains(t))
try:
- print self.variables[coordlist[0]].indepdomain.get()
- print self.variables[coordlist[0]].depdomain.get()
+ print(self.variables[coordlist[0]].indepdomain.get())
+ print(self.variables[coordlist[0]].depdomain.get())
except AttributeError:
# domains may be discrete
- print "Discrete variable domain and/or range"
+ print("Discrete variable domain and/or range")
# print self.variables[coordlist[0]].initialconditions
raise
# raise ValueError("Problem calling at these independent variable values")
@@ -465,15 +465,15 @@
[self.variables[vn] for vn in coordlist]]
except:
if checklevel > 1:
- print "\nProblem calling with coords:", coordlist
- print "Indepdendent variable values:", t
- print "Containment:", self.indepdomain.contains(t)
+ print("\nProblem calling with coords:", coordlist)
+ print("Indepdendent variable values:", t)
+ print("Containment:", self.indepdomain.contains(t))
try:
- print self.variables[coordlist[0]].indepdomain.get()
- print self.variables[coordlist[0]].depdomain.get()
+ print(self.variables[coordlist[0]].indepdomain.get())
+ print(self.variables[coordlist[0]].depdomain.get())
except AttributeError:
# domains may be discrete
- print "Discrete variable domain and/or range"
+ print("Discrete variable domain and/or range")
raise
if asmap:
coordlist.append(self.indepvarname)
@@ -601,7 +601,7 @@
assert tlo < thi, 't start point must be less than t endpoint'
if dt is not None and dt >= abs(thi-tlo):
if precise:
- print "dt = %f for interval [%f,%f]"%(dt,tlo,thi)
+ print("dt = %f for interval [%f,%f]"%(dt,tlo,thi))
raise ValueError('dt must be smaller than time interval')
else:
dt = (thi-tlo)/10.
@@ -722,8 +722,8 @@
lastins = len(tmesh_glob)
lenstart = len(start_ins)
tmesh_glob = concatenate((start_ins, tmesh_glob, end_ins))
- ins_ixs = range(lenstart) + [i+lenstart for i in ins_ixs] + \
- range(lastins+lenstart, lastins+lenstart+len(end_ins))
+ ins_ixs = list(range(lenstart)) + [i+lenstart for i in ins_ixs] + \
+ list(range(lastins+lenstart, lastins+lenstart+len(end_ins)))
tmesh_list = tmesh_glob.tolist()
for i, (t, evname) in enumerate(evtlist):
try:
@@ -750,14 +750,14 @@
if len(tmesh) > 0:
if dt is None:
- coorddict = dict(zip(coords_sorted, [m[1][ix_range] for m in \
+ coorddict = dict(list(zip(coords_sorted, [m[1][ix_range] for m in \
sortedDictValues(meshdict,
- onlykeys=coords_sorted)]))
+ onlykeys=coords_sorted)])))
if eventdata:
# insert var values at events (SLOW!)
# can only insert to lists, so have to convert coorddict
# arrays to lists first.
- for tpos in xrange(len(ins_ixs)):
+ for tpos in range(len(ins_ixs)):
tix = ins_ixs[tpos]
t = ev_ts[tpos]
x = self._FScompatibleNames(ev_pts_list[tpos])
@@ -803,7 +803,7 @@
# insert var values at events (SLOW!)
# can only insert to lists, so have to convert coorddict
# arrays to lists first.
- for tpos in xrange(len(ins_ixs)):
+ for tpos in range(len(ins_ixs)):
tix = ins_ixs[tpos]
t = ev_ts[tpos]
x = self._FScompatibleNames(ev_pts_list[tpos])
@@ -892,7 +892,7 @@
def __del__(self):
# necessary for __del__ methods of variables to be accessed
- for v in self.variables.values():
+ for v in list(self.variables.values()):
v.__del__()
@@ -908,15 +908,15 @@
outputStr = "Trajectory " + self.name
elif verbose >= 1:
outputStr = "Trajectory " + self.name + "\n of variables: " + \
- str(self._FScompatibleNamesInv(self.variables.keys()))
+ str(self._FScompatibleNamesInv(list(self.variables.keys())))
outputStr += "\n over domains: " + str(self.depdomain)
if verbose == 2:
outputStr += joinStrs(["\n"+v._infostr(1) for v in \
- self.variables.values()])
+ list(self.variables.values())])
return outputStr
def info(self, verboselevel=1):
- print self._infostr(verboselevel)
+ print(self._infostr(verboselevel))
def getEvents(self, evnames=None, asGlobalTime=True):
@@ -926,7 +926,7 @@
"""
# self.events is a dict of pointsets keyed by event name
if evnames is None:
- evnames = self.events.keys()
+ evnames = list(self.events.keys())
if isinstance(evnames, str):
# singleton
assert evnames in self.events, "Invalid event name provided: %s"%evnames
@@ -961,7 +961,7 @@
"""
result = {}
if evnames is None:
- evnames = self.events.keys()
+ evnames = list(self.events.keys())
# self.eventTimes is a dict of lists keyed by event name
if isinstance(evnames, str):
# singleton
@@ -1107,7 +1107,7 @@
def showRegimes(self):
parts = [p[1] for p in self.timePartitions]
for g, p in zip(self.modelNames, parts):
- print "Regime: %s, from t = %.5f"%(g,p)
+ print("Regime: %s, from t = %.5f"%(g,p))
def info(self):
return info(self, "Hybrid Trajectory")
@@ -1200,7 +1200,7 @@
if not isinstance(t, int):
raise TypeError("time value must be an integer"
" when treating system as a mapping")
- if t not in range(num_parts+1):
+ if t not in list(range(num_parts+1)):
raise PyDSTool_BoundsError("time value not in valid"
" partition range")
if t < num_parts:
@@ -1238,8 +1238,8 @@
trel_part = []
tval = t[tix]
if time_interval.contains(tval) is notcontained:
- print "\n** Debugging info for Hybrid Traj %s: t value, interval, tolerance ="%self.name
- print tval, time_interval.get(), time_interval._abseps
+ print("\n** Debugging info for Hybrid Traj %s: t value, interval, tolerance ="%self.name)
+ print(tval, time_interval.get(), time_interval._abseps)
raise PyDSTool_BoundsError('time value outside of '
'trajectory`s time interval '
'of validity (if checklevel was >=2 then endpoints '
@@ -1344,10 +1344,10 @@
retvals.append(val)
else:
tinterval = self.indepdomain
- print "valid t interval:", \
- tinterval.get()
- print "t in interval? -->", tinterval.contains(tval)
- print "interval abs eps = ", tinterval._abseps
+ print("valid t interval:", \
+ tinterval.get())
+ print("t in interval? -->", tinterval.contains(tval))
+ print("interval abs eps = ", tinterval._abseps)
raise ValueError('t = 'RefactoringTool: Refactored ./PyDSTool/Toolbox/syntheticdata.py
+str(tval)+' is either not in any '
'time interval defined for this '
'trajectory, or there was an out-of-range'
@@ -1417,7 +1417,7 @@
pset = self.__call__([t], coords)
pset.name = self.name + "_sample"
if doEvents:
- for evname, ev_ts in self.eventTimes.items():
+ for evname, ev_ts in list(self.eventTimes.items()):
if t in ev_ts:
pset.addlabel(0, 'Event:'+evname, {'t': t})
return pset
@@ -1459,7 +1459,7 @@
try:
pset = traj.sample(coords, dt, tlo, thi, doEvents,
False)
- except ValueError, e:
+ except ValueError as e:
if e.message[:7] in ('tlo too', 'thi too'):
# tlo or thi out of range
pass
@@ -1469,7 +1469,7 @@
try:
pset_new = traj.sample(coords, dt, tlo, thi,
doEvents, False)
- except ValueError, e:
+ except ValueError as e:
if e.message[:7] in ('tlo too', 'thi too'):
# tlo or thi out of range
pass
@@ -1508,8 +1508,8 @@
#except (PyDSTool_BoundsError, ValueError):
# r = 1000.*(t-t0)
except:
- print "Error at t=%f: "%t, sys.exc_info()[0], \
- sys.exc_info()[1]
+ print("Error at t=%f: "%t, sys.exc_info()[0], \
+ sys.exc_info()[1])
raise
try:
result = bisect(f, t1_guess-guess_tol*(t1_guess-t0),
@@ -1529,9 +1529,9 @@
if max_rval<rtol:
return abs(result-t0)
else:
- print "Did not converge. The endpoint difference at t=%f was:\n"%result, \
+ print("Did not converge. The endpoint difference at t=%f was:\n"%result, \
repr(val), \
"\nwith infinity-norm %f > %f tolerance.\n"%(max_rval,rtol), \
"Try a different starting point,", \
- "a different test variable, or reduce relative tolerance."
+ "a different test variable, or reduce relative tolerance.")
raise ValueError("Did not converge")
--- ./PyDSTool/Toolbox/syntheticdata.py (original)
+++ ./PyDSTool/Toolbox/syntheticdata.py (refactored)
@@ -40,7 +40,7 @@
rho = x/L*(roll_num*2*pi)
return (r*cos(rho), r*sin(rho))
theta = 0
- for i in xrange(N):
+ for i in range(N):
theta += cycle_rate
x = r*cos(theta)+bias_x*i
x_rolled, z_rolled = roll(x)
@@ -69,7 +69,7 @@
X[i,2:D] = array([random.normal(0,noise)]*(D-2), float)
# now do the spiral(s)
theta = sqrt(radius*radius-1)
- for i in xrange(N2):
+ for i in range(N2):
theta += cycle_rate
r = sqrt(theta*theta+0.8)
X[N1+i,:] = array([r*cos(theta)+random.normal(0,noise),
@@ -95,7 +95,7 @@
assert num_spirals in [0,1,2]
X = zeros((num_spirals*N, D), float)
theta = sqrt(radius*radius-1)
- for i in xrange(N):
+ for i in range(N):
theta += cycle_rate
r = sqrt(theta*theta+0.8)*expand_rate
X[i,:] = array([r*cos(theta)+random.normal(0,noise),
@@ -115,12 +115,12 @@
"""
X = zeros((N, D), float)
if fromcentre:
- for i in xrange(N):
- X[i,:] = array([random.uniform(-length/2., length/2.) for j in xrange(D)],
+ for i in range(N):
+ X[i,:] = array([random.uniform(-length/2., length/2.) for j in range(D)],
float)
else:
- for i in xrange(N):
- X[i,:] = array([random.uniform(0, length) for j in xrange(D)],
+ for i in range(N):
+ X[i,:] = array([random.uniform(0, length) for j in range(D)],
float)
return X
@@ -148,7 +1RefactoringTool: Refactored ./PyDSTool/Toolbox/synthetic_data.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/prep_boxplot.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/phaseplane.py
48,7 @@
else:
outsidepts += 1
## print x, xr, "outside"
- print "Number of points outside ball that were discarded = ", outsidepts
+ print("Number of points outside ball that were discarded = ", outsidepts)
return X
@@ -170,7 +170,7 @@
"""
if lengths is None:
lengths = [1.] * len(p)
- a = array([max([p[i],lengths[i]-p[i]]) for i in xrange(len(p))])
+ a = array([max([p[i],lengths[i]-p[i]]) for i in range(len(p))])
a.sort()
return a
@@ -180,7 +180,7 @@
"""
if lengths is None:
lengths = [1.] * len(p)
- a = array([min([p[i],lengths[i]-p[i]]) for i in xrange(len(p))])
+ a = array([min([p[i],lengths[i]-p[i]]) for i in range(len(p))])
a.sort()
return a
--- ./PyDSTool/Toolbox/synthetic_data.py (original)
+++ ./PyDSTool/Toolbox/synthetic_data.py (refactored)
@@ -40,7 +40,7 @@
rho = x/L*(roll_num*2*pi)
return (r*cos(rho), r*sin(rho))
theta = 0
- for i in xrange(N):
+ for i in range(N):
theta += cycle_rate
x = r*cos(theta)+bias_x*i
x_rolled, z_rolled = roll(x)
@@ -69,7 +69,7 @@
X[i,2:D] = array([random.normal(0,noise)]*(D-2), float)
# now do the spiral(s)
theta = sqrt(radius*radius-1)
- for i in xrange(N2):
+ for i in range(N2):
theta += cycle_rate
r = sqrt(theta*theta+0.8)
X[N1+i,:] = array([r*cos(theta)+random.normal(0,noise),
@@ -95,7 +95,7 @@
assert num_spirals in [0,1,2]
X = zeros((num_spirals*N, D), float)
theta = sqrt(radius*radius-1)
- for i in xrange(N):
+ for i in range(N):
theta += cycle_rate
r = sqrt(theta*theta+0.8)*expand_rate
X[i,:] = array([r*cos(theta)+random.normal(0,noise),
@@ -115,12 +115,12 @@
"""
X = zeros((N, D), float)
if fromcentre:
- for i in xrange(N):
- X[i,:] = array([random.uniform(-length/2., length/2.) for j in xrange(D)],
+ for i in range(N):
+ X[i,:] = array([random.uniform(-length/2., length/2.) for j in range(D)],
float)
else:
- for i in xrange(N):
- X[i,:] = array([random.uniform(0, length) for j in xrange(D)],
+ for i in range(N):
+ X[i,:] = array([random.uniform(0, length) for j in range(D)],
float)
return X
@@ -148,7 +148,7 @@
else:
outsidepts += 1
## print x, xr, "outside"
- print "Number of points outside ball that were discarded = ", outsidepts
+ print("Number of points outside ball that were discarded = ", outsidepts)
return X
@@ -170,7 +170,7 @@
"""
if lengths is None:
lengths = [1.] * len(p)
- a = array([max([p[i],lengths[i]-p[i]]) for i in xrange(len(p))])
+ a = array([max([p[i],lengths[i]-p[i]]) for i in range(len(p))])
a.sort()
return a
@@ -180,7 +180,7 @@
"""
if lengths is None:
lengths = [1.] * len(p)
- a = array([min([p[i],lengths[i]-p[i]]) for i in xrange(len(p))])
+ a = array([min([p[i],lengths[i]-p[i]]) for i in range(len(p))])
a.sort()
return a
--- ./PyDSTool/Toolbox/prep_boxplot.py (original)
+++ ./PyDSTool/Toolbox/prep_boxplot.py (refactored)
@@ -59,11 +59,11 @@
order = {}
# `pos` position runs from 1 to n, `ns` runs from 0 to n-1
ns = []
- for k, v in data.iteritems():
+ for k, v in data.items():
order[v['pos']] = k
ns.append(v['pos']-1)
ns.sort()
- assert ns == range(n)
+ assert ns == list(range(n))
maxD = 0
max_dimval_markers = 0
labels = []
--- ./PyDSTool/Toolbox/phaseplane.py (original)
+++ ./PyDSTool/Toolbox/phaseplane.py (refactored)
@@ -13,7 +13,7 @@
R. Clewley, 2006 - 2011
"""
-from __future__ import division
+
# itertools, operator used for _filter_consecutive function
import itertools, operator
@@ -243,7 +243,7 @@
test = q-self.history[2] # a Point
except:
# problem with self.history[2] (externally tampered with?)
- print "History is: ", self.history
+ print("History is: ", self.history)
raise RuntimeError("Invalid history object in "
"distance_to_pointset class instance")
try:
@@ -405,10 +405,10 @@
dmax = (d, i)
elif ge(d, dmax_old[0]):
dmax_old = (d,i)
- return {'min': {1: dict(zip(self._keys,dmin)),
- 2: dict(zip(self._keys,dmin_old))},
- 'max': {1: dict(zip(self._keys,dmax)),
- 2: dict(zip(self._keys,dmax_old))}}
+ return {'min': {1: dict(list(zip(self._keys,dmin))),
+ 2: dict(list(zip(self._keys,dmin_old)))},
+ 'max': {1: dict(list(zip(self._keys,dmax))),
+ 2: dict(list(zip(self._keys,dmax_old)))}}
def search_min(self, q, pts, fn, le, dmin, dmin_old):
for i, p in enumerate(pts):
@@ -418,8 +418,8 @@
dmin = (d, i)
elif le(d, dmin_old[0]):
dmin_old = (d, i)
- return {'min': {1: dict(zip(self._keys,dmin)),
- 2: dict(zip(self._keys,dmin_old))}}
+ return {'min': {1: dict(list(zip(self._keys,dmin))),
+ 2: dict(list(zip(self._keys,dmin_old)))}}
def search_max(self, q, pts, fn, ge, dmax, dmax_old):
for i, p in enumerate(pts):
@@ -429,8 +429,8 @@
dmax = (d, i)
elif ge(d, dmax_old[0]):
dmax_old = (d,i)
- return {'max': {1: dict(zip(self._keys,dmax)),
- 2: dict(zip(self._keys,dmax_old))}}
+ return {'max': {1: dict(list(zip(self._keys,dmax))),
+ 2: dict(list(zip(self._keys,dmax_old)))}}
def make_Jac(DS, varnames=None):
@@ -550,8 +550,8 @@
subdomain = filteredDict(gen.xdomain, gen.funcspec.vars)
else:
subdomain = gen._FScompatibleNames(subdomain)
- assert remain(subdomain.keys(),gen.funcspec.vars) == [] and \
- remain(gen.funcspec.vars,subdomain.keys()) == []
+ assert remain(list(subdomain.keys()),gen.funcspec.vars) == [] and \
+ remain(gen.funcspec.vars,list(subdomain.keys())) == []
if only_var is None:
do_vars = [xname, yname]
else:
@@ -570,7 +570,7 @@
y_dom = gen.xdomain[yname]
if not (isfinite(y_dom[0]) and isfinite(y_dom[1])):
raise PyDSTool_ExistError("Must specify finite range for %s"%yname)
- for varname, dom in subdomain.iteritems():
+ for varname, dom in subdomain.items():
if isinstance(dom, (tuple,list)):
if not (isfinite(dom[0]) and isfinite(dom[1])):
raise RuntimeError("Must specify a finite range for %s" % varname)
@@ -822,7 +822,7 @@
if 'fnspecs' in gen.funcspec._initargs:
old_fnspecs = gen.funcspec._initargs['fnspecs']
fnspecs, new_varspecs = resolveClashingAuxFnPars(old_fnspecs, varspecs,
- sysargs_y.pars.keys())
+ list(sysargs_y.pars.keys()))
# TEMP
# process any Jacobian functions to remove un-needed terms
if 'Jacobian' in fnspecs:
@@ -875,7 +875,7 @@
except PyDSTool_ExistError:
tries += 1
if tries == max_tries:
- print 'null_curve_y failed in forward direction'
+ print('null_curve_y failed in forward direction')
raise
else:
# try a different starting point
@@ -915,7 +915,7 @@
except PyDSTool_ExistError:
tries += 1
if tries == max_tries:
- print 'null_curve_y failed in backward direction'
+ print('null_curve_y failed in backward direction')
raise
else:
# try a different starting point
@@ -963,9 +963,9 @@
try:
fp_ixs = [findClosestPointIndex(pt, y_null) for pt in add_fp_pts]
except ValueError:
- print "Non-monotonic data computed. Try (1) reducing max_step, (2) crop_tol_pc down to zero if non-monotonicity"
- print " is at domain endpoints, or (3) normalize tolerances for fixed points with that of nullclines."
- print " Not including fixed points in nullcline data"
+ print("Non-monotonic data computed. Try (1) reducing max_step, (2) crop_tol_pc down to zero if non-monotonicity")
+ print(" is at domain endpoints, or (3) normalize tolerances for fixed points with that of nullclines.")
+ print(" Not including fixed points in nullcline data")
else:
for n, ix in enumerate(fp_ixs):
# +n offsets fact that n entries were already added
@@ -1023,7 +1023,7 @@
if 'fnspecs' in gen.funcspec._initargs:
old_fnspecs = gen.funcspec._initargs['fnspecs']
fnspecs, new_varspecs = resolveClashingAuxFnPars(old_fnspecs, varspecs,
- sysargs_x.pars.keys())
+ list(sysargs_x.pars.keys()))
# TEMP
# process any Jacobian functions to remove un-needed terms
if 'Jacobian' in fnspecs:
@@ -1073,7 +1073,7 @@
except PyDSTool_ExistError:
tries += 1
if tries == max_tries:
- print 'null_curve_x failed in forward direction'
+ print('null_curve_x failed in forward direction')
raise
else:
# try a different starting point
@@ -1099,7 +1099,7 @@
except PyDSTool_ExistError:
tries += 1
if tries == max_tries:
- print 'null_curve_x failed in backward direction'
+ print('null_curve_x failed in backward direction')
raise
else:
# try a different starting point
@@ -1135,9 +1135,9 @@
try:
fp_ixs = [findClosestPointIndex(pt, x_null) for pt in add_fp_pts]
except ValueError:
- print "Non-monotonic data computed. Try (1) reducing max_step, (2) crop_tol_pc down to zero if non-monotonicity"
- print " is at domain endpoints, or (3) normalize tolerances for fixed points with that of nullclines."
- print " Not including fixed points in nullcline data"
+ print("Non-monotonic data computed. Try (1) reducing max_step, (2) crop_tol_pc down to zero if non-monotonicity")
+ print(" is at domain endpoints, or (3) normalize tolerances for fixed points with that of nullclines.")
+ print(" Not including fixed points in nullcline data")
else:
for n, ix in enumerate(fp_ixs):
# +n offsets fact that n entries were already added
@@ -1174,14 +1174,14 @@
subdomain = filteredDict(gen.xdomain, gen.funcspec.vars)
else:
subdomain = gen._FScompatibleNames(subdomain)
- assert remain(subdomain.keys(),gen.funcspec.vars) == [] and \
- remain(gen.funcspec.vars,subdomain.keys()) == []
+ assert remain(list(subdomain.keys()),gen.funcspec.vars) == [] and \
+ remain(gen.funcspec.vars,list(subdomain.keys())) == []
# only vary over domains that are given as ranges: fixed values
# are not counted
D = 0
xdict = {}.fromkeys(gen.funcspec.vars)
fixed_vars = {}
- for xname, dom in subdomain.iteritems():
+ for xname, dom in subdomain.items():
if isinstance(dom, (tuple,list)):
if not (isfinite(dom[0]) and isfinite(dom[1])):
raise RuntimeError("Must specify a finite range for %s"%xname)
@@ -1223,7 +1223,7 @@
fprime = make_Jac_wrap(gen, xdict, x0_names)
elif jac is not None:
def Jac_wrap(x, t, pdict):
- xdict.update(dict(zip(x0_names, x)))
+ xdict.update(dict(list(zip(x0_names, x))))
argdict = filteredDict(xdict, jac._args)
argdict['t'] = t
try:
@@ -1240,8 +1240,8 @@
fp_listdict = []
d_posns = base_n_counter(n,D)
xtol = eps/10.
- for dummy_ix in xrange(n**D):
- x0 = array([x0_coords[i][d_posns[i]] for i in xrange(D)])
+ for dummy_ix in range(n**D):
+ x0 = array([x0_coords[i][d_posns[i]] for i in range(D)])
res = fsolve(Rhs_wrap,x0,(t,gen.pars),xtol=xtol,
fprime=fprime,full_output=True)
xinf_val = res[0]
@@ -1258,7 +1258,7 @@
xintervals[ix].contains(xinf_val[ix]) is not notcontained
if ok:
fps.append(xinf_val)
- fp_pt = dict(zip(x0_names, xinf_val))
+ fp_pt = dict(list(zip(x0_names, xinf_val)))
fp_pt.update(fixed_vars)
fp_listdict.append(gen._FScompatibleNamesInv(fp_pt))
d_posns.inc()
@@ -1410,9 +1410,9 @@
def info(self, verboselevel=1):
if verboselevel == 1:
- print self.__str__()
+ print(self.__str__())
elif verboselvel > 1:
- print self.__repr__()
+ print(self.__repr__())
def __copy__(self):
return Point2D(self.x, self.y, self.xname, self.yname, self._normord,
@@ -1720,8 +1720,8 @@
return nullcline(self.xname, self.yname, np.array(sample_vals),
x_relative_scale=self.x_relative_scale_fac)
except:
- print "Error cropping nullcline at sample points", sample_vals
- print "MAYBE TOO FEW VALUES SAMPLED: number was", len(sample_vals)
+ print("Error cropping nullcline at sample points", sample_vals)
+ print("MAYBE TOO FEW VALUES SAMPLED: number was", len(sample_vals))
raise
def is_monotonic(self):
@@ -1758,7 +1758,7 @@
in the given norm.
"""
# start with all indices, and remove those that are unwanted
- remaining = range(len(pts))
+ remaining = list(range(len(pts)))
for i, p in enumerate(pts):
for j in range(i+1, len(pts)):
if norm(p-pts[j],normord) < eps:
@@ -1935,8 +1935,8 @@
var_ixs.append(gen.query('vars').index(v))
fp_evaluated = array(gen.Rhs(0, gen._FScompatibleNames(pt), gen.pars))[var_ixs]
if sometrue([abs(fp_i) > eps for fp_i in fp_evaluated]):
- print "Tolerance =", eps
- print "vector field is", fp_evaluated
+ print("Tolerance =", eps)
+ print("vector field is", fp_evaluated)
raise PyDSTool_ValueError("Given point is not a fixed point of the system at given tolerance")
self.coordnames = pt.coordnames
self._classify()
@@ -2015,7 +2015,7 @@
dict_str = "{" + ",".join(entries) + "})\n"
jac_def_str = "def jac_fn(t, " + arg_str + "):\n\t" + \
"return self.gen.Jacobian(t, " + dict_str
- exec jac_def_str in locals(), globals()
+ exec(jac_def_str, locals(), globals())
return jac_fn
else:
raise NotImplementedError('Jacobian is not the right shape')
@@ -2030,7 +2030,7 @@
def _classify(self):
if self.dimension == 2:
- print "Use fixedpoint_2D class"
+ print("Use fixedpoint_2D class")
real_evals = (isreal(self.evals[0]), isreal(self.evals[1]))
equal_evals = abs(self.evals[0] - self.evals[1]) < self.eps
@@ -2130,7 +2130,7 @@
self.xvar = x
varsPP = [x, 'v']
if isinstance(model, NonHybridModel):
- self.gen = model.registry.values()[0]
+ self.gen = list(model.registry.values())[0]
elif isinstance(model, Generator.Generator):
self.gen = model
else:
@@ -2217,7 +2217,7 @@
)
DSargs.events = [thresh_ev]
if targlang == 'c':
- print "Warning! Did you delete any existing linear systems?"
+ print("Warning! Did you delete any existing linear systems?")
self.lin = Generator.Dopri_ODEsystem(DSargs)
else:
self.lin = Generator.Vode_ODEsystem(DSargs)
@@ -2713,7 +2713,7 @@
assert Bmon, "Nullcline B must be monotonic"
else:
if not Bmon:
- print "Warning: nullcline B is not monotonic in closest_perp_distance_between splines"
+ print("Warning: nullcline B is not monotonic in closest_perp_distance_between splines")
# search interior sample points of spline A first, and 1% inside endpoints
xa_search_vals = _sample_array_interior(NullcA.array[:,0], 0.01)
dists = [closest_perp_distance_on_spline(NullcA, NullcB, xa) for xa in xa_search_vals]
@@ -2950,7 +2950,7 @@
dxscaled = dx_scaled_2D(dx, rel_scale)
if isinstance(dx_gamma, dict):
assert len(dx_gamma) == 2, "Invalid value for dx_gamma"
- assert remain(dx_gamma.keys(), [1,-1]) == [], \
+ assert remain(list(dx_gamma.keys()), [1,-1]) == [], \
"Invalid value for dx_gamma"
else:
try:
@@ -2960,7 +2960,7 @@
def test_fn(x, dircode):
if verboselevel>1:
- print "Test point", x[x.coordnames[0]], x[x.coordnames[1]], "in direction", dircode, "\n"
+ print("Test point", x[x.coordnames[0]], x[x.coordnames[1]], "in direction", dircode, "\n")
gen.set(ics=x)
try:
test = gen.compute('test', dirn=dircode)
@@ -2974,26 +2974,26 @@
if events['Gamma_out_minus'] is None:
if verboselevel>1:
pts=test.sample(coords=x.coordnames)
- print "Last computed point was\n", pts[-1]
- print "...after time", pts['t'][-1]
+ print("Last computed point was\n", pts[-1])
+ print("...after time", pts['t'][-1])
plot(pts[x.coordnames[0]],pts[x.coordnames[1]],'b-')
raise RuntimeError("Did not reach Gamma surfaces")
else:
# hit Gamma_out_minus
if verboselevel>1:
- print "Reached Gamma minus at t=", events['Gamma_out_minus']['t'][0]
+ print("Reached Gamma minus at t=", events['Gamma_out_minus']['t'][0])
sgn = -1
else:
if events['Gamma_out_minus'] is None:
# hit Gamma_out_plus
if verboselevel>1:
- print "Reached Gamma plus at t=", events['Gamma_out_plus']['t'][0]
+ print("Reached Gamma plus at t=", events['Gamma_out_plus']['t'][0])
sgn = 1
else:
if verboselevel>1:
pts=test.sample(coords=x.coordnames)
- print "Last computed point was\n", pts[-1]
- print "...after time", pts['t'][-1]
+ print("Last computed point was\n", pts[-1])
+ print("...after time", pts['t'][-1])
plot(pts[x.coordnames[0]],pts[x.coordnames[1]],'b-')
raise RuntimeError("Did not reach Gamma surfaces")
return sgn
@@ -3030,7 +3030,7 @@
### w = 's' => stable branch
### w = 'u' => unstable branch
if verboselevel>0:
- print "Starting %s branch" % man_names[w]
+ print("Starting %s branch" % man_names[w])
if w == 's':
col = 'g'
w_sgn = -1
@@ -3055,7 +3055,7 @@
# determines which is "before" and which is "after" the
# event surface (time may be reversed depending on which
# manifold is being computed)
- print "Set these event directions according to your problem..."
+ print("Set these event directions according to your problem...")
gen.eventstruct.setEventDir('Gamma_out_plus', -1)
gen.eventstruct.setEventDir('Gamma_out_minus', 1)
gen.set(pars={'Gamma_out_plus_p_'+var_x: p0_plus[var_x],
@@ -3104,7 +3104,7 @@
f_ic = -w_sgn * gen.Rhs(0, ic, gen.pars) # array
for sgn in directions:
if verboselevel>0:
- print "Starting direction", sgn
+ print("Starting direction", sgn)
# PREDICTION
x0_ic = ic+w_sgn*sgn*ic_dx*f_ic/norm(f_ic, normord)
if verboselevel>1:
@@ -3126,14 +3126,14 @@
try:
x = onto_manifold(x0_ic, dx_perp, norm_to_flow,
dircode=integ_dircode)
- except RuntimeError, e:
+ except RuntimeError as e:
dx_perp *= dx_perp_fac
else:
break
if dx_perp <= dx_perp_eps:
# RuntimeError was raised and could not continue reducing dx_perp
- print "dx_perp reached lower tolerance =", dx_perp_eps
- print e
+ print("dx_perp reached lower tolerance =", dx_perp_eps)
+ print(e)
raise RuntimeError("Initial point did not converge")
else:
curve_len += norm(x-ic, normord)
@@ -3141,8 +3141,8 @@
num_pts = 1
last_x = x
if verboselevel>0:
- print "Initial point converged to (%.6f, %.6f)\n" % \
- (x[var_x], x[var_y])
+ print("Initial point converged to (%.6f, %.6f)\n" % \
+ (x[var_x], x[var_y]))
dx_perp = dx_perp_default
last_f = f_ic
# step backwards along flow
@@ -3163,23 +3163,23 @@
x_ic = last_x + w_sgn*sgn*dxscaled*f/norm(f,normord)
last_f = f
if verboselevel>1:
- print "\nStarting from point ", last_x
+ print("\nStarting from point ", last_x)
delta = w_sgn*sgn*dxscaled*f/norm(f,normord)
- print "Trying point ", x_ic, "in direction (%.6f, %.6f)\n" % (delta[0], delta[1])
+ print("Trying point ", x_ic, "in direction (%.6f, %.6f)\n" % (delta[0], delta[1]))
dx_perp = dx_perp_default
# CORRECTION
while dx_perp > dx_perp_eps:
try:
x = onto_manifold(x_ic, dx_perp, get_perp(f/norm(f,normord)),
dircode=integ_dircode)
- except RuntimeError, e:
+ except RuntimeError as e:
dx_perp *= 0.75
else:
break
if dx_perp <= dx_perp_eps:
# RuntimeError was raised and could not continue reducing dx_perp
- print "dx_perp reached lower tolerance =", dx_perp_eps
- print e
+ print("dx_perp reached lower tolerance =", dx_perp_eps)
+ print(e)
break # end while search
else:
curve_len += norm(x-last_x, normord)
@@ -3187,13 +3187,13 @@
last_x = x
num_pts += 1
if verboselevel>1:
- print "\nManifold has %i points" % num_pts
+ print("\nManifold has %i points" % num_pts)
elif verboselevel>0:
- print ".",
+ print(".", end=' ')
sys.stdout.flush()
if verboselevel>0:
# finish the line
- print " "
+ print(" ")
indepvar, piece_sorted = sortedDictLists(piece, byvalue=False)
manifold[w] = pointsToPointset(piece_sorted, indepvarname='arc_len',
indepvararray=indepvar, norm=normord)
@@ -3351,7 +3351,7 @@
except:
raise TypeError("thresh must be a 1D Point object or dictionary")
assert len(threshdict)==1, "thresh must be a 1D Point object or dictionary"
- var = thresh.keys()[0]
+ var = list(thresh.keys())[0]
a = pts[var]
t = pts['t']
ts = []
@@ -3384,7 +3384,7 @@
else:
return ts[-1]-ts[-2]
else:
- print len(ts), "is not enough periods",
+ print(len(ts), "is not enough periods", end=' ')
return NaN
@@ -3401,8 +3401,8 @@
minimize_values=range(max_index,0,-1)
"""
## Find clusters
- clusters = [map(operator.itemgetter(1), g) for k, g in \
- itertools.groupby(enumerate(indices), lambda (i,x):i-x)]
+ clusters = [list(map(operator.itemgetter(1), g)) for k, g in \
+ itertools.groupby(enumerate(indices), lambda i_x:i_x[0]-i_x[1])]
## Minimize on clusters
result = []
for c in clusters:
@@ -3517,7 +3517,7 @@
zone_width = self.pars.zone_width
except AttributeError:
zone_width = np.inf # may fail unexpectedly
- print "Warning: zone_width parameter defaulted to infinity"
+ print("Warning: zone_width parameter defaulted to infinity")
min_zone_x = x_center - zone_width
max_zone_x = x_center + zone_width
# Grow domain of zone past known sample points with same property
@@ -4000,7 +4000,7 @@
while t <= t_end:
pt = traj(t)
i += 1
- print "Frame %i, t = %.4f: step %.4f until %.4f" % (i, t, t_step, t_end)
+ print("Frame %i, t = %.4f: step %.4f until %.4f" % (i, t, t_step, t_end))
if moviename is not None:
saveplot = 'pp_fig_%03d' % i
format = 'png'
@@ -4161,8 +4161,8 @@
try:
res[i] = f(p)
except:
- print "Problem evaluating supplied function on mesh patch at " \
- "point ", p
+ print("Problem evaluating supplied function on mesh patch at " \
+ "point ", p)
raise
return res
@@ -4199,7 +4199,7 @@
## print "Min grad using ixs", ixs
use_vals = [vals[i] for i in ixs]
else:
- ixs = range(1,self.n)
+ ixs = list(range(1,self.n))
use_vals = vals
return vals, ixs, use_vals
@@ -4272,12 +4272,12 @@
if return_type == 0:
raise RuntimeError("No valid directions to point in")
else:
- return Point(dict(zip(self.p0.coordnames, [x,y])))
+ return Point(dict(list(zip(self.p0.coordnames, [x,y]))))
elif degen_exterior_higher:
if return_type == 0:
raise RuntimeError("No valid directions to point in")
else:
- return Point(dict(zip(self.p0.coordnames, [0,0])))
+ return Point(dict(list(zip(self.p0.coordnames, [0,0]))))
d1 = (Inf, NaN)
d2 = (Inf, NaN)
for i, v in enumerate(use_vals):
@@ -4378,12 +4378,12 @@
if return_type == 0:
raise RuntimeError("No valid directions to point in")
else:
- return Point(dict(zip(self.p0.coordnames, [x,y])))
+ return Point(dict(list(zip(self.p0.coordnames, [x,y]))))
elif degen_exterior_lower:
if return_type == 0:
raise RuntimeError("No valid directions to point in")
else:
- return Point(dict(zip(self.p0.coordnames, [0,0])))
+ return Point(dict(list(zip(self.p0.coordnames, [0,0]))))
d1 = (0, NaRefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/tests/test_rosenbrock.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/tests/test_quadratic.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/tests/test_powell.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/tests/test_restart_conjugate_gradient.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/tests/test_quasi_newton_step.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/tests/test_partial_step.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/tests/test_newton_step.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/tests/test_marquardt_step.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/tests/test_gradient_step.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/tests/test_goldstein_price_step.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/tests/test_conjugate_gradient_step.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/restart_conjugate_gradient.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/quasi_newton_step.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/partial_step.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/newton_step.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/marquardt_step.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/local_brute_force_1dstep.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/gradient_step.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/goldstein_price_step.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/step/goldfeld_step.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/step/conjugate_gradient_step.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/step/__init__.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/optimizer/standard_optimizer_modifying.py
N)
d2 = (0, NaN)
for i, v in enumerate(use_vals):
@@ -4438,7 +4438,7 @@
try:
test_traj = gen.compute('test')
except:
- print "Problem integrating test trajectory at i.c. ", ic
+ print("Problem integrating test trajectory at i.c. ", ic)
raise
test_pts = test_traj.sample(coords=dist_pts.all_pts.coordnames)
# distance of endpoint to pointset
@@ -4467,7 +4467,7 @@
try:
test_traj = gen.compute('test')
except:
- print "Problem integrating test trajectory at i.c. ", ic
+ print("Problem integrating test trajectory at i.c. ", ic)
raise
test_pts = test_traj.sample(coords=dist_pts.all_pts.coordnames)
# distance of endpoint to pointset
@@ -4497,7 +4497,7 @@
except (ValueError, TypeError, OverflowError):
xinf_val = NaN
except:
- print "Error in fsolve:", sys.exc_info()[0], sys.exc_info()[1]
+ print("Error in fsolve:", sys.exc_info()[0], sys.exc_info()[1])
xinf_val = NaN
else:
if result[2] in (1,2,3): #,4,5):
@@ -4541,7 +4541,7 @@
for evn in other_evnames:
gen.eventstruct.setActiveFlag(evn, False)
qpars = {}
- for parname, varname in pars_to_vars.items():
+ for parname, varname in list(pars_to_vars.items()):
qpars[parname] = q[varname]
gen.set(ics=p, tdata=tdata_local, pars=qpars)
## # temp
@@ -4564,8 +4564,8 @@
assert len(perp_ev) == 1
t_ev = perp_ev['t'][0] + tdata_local[0]
except:
- print "Event name:", iso_ev
- print perp_ev
+ print("Event name:", iso_ev)
+ print(perp_ev)
raise ValueError("No nearest point found with event")
return (perp_ev, t_ev)
--- ./PyDSTool/Toolbox/optimizers/tests/test_powell.py (original)
+++ ./PyDSTool/Toolbox/optimizers/tests/test_powell.py (refactored)
@@ -34,7 +34,7 @@
"""
Evaluates the gradient of the function
"""
- print x, self(x)
+ print(x, self(x))
return numpy.array([[2 + 120 * (x[0] - x[3]) ** 2, 20, 0, -120 * (x[0] - x[3]) ** 2], [20, 200 + 12 * (x[1] - 2 * x[2]) ** 2, -24 * (x[1] - 2 * x[2]) ** 2, 0], [0, -24 * (x[1] - 2 * x[2]) ** 2, 10 + 48 * (x[1] - 2 * x[2]) ** 2, -10], [-120 * (x[0] - x[3]) ** 2, 0, -10, -10 + 120 * (x[0] - x[3])**2]], dtype = numpy.float)
class test_Powell(NumpyTestCase):
--- ./PyDSTool/Toolbox/optimizers/step/goldfeld_step.py (original)
+++ ./PyDSTool/Toolbox/optimizers/step/goldfeld_step.py (refactored)
@@ -37,7 +37,7 @@
shift = -minEig + c
#avoiding sparse case with big nVars
- for i in xrange(point): G[i,i] += shift
+ for i in range(point): G[i,i] += shift
step = n_solve(G, -g)
--- ./PyDSTool/Toolbox/optimizers/step/__init__.py (original)
+++ ./PyDSTool/Toolbox/optimizers/step/__init__.py (refactored)
@@ -43,19 +43,19 @@
- local brute force step in 1D (experimental)
"""
-from gradient_step import *
-from conjugate_gradient_step import *
+from .gradient_step import *
+from .conjugate_gradient_step import *
-from newton_step import *
-from marquardt_step import *
-from quasi_newton_step import *
-from goldfeld_step import *
-from goldstein_price_step import *
+from .newton_step import *
+from .marquardt_step import *
+from .quasi_newton_step import *
+from .goldfeld_step import *
+from .goldstein_price_step import *
-from partial_step import *
-from restart_conjugate_gradient import *
+from .partial_step import *
+from .restart_conjugate_gradient import *
-from local_brute_force_1dstep import *
+from .local_brute_force_1dstep import *
step__all__ = ['GradientStep',
'CWConjugateGradientStep', 'DYConjugateGradientStep', 'DConjugateGradientStep', 'FRConjugateGradientStep', 'PRPConjugateGradientStep', 'FRPRPConjugateGradientStep',
--- ./PyDSTool/Toolbox/optimizers/optimizer/standard_optimizer_modifying.py (original)
+++ ./PyDSTool/Toolbox/optimizers/optimizer/standard_optimizRefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/optimizer/standard_optimizer.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/optimizer/optimizer.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/optimizer/__init__.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/wolfe_powell_rule.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/tests/test_wolfe_powell_rule.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/tests/test_strong_wolfe_powell_rule.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/tests/test_simple_line_search.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/tests/test_quadratic_interpolation.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/tests/test_goldstein_rule.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/tests/test_golden_section.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/tests/test_fixed_last_step_modifier.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/tests/test_fibonacci_section.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/tests/test_damped_line_search.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/tests/test_cubic_interpolation.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/tests/test_backtracking_search.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/tests/test_adaptive_last_step_modifier.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/strong_wolfe_powell_rule.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/simple_line_search.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/line_search/scaled_line_search.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/quadratic_interpolation.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/hyperbolic_line_search.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/goldstein_rule.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/golden_section.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/fixed_last_step_modifier.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/fibonacci_section.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/damped_line_search.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/cubic_interpolation.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_search.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_non_monotone_search.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/backtracking_search.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/line_search/adaptive_last_step_modifier.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/line_search/__init__.py
er_modifying.py (refactored)
@@ -6,7 +6,7 @@
A standard optimizer with a special object that modifies the resulting set of parameters
"""
-import optimizer
+from . import optimizer
class StandardOptimizerModifying(optimizer.Optimizer):
"""
--- ./PyDSTool/Toolbox/optimizers/optimizer/standard_optimizer.py (original)
+++ ./PyDSTool/Toolbox/optimizers/optimizer/standard_optimizer.py (refactored)
@@ -6,7 +6,7 @@
A standard optimizer
"""
-import optimizer
+from . import optimizer
class StandardOptimizer(optimizer.Optimizer):
"""
@@ -60,7 +60,7 @@
else:
# this would include self.optimalPoint if the lowest was found by the linesearch
new_pars = pest.pars_dict_to_array(pest.log[pest._lowest_res_log_ix].pars)
- print "*** CHOSE pars with residual %.8f" % pest.log[pest._lowest_res_log_ix].residual_norm
+ print("*** CHOSE pars with residual %.8f" % pest.log[pest._lowest_res_log_ix].residual_norm)
self.state['new_parameters'] = new_pars
self.state['new_value'] = self.function(new_pars)
--- ./PyDSTool/Toolbox/optimizers/optimizer/__init__.py (original)
+++ ./PyDSTool/Toolbox/optimizers/optimizer/__init__.py (refactored)
@@ -16,8 +16,8 @@
- modifies the resulting parameters
"""
-from standard_optimizer import *
-from standard_optimizer_modifying import *
+from .standard_optimizer import *
+from .standard_optimizer_modifying import *
optimizer__all__ = ['StandardOptimizer', 'StandardOptimizerModifying']
--- ./PyDSTool/Toolbox/optimizers/line_search/scaled_line_search.py (original)
+++ ./PyDSTool/Toolbox/optimizers/line_search/scaled_line_search.py (refactored)
@@ -89,9 +89,9 @@
# stepSize = 0.0005
init_step = stepSize
while not_done:
- print "\nLinestep: i =", i, "step size =", stepSize, "direction =\n", direction
+ print("\nLinestep: i =", i, "step size =", stepSize, "direction =\n", direction)
p = origin + i * stepSize * direction
- print "Testing p = ", p
+ print("Testing p = ", p)
new_value = fun(p)
if new_value < old_value:
i += 1
--- ./PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_search.py (original)
+++ ./PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_search.py (refactored)
@@ -24,7 +24,7 @@
state0 = {'direction' : g0}
x1 = lineSearch(origin = x0, state = state0, function = function)
- print x1
+ print(x1)
s0 = x1 - x0
y0 = state['gradient'] - g0
@@ -37,7 +37,7 @@
yk_ = y0
gk_ = state['gradient']
- for k in xrange(maxIter):
+ for k in range(maxIter):
alpha_k = dot(sk_, sk_) / dot(sk_,yk_)
sk_ = -alpha_k * gk_
xk += sk_
@@ -46,7 +46,7 @@
yk_ = gk_ - gk_prev
#if norm(gk_) < self.gradtol: return xk
if norm(gk_) <= 1e-6:
- print 'k=', k
+ print('k=', k)
return xk
return xk
@@ -58,6 +58,6 @@
x0 = sin(arange(1000))
fun = Function()
x_opt = BarzilaiBorwein(fun, x0)
- print x_opt
- print fun(x_opt)
+ print(x_opt)
+ print(fun(x_opt))
--- ./PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_non_monotone_search.py (original)
+++ ./PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_non_monotone_search.py (refactored)
@@ -42,7 +42,7 @@
xk = x0.copy()
last_M_iter_objFun_values = []
- for k in xrange(maxIter):
+ for k in range(maxIter):
gk = function.gradient(xk)
if norm(gk) <= gradtol: break
@@ -77,6 +77,6 @@
x0 = sin(arange(300))
fun = Function()
x_opt = BarzilaiBorwein_nonmonotone(fun, x0)
- print x_opt
- print fun(x_opt)
+ print(x_opt)
+ print(fun(x_opt))
--- ./PyDSTool/Toolbox/optimizers/line_search/__init__.py (original)
+++ ./PyDSTool/Toolbox/optimizers/line_search/__init__.py (refactored)
@@ -35,24 +35,24 @@
- modified the last step length with a fixed factor
"""
-from simple_line_search import *
-from hyperbolic_line_search import *
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/helpers/tests/test_quadratic.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/helpers/tests/test_levenberg_marquardt.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/helpers/tests/test_finite_difference.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/helpers/quadratic.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/helpers/levenberg_marquardt.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/helpers/finite_difference.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/helpers/__init__.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/defaults.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/criterion/tests/test_information_criteria.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/criterion/tests/test_facilities.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/criterion/tests/test_criteria.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/criterion/tests/test_composite_criteria.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/criterion/information_criteria.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/criterion/facilities.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/optimizers/criterion/criteria.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/criterion/composite_criteria.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/criterion/__init__.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/optimizers/__init__.py
-from damped_line_search import *
-from backtracking_search import *
+from .simple_line_search import *
+from .hyperbolic_line_search import *
+from .damped_line_search import *
+from .backtracking_search import *
-from wolfe_powell_rule import *
-from strong_wolfe_powell_rule import *
-from goldstein_rule import *
+from .wolfe_powell_rule import *
+from .strong_wolfe_powell_rule import *
+from .goldstein_rule import *
-from golden_section import *
-from fibonacci_section import *
-from quadratic_interpolation import *
-from cubic_interpolation import *
+from .golden_section import *
+from .fibonacci_section import *
+from .quadratic_interpolation import *
+from .cubic_interpolation import *
-from adaptive_last_step_modifier import *
-from fixed_last_step_modifier import *
+from .adaptive_last_step_modifier import *
+from .fixed_last_step_modifier import *
-from scaled_line_search import *
+from .scaled_line_search import *
line_search__all__ = ['SimpleLineSearch', 'HyperbolicLineSearch', 'DampedLineSearch', 'BacktrackingSearch',
'WolfePowellRule', 'StrongWolfePowellRule', 'GoldsteinRule',
--- ./PyDSTool/Toolbox/optimizers/helpers/levenberg_marquardt.py (original)
+++ ./PyDSTool/Toolbox/optimizers/helpers/levenberg_marquardt.py (refactored)
@@ -2,7 +2,7 @@
# Matthieu Brucher
# Last Change : 2007-08-23 10:12
-import quadratic
+from . import quadratic
import numpy
class LMQuadratic(quadratic.Quadratic):
--- ./PyDSTool/Toolbox/optimizers/helpers/finite_difference.py (original)
+++ ./PyDSTool/Toolbox/optimizers/helpers/finite_difference.py (refactored)
@@ -1,4 +1,4 @@
-from __future__ import division
+
from PyDSTool import common
import numpy as np
--- ./PyDSTool/Toolbox/optimizers/helpers/__init__.py (original)
+++ ./PyDSTool/Toolbox/optimizers/helpers/__init__.py (refactored)
@@ -15,9 +15,9 @@
- also, versions with in-built caching of previous values
"""
-from quadratic import *
+from .quadratic import *
-from finite_difference import *
+from .finite_difference import *
helpers__all__ = ['Quadratic', 'FiniteDifferencesFunction',
'ForwardFiniteDifferences',
--- ./PyDSTool/Toolbox/optimizers/criterion/facilities.py (original)
+++ ./PyDSTool/Toolbox/optimizers/criterion/facilities.py (refactored)
@@ -8,8 +8,8 @@
__all__ = ['criterion']
-from criteria import IterationCriterion, RelativeValueCriterion, RelativeParametersCriterion, GradientCriterion
-from composite_criteria import OrComposition
+from .criteria import IterationCriterion, RelativeValueCriterion, RelativeParametersCriterion, GradientCriterion
+from .composite_criteria import OrComposition
def criterion(**kwargs):
"""
--- ./PyDSTool/Toolbox/optimizers/criterion/composite_criteria.py (original)
+++ ./PyDSTool/Toolbox/optimizers/criterion/composite_criteria.py (refactored)
@@ -29,7 +29,7 @@
"""
Collects the different criteria
"""
- self.criteria = kwargs.values() + list(args)
+ self.criteria = list(kwargs.values()) + list(args)
def __call__(self, state, **kwargs):
"""
@@ -46,7 +46,7 @@
"""
Collects the different criteria
"""
- self.criteria = kwargs.values() + list(args)
+ self.criteria = list(kwargs.values()) + list(args)
def __call__(self, state, **kwargs):
"""
--- ./PyDSTool/Toolbox/optimizers/criterion/__init__.py (original)
+++ ./PyDSTool/Toolbox/optimizers/criterion/__init__.py (refactored)
@@ -38,10 +38,10 @@
- Identical to AICCriterion except that a number of increases are tolerated
"""
-from criteria import *
-from composite_criteria import *
-from information_criteria import *
-from facilities import *
+from .criteria import *
+from .composite_criteria import *
+from .information_criteria import *
+from .facilities import *
criterion__all__ = ['IterationCriterion', 'MonotonyCriterion', 'RelativeValueCriterion', 'AbsoluteValueCriterion', 'RelativeParametersCriterion', 'AbsoluteParametersCriterion', 'GradientCriterion',
'OrComposition', 'AndComposition',
--- ./PyDSTool/Toolbox/optimRefactoringTool: Refactored ./PyDSTool/Toolbox/neuro_data.py
izers/__init__.py (original)
+++ ./PyDSTool/Toolbox/optimizers/__init__.py (refactored)
@@ -14,12 +14,12 @@
mod_path()
-import defaults
-import criterion
-import line_search
-import optimizer
-import step
-import helpers
+from . import defaults
+from . import criterion
+from . import line_search
+from . import optimizer
+from . import step
+from . import helpers
__all__= ['defaults', 'criterion', 'line_search', 'optimizer', 'step', 'helpers']
--- ./PyDSTool/Toolbox/neuro_data.py (original)
+++ ./PyDSTool/Toolbox/neuro_data.py (refactored)
@@ -112,7 +112,7 @@
thi=self.pars.tlo+self.pars.width_tol)
loc_extrema = find_internal_extrema(pts)
if self.pars.verbose_level > 0:
- print loc_extrema
+ print(loc_extrema)
max_val_ix, xmax = loc_extrema['local_max']
global_max_val_ix, global_xmax = loc_extrema['global_max']
min_val_ix, xmin = loc_extrema['local_min']
@@ -182,7 +182,7 @@
self.pars.thi = pts.indepvararray[-1]
loc_extrema = find_internal_extrema(pts, self.pars.noise_tol)
if self.pars.verbose_level > 0:
- print loc_extrema
+ print(loc_extrema)
## plot spike and quadratic fit
#plot(pts.indepvararray, pts[self.super_pars.burst_coord], 'go-')
#show()
@@ -211,8 +211,8 @@
thresh_pc = 0.15
thresh = (xmin + thresh_pc*(xmax-xmin))
if self.pars.verbose_level > 0:
- print "xmin used =", xmin
- print "thresh = ", thresh
+ print("xmin used =", xmin)
+ print("thresh = ", thresh)
# Define extent of spike for purposes of quadratic fit ...
evs_found = self.pars.ev.searchForEvents(trange=[self.pars.tlo,
self.pars.thi],
@@ -233,10 +233,10 @@
ixlo = pts.find(tmax-dt, end=0)
ixhi = pts.find(tmax+dt, end=1)
if self.pars.verbose_level > 0:
- print "ixlo =", ixlo, "ixhi =", ixhi
- print "tlo =",tmax-dt, "thi =",tmax+dt
- print pts[ixlo], pts[ixhi]
- print "\nget_spike tests:", test1, test2, test3
+ print("ixlo =", ixlo, "ixhi =", ixhi)
+ print("tlo =",tmax-dt, "thi =",tmax+dt)
+ print(pts[ixlo], pts[ixhi])
+ print("\nget_spike tests:", test1, test2, test3)
self.results.ixlo = ixlo
self.results.ixhi = ixhi
self.results.ixmax = max_val_ix
@@ -249,7 +249,7 @@
def finish(self, traj):
# function of traj, not target
if self.pars.verbose_level > 0:
- print "Finishing spike processing..."
+ print("Finishing spike processing...")
pts = self.results.spike_pts
coord = self.pars.coord
xlo = pts[0][0]
@@ -477,7 +477,7 @@
xrs = burst_pts[self.pars.burst_coord]
trs = burst_pts.indepvararray
if max(x)-min(x) < 5:
- print "\n\n Not a bursting trajectory!!"
+ print("\n\n Not a bursting trajectory!!")
raise ValueError("Not a bursting trajectory")
b, a = self.pars.filt_coeffs_LP
xf = filtfilt(b, a, xrs)
@@ -504,7 +504,7 @@
# get_burst_spikes if done accurately
#self.results.spike_times = self.results.burst_est.spike_ts
if self.pars.verbose_level > 0:
- print "Spikes found at (approx) t=", self.results.burst_est.spike_ts
+ print("Spikes found at (approx) t=", self.results.burst_est.spike_ts)
if self.results.burst_est.spike_ts[0] < self.pars.shrink_end_time_thresh:
# kludgy way to ensure that another burst doesn't encroach
if not hasattr(self.pars, 'shrunk'):
@@ -548,7 +548,7 @@
"""
def _local_init(self):
assert len(self.subfeatures) == 2
- assert remain(self.subfeatures.keys(),
+ assert remain(list(self.subfeatures.keys()),
['is_spike_data', 'is_spike_model']) == []
def postprocess_ref_traj(RefactoringTool: Refactored ./PyDSTool/Toolbox/neuralcomp.py
self):
@@ -574,7 +574,7 @@
satisfied = True
for spike_num, spike_ix in enumerate(burst_est.spike_ixs):
if self.pars.verbose_level > 0:
- print "\n Starting spike", spike_num+1
+ print("\n Starting spike", spike_num+1)
is_spike.super_pars.burst_coord = self.super_pars.burst_coord
# step back 10% of estimated period
try:
@@ -586,7 +586,7 @@
is_spike.pars.tlo = burst_est.t[spike_ix] - \
is_spike.pars.width_tol / 2.
if self.pars.verbose_level > 0:
- print "new tlo =", is_spike.pars.tlo
+ print("new tlo =", is_spike.pars.tlo)
# would prefer to work this out self-consistently...
#is_spike.pars.fit_width_max = ?
new_sat = is_spike(traj)
@@ -596,7 +596,7 @@
spike_times.append(is_spike.results.spike_time)
spike_vals.append(is_spike.results.spike_val)
if self.pars.verbose_level > 0:
- print "Spike times:", spike_times
+ print("Spike times:", spike_times)
return spike_times, spike_vals
@@ -669,7 +669,7 @@
vals = burst_pts[self.super_pars.burst_coord]
inter_spike_ixs = [(burst_est.spike_ixs[i-1],
burst_est.spike_ixs[i]) \
- for i in xrange(1, len(burst_est.spike_ixs))]
+ for i in range(1, len(burst_est.spike_ixs))]
# should really use quadratic fit to get an un-biased minimum
trough_ixs = [npy.argmin(vals[ix_lo:ix_hi])+ix_lo for ix_lo, ix_hi in \
inter_spike_ixs]
@@ -696,7 +696,7 @@
spike_ixs.append(tix)
inter_spike_ixs = [(spike_ixs[i-1],
spike_ixs[i]) \
- for i in xrange(1, len(ts))]
+ for i in range(1, len(ts))]
# min and max events in model mean that these are recorded
# accurately in the pointsets already
trough_ixs = [npy.argmin(vals[ix_lo:ix_hi])+ix_lo for ix_lo, ix_hi in \
@@ -730,10 +730,10 @@
burst_est = self.super_pars.ref_burst_est
# find approximate (integer) mid-point index between spikes
mid_isi_ixs = [int(0.5*(burst_est.spike_ixs[i-1]+burst_est.spike_ixs[i])) \
- for i in xrange(1, len(burst_est.spike_ixs))]
+ for i in range(1, len(burst_est.spike_ixs))]
isi_t = [ts[i] for i in mid_isi_ixs]
isi_vals = [ts[burst_est.spike_ixs[i]]-ts[burst_est.spike_ixs[i-1]] for \
- i in xrange(1, len(burst_est.spike_ixs))]
+ i in range(1, len(burst_est.spike_ixs))]
self.ref_traj = numeric_to_traj([isi_vals], 'isi_envelope',
self.super_pars.burst_coord, isi_t,
burst_pts.indepvarname, discrete=False)
@@ -746,7 +746,7 @@
# ignore target
ts = self.super_results.spike_times
tname = self.super_pars.burst_coord_pts.indepvarname
- isi_vals = [ts[i]-ts[i-1] for i in xrange(1, len(ts))]
+ isi_vals = [ts[i]-ts[i-1] for i in range(1, len(ts))]
self.results.burst_isi_env = numeric_to_traj([isi_vals],
'isi_envelope',
self.super_pars.burst_coord,
@@ -927,7 +927,7 @@
self.spike_ixs = spike_ixs
self.spike_ts = t[spike_ixs]
self.ISIs = [self.spike_ts[i]-self.spike_ts[i-1] for \
- i in xrange(1, len(spike_ixs))]
+ i in range(1, len(spike_ixs))]
self.mean_ISI = npy.mean(self.ISIs)
self.std_ISI = npy.std(self.ISIs)
self.num_spikes = len(spike_ixs)
--- ./PyDSTool/Toolbox/neuralcomp.py (original)
+++ ./PyDSTool/Toolbox/neuralcomp.py (refactored)
@@ -10,7 +10,7 @@
Rob Clewley, September 2005.
"""
-from __future__ import division
RefactoringTool: No changes to ./PyDSTool/Toolbox/model_primitives.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/mechmatlib.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/makeSloppyModel.py
+
from PyDSTool import *
from copy import copy
@@ -1004,13 +1004,13 @@
return inp
else:
return c.name+'.'+inp
- for targ, inputs in c.gamma1.items():
+ for targ, inputs in list(c.gamma1.items()):
proc_targ = process_targ_name(targ)
if proc_targ not in dssrt_inputs:
dssrt_inputs[proc_targ] = args(gamma1=[], gamma2=[])
dssrt_inputs[proc_targ].gamma1.extend([process_targ_name(i) \
for i in inputs])
- for targ, inputs in c.gamma2.items():
+ for targ, inputs in list(c.gamma2.items()):
proc_targ = process_targ_name(targ)
if proc_targ not in dssrt_inputs:
dssrt_inputs[proc_targ] = args(gamma1=[], gamma2=[])
@@ -1195,7 +1195,7 @@
raise TypeError("threshold function must be a string or a "
"QuantSpec")
if threshfun[0] not in funbody:
- print "Warning: voltage name %s does not appear in function body!"%threshfun[0]
+ print("Warning: voltage name %s does not appear in function body!"%threshfun[0])
f = Fun(funbody, [threshfun[0]], 'thresh')
assert len(f.signature) == 1, \
'threshold function must be a function of a single argument (voltage)'
--- ./PyDSTool/Toolbox/makeSloppyModel.py (original)
+++ ./PyDSTool/Toolbox/makeSloppyModel.py (refactored)
@@ -13,25 +13,25 @@
def makeSloppyModel(modelName, modelDict, targetGen, globalRefs=None,
algParams=None, silent=False):
if targetGen not in allODEgens:
- print 'Valid target ODE solvers: ' + ", ".join(allODEgens)
+ print('Valid target ODE solvers: ' + ", ".join(allODEgens))
raise ValueError('Invalid target ODE solver')
sModelSpec = sloppyModel(modelName)
if not silent:
- print "Building sloppy model '%s'"%modelName
+ print("Building sloppy model '%s'"%modelName)
# first pass to collect names
varnames = []
- for odeName in modelDict['odes'].keys():
+ for odeName in list(modelDict['odes'].keys()):
varnames.append(odeName)
parnames = []
if 'parameters' in modelDict:
- for parName in modelDict['parameters'].keys():
+ for parName in list(modelDict['parameters'].keys()):
parnames.append(parName)
pdomains = {}
xdomains = {}
if 'domains' in modelDict:
- for name, dom in modelDict['domains'].iteritems():
+ for name, dom in modelDict['domains'].items():
if name in parnames:
pdomains[name] = dom
elif name in varnames:
@@ -40,9 +40,9 @@
raise ValueError("Name %s unknown in domain specs"%name)
- for odeName, expr in modelDict['odes'].iteritems():
+ for odeName, expr in modelDict['odes'].items():
if not silent:
- print 'Adding ODE: ', odeName
+ print('Adding ODE: ', odeName)
if odeName in xdomains:
sModelSpec.add(Var(expr, odeName, specType='RHSfuncSpec',
domain=xdomains[odeName]))
@@ -51,40 +51,40 @@
auxvarnames = []
if 'assignments' in modelDict:
- for assgnName, expr in modelDict['assignments'].iteritems():
+ for assgnName, expr in modelDict['assignments'].items():
if not silent:
- print 'Adding assignment: ', assgnName
+ print('Adding assignment: ', assgnName)
sModelSpec.add(Var(expr, assgnName, specType='ExpFuncSpec'))
auxvarnames.append(assgnName)
if 'parameters' in modelDict:
- for parName, val in modelDict['parameters'].iteritems():
+ for parName, val in modelDict['parameters'].items():
if not silent:
- print 'Adding parameter: ', parName, "=", val
+ print('Adding parameter: ', parName, "=", val)
if parName in pdRefactoringTool: Refactored ./PyDSTool/Toolbox/fracdim.py
omains:
sModelSpec.add(Par(str(val), parName, domain=pdomains[parName]))
else:
sModelSpec.add(Par(str(val), parName))
auxfndict = {}
- for funSig, expr in modelDict['functions'].iteritems():
+ for funSig, expr in modelDict['functions'].items():
assert ')' == funSig[-1]
assert '(' in funSig
major = funSig.replace(')','').replace(' ','').split('(')
args = major[1].split(',')
name = major[0]
if not silent:
- print 'Adding function: ', name, " of arguments:", args
+ print('Adding function: ', name, " of arguments:", args)
sModelSpec.add(Fun(expr, args, name))
auxfndict[name] = (args, expr)
if globalRefs is None:
globalRefs = []
if not sModelSpec.isComplete(globalRefs):
- print "Model retains free names: " + ", ".join(sModelSpec.freeSymbols)
- print "These must be resolved in the specification before continuing."
- print "If one of these is time, then include it explicitly as an"
- print "entry in the argument list ('globalRefs' key)"
+ print("Model retains free names: " + ", ".join(sModelSpec.freeSymbols))
+ print("These must be resolved in the specification before continuing.")
+ print("If one of these is time, then include it explicitly as an")
+ print("entry in the argument list ('globalRefs' key)")
raise ValueError('Incomplete model specification')
targetlang = theGenSpecHelper(targetGen).lang
# single-generator model so give both same name
@@ -96,11 +96,11 @@
'target': targetGen,
'algparams': algParams}})
if not silent:
- print "Adding events with default tolerances..."
+ print("Adding events with default tolerances...")
argDict={'precise': True, 'term': True}
evcount = 0
if 'events' in modelDict:
- for evspec, mappingDict in modelDict['events'].iteritems():
+ for evspec, mappingDict in modelDict['events'].items():
if evspec[:2] == 'lt':
dircode = -1
elif evspec[:2] == 'gt':
@@ -121,6 +121,6 @@
'pars': parnames})
sModel.mapEvent(genName, evname, genName, evmap)
if not silent:
- print "Building target model with default settings"
+ print("Building target model with default settings")
return sModel.getModel()
--- ./PyDSTool/Toolbox/fracdim.py (original)
+++ ./PyDSTool/Toolbox/fracdim.py (refactored)
@@ -6,7 +6,7 @@
(c) 2005, 2006. Robert Clewley, John Guckenheimer.
"""
-from __future__ import division
+
from PyDSTool import *
from PyDSTool.common import _seq_types
from PyDSTool.Toolbox.data_analysis import *
@@ -34,12 +34,12 @@
npts = size(data,0)
d = zeros((npts*(npts-1)/2,), 'd') # size of upper triangle (no diagonal) of m vs. m matrix
# max ix for each i in expression for d is (i-1)*(i-2)/2 + (i-2)
- for i in xrange(1,npts):
- for j in xrange(i-1):
+ for i in range(1,npts):
+ for j in range(i-1):
d[(i-1)*(i-2)/2+j] = norm(data[i]-data[j], which_norm)
d.sort()
logd = log(d).ravel()
- logv = log(range(1,len(d)+1))
+ logv = log(list(range(1,len(d)+1)))
nan_ixs = isfinite(logd)
logd = extract(nan_ixs, logd)
logv = extract(nan_ixs, logv)
@@ -55,15 +55,15 @@
dsize = npts*(npts-1)/2
d = zeros((dsize,), 'd') # size of upper triangle (no diagonal) of m vs. m matrix
# max ix for each i in expression for d is (i-1)*(i-2)/2 + (i-2)
- for i in xrange(1,npts):
- for j in xrange(i-1):
+ for i in range(1,npts):
+ for j in range(i-1):
ix = (i-1)*(i-2)/2+j
if mod(ix,inforate) == 0:
dump_progress(ix, dsize)
d[ix] = norm(data[i]-data[j])
d.sort()
logd = log(d).ravel()
- logv = log(range(1,len(d)+1))
+ logv = log(list(range(1,len(d)+1)))
nan_ixs = isfinite(logd)
logd = extract(nan_ixs, logd)
logv = extract(nan_ixs, logv)
@@ -73,7 +73,7 @@
def timeseq(time, covering, refpt):
"""Extract time sequence from a covering"""
ts = time.take(covering[refpt][3], 0)
- print "time sequence min = %f, max = %f"%(min(ts),max(ts))
+ print("time sequence min = %f, max = %f"%(min(ts),max(ts)))
return ts
@@ -94,8 +94,8 @@
point -> reference points whose neighbourhoods include it
"""
covering = {}
- covered = {}.fromkeys(range(len(data)),None)
- not_covered = covered.keys()
+ covered = {}.fromkeys(list(range(len(data))),None)
+ not_covered = list(covered.keys())
if remain_tol > len(data):
remain_tol = 0
makerefpt_ixs = []
@@ -105,8 +105,8 @@
refptix = 0 # initial value
N = size(data,0)
start_ix = int(round(sqrt(N)))
- print "N = ", N, "start ix = ", start_ix
- logv_raw = log(range(1,N+1))
+ print("N = ", N, "start ix = ", start_ix)
+ logv_raw = log(list(range(1,N+1)))
done = False
unsuccessful = []
if step is None:
@@ -116,21 +116,21 @@
# treat as %age of # data points
ixstep = int(math.ceil(len(d)*step))
if not quiet:
- print "Using index step %i out of %i points"%(ixstep, len(d))
+ print("Using index step %i out of %i points"%(ixstep, len(d)))
else:
ixstep = step
else:
raise ValueError("Invalid step argument")
while not done:
if not quiet:
- print "\n*************\nCalculating distances and point-wise dimension around pt %i ..."%refptix
+ print("\n*************\nCalculating distances and point-wise dimension around pt %i ..."%refptix)
logv, logd, d, d_inv_dict = log_distances_with_D(data, refptix, logv_raw)
d_inv_keys = sortedDictKeys(d_inv_dict)
d_inv_vals = sortedDictValues(d_inv_dict)
d_inv = Pointset(indepvararray=d_inv_keys, indepvartype=Float,
coordarray=d_inv_vals, coordtype=Int, tolerance=5e-5)
if not quiet:
- print "Finding self-consistent neighbourhood",
+ print("Finding self-consistent neighbourhood", end=' ')
# search from min_ix -> end, increasing hiix from loix+1 until dimensionality
# (slope) stabilizes to within an absolute tolerance and does not grow larger
# than a different tolerance
@@ -139,7 +139,7 @@
old_dim = None
hiix = start_ix
if not quiet:
- print "Start ix = ", start_ix
+ print("Start ix = ", start_ix)
loix=start_ix-2
nhd_too_small = False
ref_dim = -1
@@ -154,7 +154,7 @@
weight='')
all_res.append(residual)
if not quiet and mod(hiix,50) == 0:
- print ".",
+ print(".", end=' ')
if old_dim is not None:
sd = std(all_res)
## if residual > max_res:
@@ -174,10 +174,10 @@
weight='lo', w=wlo)
all_res.append(residual)
if not quiet:
- print "(%i,%i)"%(loix,hiix),
- print "dim=%.4f, residual = %.4f"%(dim,residual)
+ print("(%i,%i)"%(loix,hiix), end=' ')
+ print("dim=%.4f, residual = %.4f"%(dim,residual))
if not quiet and mod(hiix,50) == 0:
- print ".",
+ print(".", end=' ')
try:
sd = std(all_res)
except:
@@ -188,20 +188,20 @@
## not_done = False
if sd > max_std:
if not quiet:
- print "residuals s.d. > max_std"
+ print("residuals s.d. > max_std")
not_done = False
old_dim = dim
nhd_too_small = hiix-loix < min_nhd_size
if not quiet:
- print "nhd_too_small = ", nhd_too_small
+ print("nhd_too_small = ", nhd_too_small)
if nhd_too_small:
if not quiet:
- print "Neighbourhood too small. Moving to a different reference point..."
+ print("Neighbourhood too small. Moving to a different reference point...")
unsuccessful.append(refptix)
else:
if not quiet:
- print "\nDimension = %f"%dim
- print "Found best fit line from relative ix %i to %i (radius %f)"%(loix, hiix, d[hiix])
+ print("\nDimension = %f"%dim)
+ print("Found best fit line from relative ix %i to %i (radius %f)"%(loix, hiix, d[hiix]))
# consolidate results in terms of global index positions in data
covered_ixs = [d_inv(d[ix])[0] for ix in range(loix, hiix+1)]
covered_ixs.append(refptix)
@@ -225,7 +225,7 @@
# find new ref pt in not_covered and repeat
num_uncovered = len(not_covered)
## if not quiet:
- print "%i points left to cover"%(num_uncovered+len(makerefpt_ixs))
+ print("%i points left to cover"%(num_uncovered+len(makerefpt_ixs)))
if num_uncovered < remain_tol:
if len(makerefpt_ixs) == 0:
done = True
@@ -252,14 +252,14 @@
max_radius_ratio=1.5):
"""Find a single neighbourhood around a reference point."""
covering = {}
- covered = {}.fromkeys(range(len(data)),None)
+ covered = {}.fromkeys(list(range(len(data))),None)
if initref is not None:
refptix = initref
else:
refptix = 0 # initial value
- logv_raw = log(range(1,size(data,0)+1))
+ logv_raw = log(list(range(1,size(data,0)+1)))
if not quiet:
- print "\n*************\nCalculating distances and point-wise dimension around pt %i ..."%refptix
+ print("\n*************\nCalculating distances and point-wise dimension around pt %i ..."%refptix)
doplot = 1
else:
doplot = 0
@@ -269,7 +269,7 @@
d_inv = Pointset(indepvararray=d_inv_keys, indepvartype=Float,
coordarray=d_inv_vals, coordtype=Int, tolerance=5e-5)
if not quiet:
- print "Finding self-consistent neighbourhood",
+ print("Finding self-consistent neighbourhood", end=' ')
# search from min_ix -> end, increasing hiix from loix+1 until dimensionality
# (slope) stabilizes to within an absolute tolerance and does not grow larger
# than a different tolerance
@@ -286,7 +286,7 @@
# treat as %age of # data points
ixstep = int(math.ceil(len(d)*step))
if not quiet:
- print "Using index step %i out of %i points"%(ixstep, len(d))
+ print("Using index step %i out of %i points"%(ixstep, len(d)))
else:
ixstep = step
else:
@@ -307,7 +307,7 @@
## if hiix - loix > min_nhd_size:
all_res.append(residual)
if not quiet:
- print "Dim = %.3f in [%i,%i], Residual = %.4f "%(dim,loix,hiix,residual),
+ print("Dim = %.3f in [%i,%i], Residual = %.4f "%(dim,loix,hiix,residual), end=' ')
plot([logd[loix],logd[hiix]],[logd[loix]*pfit[0]+pfit[1],logd[hiix]*pfit[0]+pfit[1]])
## if mod(hiix,50) == 0:
## print ".",
@@ -315,12 +315,12 @@
## err = abs(dim-old_dim)/dim
sd = std(all_res)
if not quiet:
- print "S.d. = %.4f "%sd
+ print("S.d. = %.4f "%sd)
if residual > max_res:
- print "residual > max_res"
+ print("residual > max_res")
not_done = False
if sd > max_std:
- print "residuals s.d. > max_std"
+ print("residuals s.d. > max_std")
not_done = False
## if err > max_err and hiix-loix > min_nhd_size/4:
## if not quiet:
@@ -345,13 +345,13 @@
old_dim = dim
nhd_too_small = nhd_too_small or hiix-loix < min_nhd_size
if nhd_too_small:
- print "Neighbourhood too small. Try a different starting index or a new reference point ..."
- print "Dim found over ixs [%i, %i] = %.4f"%(loix,hiix,dim)
+ print("Neighbourhood too small. Try a different starting index or a new reference point ...")
+ print("Dim found over ixs [%i, %i] = %.4f"%(loix,hiix,dim))
raise RuntimeError
else:
if not quiet:
- print "\nDimension = %f"%dim
- print "Found best fit line from relative ix %i to %i (radius %f)"%(loix, hiix, d[hiix])
+ print("\nDimension = %f"%dim)
+ print("Found best fit line from relative ix %i to %i (radius %f)"%(loix, hiix, d[hiix]))
# consolidate results in terms of global index positions in data
covered_ixs = [d_inv(d[ix])[0] for ix in range(loix, hiix+1)]
covered_ixs.append(refptix)
@@ -446,15 +446,15 @@
rhiy = zeros((len(covering),1),'f')
drange = arange(0, maxD+1, bin_width, 'd').tolist()
dbins = data_bins('D', drange)
- cover_by_dimix = {}.fromkeys(range(len(drange)))
+ cover_by_dimix = {}.fromkeys(list(range(len(drange))))
for dix in range(len(drange)):
cover_by_dimix[dix] = []
- cover_by_size_dict = {}.fromkeys(range(len(covered)+1))
+ cover_by_size_dict = {}.fromkeys(list(range(len(covered)+1)))
ix = 0
integral = 0
largest = 0
try:
- for p, (d, rlo, rhi, l) in covering.iteritems():
+ for p, (d, rlo, rhi, l) in covering.items():
dx[ix] = d
rloy[ix] = rlo
rhiy[ix] = rhi
@@ -471,7 +471,7 @@
except ValueError:
# No max radius information available!
# compatible with old version of covering that does not return rhi
- for p, (d, rlo, l) in covering.iteritems():
+ for p, (d, rlo, l) in covering.items():
dx[ix] = d
rloy[ix] = rlo
rhiy[ix] = 0
@@ -485,19 +485,19 @@
ly[ix] = lenl
integral += lenl
ix += 1
- print "\nNeighbourhood statistics:"
- print "There are %i neighbourhoods to this covering"%len(covering)
- print "Largest neighbourhood has %i points"%largest
- cover_by_size = [di for di in cover_by_size_dict.iteritems() if di[1] is not None]
+ print("\nNeighbourhood statistics:")
+ print("There are %i neighbourhoods to this covering"%len(covering))
+ print("Largest neighbourhood has %i points"%largest)
+ cover_by_size = [di for di in cover_by_size_dict.items() if di[1] is not None]
cover_by_size.sort()
csizes = [c[0] for c in cover_by_size]
if nhd_size_thresh is None:
s = std(csizes)
sm = s_frac*s
m = mean(csizes)
- print "Std. dev. of cover_by_size =", s
- print "Max size found =", max(csizes)
- print "Mean size found =", m
+ print("Std. dev. of cover_by_size =", s)
+ print("Max size found =", max(csizes))
+ print("Mean size found =", m)
## # find largest index of set of covering nhds such that its size
## # is smaller than s_frac% of the std deviation of the sizes
## for i in range(len(cover_by_size)):
@@ -510,11 +510,11 @@
## print "N'hood size threshold used = mean(cover_by_sizes restricted to %.3f of 1st std. dev.)"%s_frac
## print " =", nhd_size_thresh
nhd_size_thresh = m-sm
- print "N'hood size threshold used = mean - %.3f of std. dev."%s_frac
- print " =", nhd_size_thresh
+ print("N'hood size threshold used = mean - %.3f of std. dev."%s_frac)
+ print(" =", nhd_size_thresh)
else:
if nhd_size_thresh > 0:
- print "N'hood size threshold set by user =", nhd_size_thresh
+ print("N'hood size threshold set by user =", nhd_size_thresh)
if nhd_max_plot_size is None:
## # 2 * original set sizes mean
## try:
@@ -523,14 +523,14 @@
## nhd_max_plot_size = largest
## print "Using max plot nhd size = 2*mean(cover_by_sizes) =", nhd_max_plot_size
nhd_max_plot_size = largest
- print "Using max plot nhd size of largest neighbourhood found =", nhd_max_plot_size
- else:
- print "Using max plot nhd size set by user =", nhd_max_plot_size
+ print("Using max plot nhd size of largest neighbourhood found =", nhd_max_plot_size)
+ else:
+ print("Using max plot nhd size set by user =", nhd_max_plot_size)
# reverse so that largest first for returning to user
cover_by_size.reverse()
filtered_ixs = []
try:
- for p, (d, rlo, rhi, l) in covering.iteritems():
+ for p, (d, rlo, rhi, l) in covering.items():
if d <= maxD:
dix = dbins.resolve_bin_index(d)
if len(l) > nhd_size_thresh:
@@ -543,7 +543,7 @@
cover_by_dimix[dix].append(p)
except ValueError:
# compatible with old version of covering that does not return rhi
- for p, (d, rlo, l) in covering.iteritems():
+ for p, (d, rlo, l) in covering.items():
if d <= maxD:
dix = dbins.resolve_bin_index(d)
if len(l) > nhd_size_thresh:
@@ -595,7 +595,7 @@
fontmath = args(fontsize=22,fontname='Times')
fonttext = args(fontsize=18,fontname='Times')
# make plot
- print "Plotting histograms to figure", fignum
+ print("Plotting histograms to figure", fignum)
assert num_panels in [2,4], "num_panels argument must be 2 or 4"
figure(fignum)
if num_panels == 4:
@@ -637,7 +637,7 @@
else:
subplot(2,1,2)
dbx = dbins.midpoints.tolist()
- dby = dbins.values()
+ dby = list(dbins.values())
bar(dbx, dby, color='b', width=dbx[1]-dbx[0])
for panel in range(num_panels):
figure(fignum).axes[panel].set_xlim([dmin,dmax])
@@ -649,7 +649,7 @@
# assumes will not be more than 100 times!
cbins = zeros((100,),'i')
max_used = 0
- for clist in covered.itervalues():
+ for clist in covered.values():
try:
n = len(clist)
except TypeError:
@@ -698,13 +698,13 @@
m = dbins[:tail_ix].mean()
s = dbins[:tail_ix].std()
except:
- print "Tail found at index %i and D = %.3f"%(tail_ix,d_est)
- print " -- problem computing mean and std dev for this mode"
- print " so calculating for whole data set"
+ print("Tail found at index %i and D = %.3f"%(tail_ix,d_est))
+ print(" -- problem computing mean and std dev for this mode")
+ print(" so calculating for whole data set")
m = dbins.mean()
s = dbins.std()
- print "Estimate dimension to be (to resolution of histogram bin width):", d_est
- print " with histogram mean D = %.5f and std dev D = %.5f"%(m, s)
+ print("Estimate dimension to be (to resolution of histogram bin width):", d_est)
+ print(" with histogram mean D = %.5f and std dev D = %.5f"%(m, s))
return {"D_tail": d_est, "D_mean": m, "D_std": s}, \
dbins, cover_by_dimix, cover_by_size, cbu, filtered_ixs, integral
@@ -713,7 +713,7 @@
"""Returns the list of indices in covering for which the neighbourhood
size was larger than the threshold for dimension binning."""
fixs=[]
- for p, ixlist in cover_by_dimix.iteritems():
+ for p, ixlist in cover_by_dimix.items():
fixs.extend(ixlist)
fixs.sort()
return fixs
@@ -743,7 +743,7 @@
for i, cdata in enumerate(central_data):
dc[i]=norm(c_mean-cdata)
ds = []
- for i in xrange(len(data)):
+ for i in range(len(data)):
if i not in outliers:
ds.append(norm(data[i]-data[outliers[0]]))
ds = array(ds)
@@ -765,10 +765,10 @@
rfun = lambda rh, rl: rh-rl
radii = {}
if ixs is None:
- for p, (d, rlo, rhi, l) in covering.iteritems():
+ for p, (d, rlo, rhi, l) in covering.items():
radii[p] = rfun(rhi,rlo)
else:
- for p, (d, rlo, rhi, l) in covering.iteritems():
+ for p, (d, rlo, rhi, l) in covering.items():
if p in ixs:
radii[p] = rfun(rhi,rlo)
return radii
@@ -785,14 +785,14 @@
test = lambda r: r < rhi
else:
test = lambda r: r > rlo and r < rhi
- rfilt = [(ix,r) for (ix, r) in radii.iteritems() if test(r)]
+ rfilt = [(ix,r) for (ix, r) in radii.items() if test(r)]
return rfilt, [covering[rinfo[0]][0] for rinfo in rfilt]
def plot_radius_distribution(radii, max_radius, radius_bin_width):
"""Expects radii dictionary, as returned by get_cover_radii.
Returns figure handle."""
- rads = array(radii.values())
+ rads = array(list(radii.values()))
dbins = data_bins('r', arange(0, max_radius+radius_bin_width, radius_bin_width))
dbins.bin(rads)
dbx, dby = dbins.to_array()
@@ -811,7 +811,7 @@
If rwidth=0 (default) then no data binning is done.
Returns figure handle."""
- rlo, rhi = extent(radii.values())
+ rlo, rhi = extent(list(radii.values()))
assert rlo > 0 and rhi > rlo
f=figure()
if rwidth > 0:
@@ -837,7 +837,7 @@
r_max - r_min.
Returns figure handle."""
- rlo, rhi = extent(radii.values())
+ rlo, rhi = extent(list(radii.values()))
assert rlo > 0 and rhi > rlo
f = figure()
rs, ds = filter_by_radius(covering, radii, 0, rhi)
@@ -1054,7 +1054,7 @@
N=size(data,0)
assert Delta > 1
assert N > Delta*startix
- logv_raw = log(range(1,N+1))
+ logv_raw = log(list(range(1,N+1)))
logv, logd, d, d_inv_dict = log_distances_with_D(data, refptix, logv_raw)
hi_slope = 0
lo_slope = 1e10
@@ -1116,10 +1116,10 @@
col = array([0.3,0.3,0.3])
else:
raise "invalid color source"
- print "Expect %i dots when finished:"%int(num_refpts/50)
+ print("Expect %i dots when finished:"%int(num_refpts/50))
for i in range(num_refpts):
if mod(i,50) == 49:
- print ".",
+ print(".", end=' ')
slope_by_loix, lo, loix, hi, hiix, logv, logd = slope_range(data,
refpts[i], startix=startix, stopix=stopix,
Delta=Delta, step=step, maxD=maxD)
@@ -1163,19 +1163,19 @@
stats['max_slope']['min']=min(plotdata[:,1])
stats['min_slope']['max']=max(plotdata[:,0])
stats['max_slope']['max']=max(plotdata[:,1])
- print "\n"
+ print("\n")
return (plotdata, s, colors, c, ixdata, stats, handle)
def sorted_by_slope(plotdata, select=0):
"""select: 0 = rmin, 1 = rmax"""
ixs = argsort(plotdata, 0)[:,select]
- return zip(take(plotdata, ixs, 0)[:,select], ixs)
+ return list(zip(take(plotdata, ixs, 0)[:,select], ixs))
def sorted_by_radius(colors, select=0):
"""select: 0 = rmin, 1 = rmax"""
ixs = argsort(colors, 0)[:,select]
- return zip(take(colors, ixs, 0)[:,select], ixs)
+ return list(zip(take(colors, ixs, 0)[:,select], ixs))
def find_from_sorted(x, v, next_largest=1, indices=None):
if isinstance(v, _seq_types):
@@ -1252,8 +1252,8 @@
Engineering, 2007.
"""
pde_name = 'PD_E-'+a.name
- if 'N' in a.keys():
- if 'stopix' in a.keys():
+ if 'N' in list(a.keys()):
+ if 'stopix' in list(a.keys()):
if a.stopix is not None:
a.stopix = int(round(0.7*a.N))
else:
@@ -1262,14 +1262,14 @@
a.step = int(round(0.005*a.N))
else:
a.N = None
- if 'stopix' not in a.keys():
+ if 'stopix' not in list(a.keys()):
a.stopix = None
try:
if force:
raise ValueError
data, pde_args, plotdata, ssorted, colors, \
csorted, ixdata, sstats = loadObjects(pde_name)
- print "Loaded data set and stats for %s"%a.name
+ print("Loaded data set and stats for %s"%a.name)
# don't check the data field
if filteredDict(a, ['data','bin_width'], neg=True) != \
filteredDict(pde_args, ['data','bin_width'], neg=True):
@@ -1283,10 +1283,10 RefactoringTool: Refactored ./PyDSTool/Toolbox/event_driven_simulator.py
@@
try:
data = eval(a.data_gen_str, globals(), a.data_gen_fun)
except:
- print "Problem re-calculating data from given information"
+ print("Problem re-calculating data from given information")
else:
data = a.data
- print "Recalculating PD-E for %s"%a.name
+ print("Recalculating PD-E for %s"%a.name)
try:
csource=a.color_source
except AttributeError:
@@ -1313,7 +1313,7 @@
save_info='result_'+a.name
else:
save_info=''
- if 'show_seq' in a.keys():
+ if 'show_seq' in list(a.keys()):
show_seq = a['show_seq']
else:
show_seq = False
--- ./PyDSTool/Toolbox/event_driven_simulator.py (original)
+++ ./PyDSTool/Toolbox/event_driven_simulator.py (refactored)
@@ -60,7 +60,7 @@
#print "\n ** ", self.name, "received state:", state
self.in_vals.update(state)
# poll inputs
- for name, connxn in self.inputs.items():
+ for name, connxn in list(self.inputs.items()):
self.in_vals[connxn.input.name] = connxn.poll()
#print "... passing input values", self.in_vals
self.next_t = self.map(self.in_vals)
@@ -129,17 +129,17 @@
nodes[n] = new_node
# fill in inputs and outputs dictionaries for each type
- for cn, c in connxns.items():
+ for cn, c in list(connxns.items()):
cobj = mspec.components[cn]
targs = [head(t) for t in cobj.connxnTargets]
- c.outputs = dict(zip(targs, [nodes[t] for t in targs]))
+ c.outputs = dict(list(zip(targs, [nodes[t] for t in targs])))
for t in targs:
nodes[t].inputs[cn] = c
- for nn, n in nodes.items():
+ for nn, n in list(nodes.items()):
nobj = mspec.components[nn]
targs = [head(t) for t in nobj.connxnTargets]
- n.outputs = dict(zip(targs, [connxns[t] for t in targs]))
+ n.outputs = dict(list(zip(targs, [connxns[t] for t in targs])))
for t in targs:
connxns[t].input = n
@@ -207,22 +207,22 @@
# don't really need the connections, but just as a reference
self.connections = connections
if state is None:
- self.state = dict(zip(nodes.keys(), [NaN for n in nodes]))
+ self.state = dict(list(zip(list(nodes.keys()), [NaN for n in nodes])))
else:
self.state = state
self.curr_t = 0
self.history = {}
self.verbosity = 0
- self.Q = FIFOqueue_uniquenode(nodes.keys())
+ self.Q = FIFOqueue_uniquenode(list(nodes.keys()))
def set_node_state(self):
- for name, n in self.nodes.items():
+ for name, n in list(self.nodes.items()):
n.last_t = self.state[name]
def validate(self):
- for name, n in self.nodes.items():
+ for name, n in list(self.nodes.items()):
assert isinstance(n, node)
- for name, connxn in self.connections.items():
+ for name, connxn in list(self.connections.items()):
assert isinstance(connxn, connection)
assert sortedDictKeys(self.state) == sortedDictKeys(self.nodes), \
"Invalid or missing node state in history argument"
@@ -244,7 +244,7 @@
while not done:
last_state = self.state.copy()
- print "\n ***", self.curr_t, self.history[self.curr_t][0], self.state
+ print("\n ***", self.curr_t, self.history[self.curr_t][0], self.state)
next_t = Inf
iters = 1
@@ -255,17 +255,17 @@
try:
proj_state = self.compile_next_state(nodes)
except PyDSTool_BoundsError:
- print "Maps borked at", self.curr_t
+ print("Maps borked at", self.curr_t)
done = True
break
- print "Projected:", proj_state
- for node, t in proj_state.items():
+ print("Projected:", proj_state)
+ for node, t in list(proj_state.items())RefactoringTool: Refactored ./PyDSTool/Toolbox/dssrt.py
:
if t > self.curr_t:
self.Q.push(t, node)
# self.state[next_node] = self.Q.next_t
if self.verbosity > 0:
- print "Took %i iterations to stabilize" % iters
+ print("Took %i iterations to stabilize" % iters)
self.display()
t, next_node = self.Q.pop()
@@ -281,7 +281,7 @@
self.state = next_state.copy()
if self.verbosity > 0:
- print "Next node is", next_node, "at time ", self.curr_t
+ print("Next node is", next_node, "at time ", self.curr_t)
done = self.curr_t >= t_end
continue
@@ -305,7 +305,7 @@
## min_ix = i
if min_ix is None:
# no further events possible
- print "No further events possible, stopping!"
+ print("No further events possible, stopping!")
break
## if min_val < self.curr_t:
## # clear later history
@@ -321,7 +321,7 @@
self.state = (next_node, next_state)
if self.verbosity > 0:
- print "Next node is", next_node, "at time ", self.curr_t
+ print("Next node is", next_node, "at time ", self.curr_t)
done = self.curr_t >= t_end
ts, state_dicts = sortedDictLists(self.history, byvalue=False)
@@ -335,23 +335,23 @@
def compile_next_state(self, nodes):
vals = {}
- for name, n in nodes.items():
+ for name, n in list(nodes.items()):
vals[name] = n.poll(self.state)
return vals
def display(self):
- print "\n****** t =", self.curr_t
+ print("\n****** t =", self.curr_t)
info(self.state, "known state")
- print "\nNodes:"
- for name, n in self.nodes.items():
+ print("\nNodes:")
+ for name, n in list(self.nodes.items()):
#n.poll(self.state)
- print name
- for in_name, in_val in n.in_vals.items():
- print " Input", in_name, ": ", in_val
+ print(name)
+ for in_name, in_val in list(n.in_vals.items()):
+ print(" Input", in_name, ": ", in_val)
def extract_history_events(self):
- node_names = self.nodes.keys()
- node_events = dict(zip(node_names, [None]*len(node_names)))
+ node_names = list(self.nodes.keys())
+ node_events = dict(list(zip(node_names, [None]*len(node_names))))
ts = sortedDictKeys(self.history)
old_node, old_state = self.history[ts[0]]
# deal with initial conditions first
@@ -366,8 +366,8 @@
def display_raster(self, new_figure=True):
h = self.history
ts = sortedDictKeys(h)
- node_names = self.nodes.keys()
- print "\n\nNode order in plot (bottom to top) is", node_names
+ node_names = list(self.nodes.keys())
+ print("\n\nNode order in plot (bottom to top) is", node_names)
if new_figure:
figure()
t0 = ts[0]
@@ -387,7 +387,7 @@
"""seq_dict maps string symbols to increasing-ordered sequences of times.
Returns a single list of (symbol, time) pairs ordered by time."""
out_seq = []
- symbs = seq_dict.keys()
+ symbs = list(seq_dict.keys())
next_s = None
indices = {}
for s in symbs:
--- ./PyDSTool/Toolbox/dssrt.py (original)
+++ ./PyDSTool/Toolbox/dssrt.py (refactored)
@@ -7,7 +7,7 @@
Robert Clewley, 2009
"""
-from __future__ import division
+
from PyDSTool import common
from PyDSTool import utils
@@ -21,7 +21,8 @@
import numpy as np
import scipy as sp
import copy
-import cStringIO, operator
+import io, operator
+from functools import reduce
#############
@@ -338,7 +339,7 @@
trans_earliest_t0s = [min_tstart]*len(criteria_list)
glob_earliest_t0_ixs = [None]*len(criteria_list)
glob_earliest_t0s = [min_tstart]*len(criteria_list)
- crit_ixs = range(len(criteria_list))
+ crit_ixs = list(range(len(criteria_list)))
re_run = crit_ixs[:] # initial copy
re_run_glob = []
re_run_trans = []
@@ -623,7 +624,7 @@
return str1 + str2 + str3
def info(self, verboselevel=1):
- print self._infostr(verboselevel)
+ print(self._infostr(verboselevel))
def __str__(self):
return self._infostr(0)
@@ -754,14 +755,14 @@
def check_opts(opts):
def_vals = {'use_order': True, 'speed_fussy': True}
- ok_keys = def_vals.keys()
+ ok_keys = list(def_vals.keys())
if opts is None:
return common.args(**def_vals)
else:
for k in ok_keys:
- if k not in opts.keys():
+ if k not in list(opts.keys()):
opts[k] = def_vals[k]
- rem_keys = common.remain(opts.keys(), ok_keys)
+ rem_keys = common.remain(list(opts.keys()), ok_keys)
if rem_keys != []:
raise ValueError("Invalid options passed in opts argument: %s" % rem_keys)
else:
@@ -818,7 +819,7 @@
all_modulatory = {}
ep_start = 0
complete_epoch = False
- for i in xrange(self.num_pts):
+ for i in range(self.num_pts):
# ignore_change is used to avoid single time-point epochs:
# it ensures 'old' actives and time scale sets don't get updated for
# the single time-point change
@@ -859,7 +860,7 @@
# ignore epoch made up of single time point
ignore_change = True
act_vars = old_actives
- mod_vars = all_modulatory.keys()
+ mod_vars = list(all_modulatory.keys())
i_stop = i
if ignore_change:
old_fast = fast
@@ -868,12 +869,12 @@
old_fast = common.makeSeqUnique(utils.union(old_fast,fast))
old_slow = common.makeSeqUnique(utils.union(old_slow,slow))
if old_actives == actives and i < self.num_pts-1:
- all_modulatory.update(dict(zip(modulatory,enumerate(modulatory))))
+ all_modulatory.update(dict(list(zip(modulatory,enumerate(modulatory)))))
else:
# epoch changed or we reached the last point
if old_actives == [] and self.num_pts > 1:
# first epoch: don't make an epoch object until it ends
- all_modulatory.update(dict(zip(modulatory,enumerate(modulatory))))
+ all_modulatory.update(dict(list(zip(modulatory,enumerate(modulatory)))))
elif ignore_singleton and i - ep_start == 1 and i < self.num_pts-1:
# ignore epoch made up of single time point
if common.intersect(modulatory, old_actives) != []:
@@ -882,7 +883,7 @@
# continue
#raise ValueError("Reduce step size! Single time-point epochs are not allowed")
old_actives = common.remain(old_actives, common.intersect(modulatory, old_actives))
- all_modulatory.update(dict(zip(modulatory,enumerate(modulatory))))
+ all_modulatory.update(dict(list(zip(modulatory,enumerate(modulatory)))))
ignore_change = True
else:
if self.num_pts == 1:
@@ -891,7 +892,7 @@
i_stop = 1
else:
act_vars = old_actives
- mod_vars = all_modulatory.keys()
+ mod_vars = list(all_modulatory.keys())
i_stop = i
complete_epoch = True
if ignore_change:
@@ -951,8 +952,8 @@
focus_taus = taus[self.focus_var]
rel_taus = taus/focus_taus
cs = taus.coordnames
- ixs = xrange(len(cs))
- n = xrange(len(taus))
+ ixs = range(len(cs))
+ n = range(len(taus))
# these tests can never select focus_var which has
# been normalized to tau = 1
slow_test = rel_taus/gamma > 1
@@ -1110,12 +1111,12 @@
if isinstance(model, HybridModel):
# check that there is a single sub-model (not a true hybrid system)
assert len(model.registry) == 1
- self.model = model.registry.values()[0]
- self.gen = self.model.registry.values()[0]
+ self.model = list(model.registry.values())[0]
+ self.gen = list(self.model.registry.values())[0]
elif isinstance(model, NonHybridModel):
assert len(model.registry) == 1
self.model = model
- self.gen = self.model.registry.values()[0]
+ self.gen = list(self.model.registry.values())[0]
else:
# assume generator
self.model = None
@@ -1132,7 +1133,7 @@
# has no activation variable, will not be present in
# the FScompatMap, so use this opportunity to update
# the mapping
- for k, gam_inps in inputs.items():
+ for k, gam_inps in list(inputs.items()):
gamma1 = []
try:
for i in gam_inps.gamma1:
@@ -1159,7 +1160,7 @@
self.gamma2[k] = gamma2
# all_vars includes 'mock' variables
# given by auxiliary functions
- self.all_vars = inputs.keys()
+ self.all_vars = list(inputs.keys())
else:
# deduce them from the dependencies in the
# ModelSpec dict
@@ -1170,9 +1171,9 @@
#self.gamma1 = ?
#self.gamma2 = ?
# Can expect only mspec
- self._init_from_MSpec(self.model._mspecdict.values()[0]['modelspec'])
+ self._init_from_MSpec(list(self.model._mspecdict.values())[0]['modelspec'])
all_inputs = []
- for ins in self.gamma1.values() + self.gamma2.values():
+ for ins in list(self.gamma1.values()) + list(self.gamma2.values()):
try:
all_inputs.extend(ins)
except TypeError:
@@ -1223,7 +1224,7 @@
d = {}
fspecs = self.gen.funcspec._auxfnspecs
fn_base = 'dssrt_fn_'
- for var, tau in self.tau_refs.items():
+ for var, tau in list(self.tau_refs.items()):
if tau is None:
continue
# signature for the aux fn is in the Generator's FuncSpec, e.g.
@@ -1258,7 +1259,7 @@
sig[ix] = inp
d[tau.replace('.','_')] = fname+'(' + ",".join(sig) + ')'
- for var, inf in self.inf_refs.items():
+ for var, inf in list(self.inf_refs.items()):
if inf is None:
continue
# signature for the aux fn is in the Generator's FuncSpec, e.g.
@@ -1297,23 +1298,23 @@
FScMap = self._FScompatMap
self.taus = {}
self.taus_direct = {}
- for k, v in self.tau_refs.items():
+ for k, v in list(self.tau_refs.items()):
self.taus[k], self.taus_direct[k] = self._process_expr(FScMap(v))
self.infs = {}
self.infs_direct = {}
- for k, v in self.inf_refs.items():
+ for k, v in list(self.inf_refs.items()):
self.infs[k], self.infs_direct[k] = self._process_expr(FScMap(v))
self.psis = {}
self.psis_direct = {}
- for k, vdict in self.psi_refs.items():
+ for k, vdict in list(self.psi_refs.items()):
if vdict is None:
self.psis[k], self.psis_direct[k] = (None, None)
else:
self.psis[k] = {}
self.psis_direct[k] = {}
- for inp, psiv in vdict.items():
+ for inp, psiv in list(vdict.items()):
self.psis[k][inp], self.psis_direct[k][inp] = \
self._process_expr(FScMap(psiv))
@@ -1363,11 +1364,11 @@
else:
# test for valid math expression
# - may include auxiliary function call (with arguments)
- fnames = self.gen.auxfns.keys()
- themap = dict(self.gen.auxfns.items())
- themap.update(dict(self.gen.inputs.items()))
+ fnames = list(self.gen.auxfns.keys())
+ themap = dict(list(self.gen.auxfns.items()))
+ themap.update(dict(list(self.gen.inputs.items())))
defs = {'refpars': self.pars}
- pnames = self.pars.keys()
+ pnames = list(self.pars.keys())
pvals = ['refpars["%s"]' % pn for pn in pnames]
# parmap = dict(zip(pnames,
# [Symbolic.expr2fun(v, **defs) for v in pvals]))
@@ -1375,9 +1376,9 @@
val = expr # retained in case revert to replaceCallsWithDummies(...)
#dummies = {}
val_q = Symbolic.QuantSpec('__expr__', val)
- mapping = dict(zip(pnames, pvals))
+ mapping = dict(list(zip(pnames, pvals)))
used_inputs = utils.intersect(val_q.parser.tokenized,
- self.gen.inputs.keys())
+ list(self.gen.inputs.keys()))
for inp in used_inputs:
# turn into a function of t
mapping[inp] = inp + '(t)'
@@ -1454,8 +1455,8 @@
try:
return f(**common.filteredDict(ptFS, args))
except:
- print f._args
- print f._call_spec
+ print(f._args)
+ print(f._call_spec)
raise
@@ -1474,8 +1475,8 @@
try:
return f(**common.filteredDict(ptFS, args))
except:
- print f._args
- print f._call_spec
+ print(f._args)
+ print(f._call_spec)
raise
@@ -1500,8 +1501,8 @@
try:
return f(**common.filteredDict(ptFS, args))
except:
- print f._args
- print f._call_spec
+ print(f._args)
+ print(f._call_spec)
raise
@@ -1515,7 +1516,7 @@
if focus:
vars = [self.focus_var]
else:
- vars = self.taus.keys()
+ vars = list(self.taus.keys())
pts = self._FScompatMap(self.pts)
# ptvals = dict(self.pts)
# # permit access from external inputs or other autonomous functions
@@ -1531,8 +1532,8 @@
vals['tau_'+k] = np.array([f(**common.filteredDict(pt, args)) \
for pt in pts])
except:
- print f._args
- print f._call_spec
+ print(f._args)
+ print(f._call_spec)
raise
inf_info = self.infs[k]
if inf_info is None:
@@ -1543,8 +1544,8 @@
vals['inf_'+k] = np.array([f(**common.filteredDict(pt, args)) \
for pt in pts])
except:
- print f._args
- print f._call_spec
+ print(f._args)
+ print(f._call_spec)
raise
# we know that taus and infs have same set of keys -- the variable names
self.tau_inf_vals.update(vals)
@@ -1597,8 +1598,8 @@
psis[inp] = np.array([f(*val_array.flatten()) \
for val_array in all_coords[:,[arg_ixs]]])
except:
- print f._args
- print f._call_spec
+ print(f._args)
+ print(f._call_spec)
raise
self.psi_vals[fv] = psis
@@ -1611,7 +1612,7 @@
all_vals = {}
all_vals.update(self.tau_inf_vals)
base='psi_'+fv
- for inp, psis in self.psi_vals[fv].items():
+ for inp, psis in list(self.psi_vals[fv].items()):
all_vals[base+'_'+inp] = psis
self.psi_pts = Pointset(indepvararray=self.times, coorddict=all_vals)
@@ -1644,7 +1645,7 @@
ics=common.filteredDict(gen.initialconditions,vars),
varspecs=varspecs, auxvars=gen.funcspec._initargs['auxvars'],
fnspecs=gen.funcspec._initargs['fnspecs'])
- nan_auxs = [xname for xname, val in gen.initialconditions.iteritems() if not np.isfinite(val)]
+ nan_auxs = [xname for xname, val in gen.initialconditions.items() if not np.isfinite(val)]
sysargs.pars.update(common.filteredDict(gen.initialconditions, vars+nan_auxs, neg=True))
return Vode_ODEsystem(sysargs)
@@ -1654,7 +1655,7 @@
def get_taus(pts, tau_names):
"""pts can be a Point or Pointset"""
# filter this way in case there are None entries in tau_names.values()
- clist = [cname for cname in pts.coordnames if cname in tau_names.values()]
+ clist = [cname for cname in pts.coordnames if cname in list(tau_names.values())]
t = pts[clist]
t.mapNames(parseUtils.symbolMapClass(common.invertMap(tau_names)))
return t
@@ -1662,7 +1663,7 @@
def get_infs(pts, inf_names):
"""pts can be a Point or Pointset"""
# filter this way in case there are None entries in inf_names.values()
- clist = [cname for cname in pts.coordnames if cname in inf_names.values()]
+ clist = [cname for cname in pts.coordnames if cname in list(inf_names.values())]
i = pts[clist]
i.mapNames(parseUtils.symbolMapClass(common.invertMap(inf_names)))
return i
@@ -1684,7 +1685,7 @@
try:
vals = pts[ix0:ix1].coordarray.copy()
except ValueError:
- print ix0, ix1
+ print(ix0, ix1)
raise
ts = pts.indepvararray[ix0:ix1].copy()
if reset_t0 is not None:
@@ -1700,10 +1701,10 @@
# don't start i at 0 b/c will be in middle of an epoch
for i, ep0 in enumerate(epochs[1:-1]):
if verbose:
- print "start epoch = ", i+1
+ print("start epoch = ", i+1)
for j, ep in enumerate(epochs[i+1:]):
if verbose:
- print "end epoch =", i+j+1
+ print("end epoch =", i+j+1)
try:
res = [epochs[k]==epochs[k+j+1] for k in range(i,j)]
except IndexError:
@@ -1711,10 +1712,10 @@
continue
else:
if verbose:
- print i, j, res
+ print(i, j, res)
if np.all(res) and j > i+1:
if verbose:
- print "Found period between epochs", i+1, j+2+i, " len=", j+1
+ print("Found period between epochs", i+1, j+2+i, " len=", j+1)
cycle_len = j+1
ixs = [i+1, i+j+2]
return cycle_len, ixs
@@ -1811,7 +1812,7 @@
# split_ixs is a list
if not range_tuple[0] < range_tuple[1]:
raise ValueError("Range tuple not in increasing order")
- if not np.alltrue(ix in xrange(range_tuple[0],range_tuple[1]) \
+ if not np.alltrue(ix in range(range_tuple[0],range_tuple[1]) \
for ix in split_ixs):
raise ValueError("Split indices out of range")
if range_tuple[0] in split_ixs or range_tuple[1] in split_ixs:
@@ -1880,7 +1881,7 @@
def show_epochs(eps):
"Small utility to print more detailed information about epochs"
for i, ep in enumerate(eps):
- print i,
+ print(i, end=' ')
ep.info()
@@ -1912,16 +1913,16 @@
cols.append(c+s)
if len(do_vars) > len(cols):
raise ValueError("Max number of permitted variables for these colors/styles is %i"%len(cols))
- print "Color scheme:"
+ print("Color scheme:")
if do_log:
for i, v in enumerate(do_vars):
if root+v in pts.coordnames:
- print " ", v, cols[i]
+ print(" ", v, cols[i])
plot(ts, np.log(pts[root+v]), cols[i])
else:
for i, v in enumerate(do_vars):
if root+v in pts.coordnames:
- print " ", v, cols[i]
+ print(" ", v, cols[i])
RefactoringTool: Refactored ./PyDSTool/Toolbox/data_analysis.py
plot(ts, pts[root+v], cols[i])
# ---------------------------------------------------------------------------
@@ -2016,7 +2017,7 @@
s2[(a,a)] = MATCH #VCLOSE
s2[(a,'_')] = CLOSE
- for k, v in s1.score_dict.iteritems():
+ for k, v in s1.score_dict.items():
if v is None:
d_common = len(common.intersect(alphabet.dynamic_vars, strip_speed(k)))
# s.score_dict[k] = MISMATCH
@@ -2376,7 +2377,7 @@
d = [] # Table with the full distance matrix
- current = range(n+1)
+ current = list(range(n+1))
d.append(current)
for i in range(1,m+1):
@@ -2496,9 +2497,9 @@
workstr1 = workstr1[:index]+JARO_MARKER_CHAR+workstr1[index+1:]
if (common1 != common2):
- print 'Jaro: Wrong common values for strings "%s" and "%s"' % \
+ print('Jaro: Wrong common values for strings "%s" and "%s"' % \
(str1, str2) + ', common1: %i, common2: %i' % (common1, common2) + \
- ', common should be the same.'
+ ', common should be the same.')
common1 = float(common1+common2) / 2.0 ##### This is just a fix #####
if (common1 == 0):
@@ -2529,7 +2530,7 @@
eps1 = epseq1[i]
eps2 = epseq2[i]
str_table.append([",".join(eps1), ",".join(eps2)])
- print indent(str_table)
+ print(indent(str_table))
def indent(rows, hasHeader=False, headerChar='-', delim=' | ', justify='left',
separateRows=False, prefix='', postfix='', wrapfunc=lambda x:x):
@@ -2550,26 +2551,25 @@
# closure for breaking logical rows to physical, using wrapfunc
def rowWrapper(row):
newRows = [wrapfunc(item).split('\n') for item in row]
- return [[substr or '' for substr in item] for item in map(None,*newRows)]
+ return [[substr or '' for substr in item] for item in list(*newRows)]
# break each logical row into one or more physical ones
logicalRows = [rowWrapper(row) for row in rows]
# columns of physical rows
- columns = map(None,*reduce(operator.add,logicalRows))
+ columns = list(*reduce(operator.add,logicalRows))
# get the maximum of each column by the string length of its items
maxWidths = [max([len(str(item)) for item in column]) for column in columns]
rowSeparator = headerChar * (len(prefix) + len(postfix) + sum(maxWidths) + \
len(delim)*(len(maxWidths)-1))
# select the appropriate justify method
justify = {'center':str.center, 'right':str.rjust, 'left':str.ljust}[justify.lower()]
- output=cStringIO.StringIO()
- if separateRows: print >> output, rowSeparator
+ output=io.StringIO()
+ if separateRows: print(rowSeparator, file=output)
for physicalRows in logicalRows:
for row in physicalRows:
- print >> output, \
- prefix \
+ print(prefix \
+ delim.join([justify(str(item),width) for (item,width) in zip(row,maxWidths)]) \
- + postfix
- if separateRows or hasHeader: print >> output, rowSeparator; hasHeader=False
+ + postfix, file=output)
+ if separateRows or hasHeader: print(rowSeparator, file=output); hasHeader=False
return output.getvalue()
--- ./PyDSTool/Toolbox/data_analysis.py (original)
+++ ./PyDSTool/Toolbox/data_analysis.py (refactored)
@@ -4,7 +4,7 @@
Robert Clewley, August 2006
"""
-from __future__ import division
+
from PyDSTool.Points import Point, Pointset
from PyDSTool.Interval import Interval
from PyDSTool.utils import intersect, filteredDict
@@ -86,8 +86,7 @@
#x must be bigger than edge
if x.size < edge:
- raise ValueError, \
- "Input vector needs to be bigger than 3 * max(len(a),len(b)."
+ raise ValueError("Input vector needs to be bigger than 3 * max(len(a),len(b).")
if len(a) < ntaps:
a=r_[a,zeros(len(b)-len(a))]
@@ -132,8 +131,8 @@
if type(refpt) != int:
refpt = refpt[0]
pca[refpt] = doPCA(nhd(data, covering, refpt), tol)
- print "PCA eigenvalues for nhd #%i:"%refpt
- print pca[refpt].d
+ print("PCA eigenvalues for nhd #%i:"%refpt)
+ print(pca[refpt].d)
return len(pca[refpt].d)
@@ -156,7 +155,7 @@
spec[i] = norm(p.d[:i])
res = transpose(sqrt(spec[-1]**2-spec**2)/spec[-1])[0]
if not silent:
- print "L2-norm of PCA spectrum =", spec[-1]
+ print("L2-norm of PCA spectrum =", spec[-1])
if newfig:
figure()
style='k'+marker
@@ -197,7 +196,7 @@
assert sampleix >= 0
d = zeros((npts-1,), 'd')
if rank(m) == 3:
- for i in xrange(npts):
+ for i in range(npts):
if sampleix != i:
try:
d[i] = norm(m[sampleix,:,:]-m[i,:,:])
@@ -206,7 +205,7 @@
# so use the empty i=pix position (ordering doesn't matter)
d[sampleix] = norm(m[sampleix,:,:]-m[i,:,:])
elif rank(m) == 2:
- for i in xrange(npts):
+ for i in range(npts):
if sampleix != i:
try:
d[i] = norm(m[sampleix,:]-m[i,:])
@@ -225,11 +224,11 @@
# just sort
d.sort()
if not quiet:
- print "Chose reference point %i"%sampleix
- print "Min distance = %f, max distance = %f"%(d[0], d[-1])
+ print("Chose reference point %i"%sampleix)
+ print("Min distance = %f, max distance = %f"%(d[0], d[-1]))
logd = log(d).ravel()
if logv is None:
- logv = log(range(1,len(d)+1))
+ logv = log(list(range(1,len(d)+1)))
nan_ixs = isfinite(logd) # mask, not a list of indices
logd = extract(nan_ixs, logd)
logv = extract(nan_ixs, logv)
@@ -268,7 +267,7 @@
# but offset second stage indices in dk so there's a total of n-1
# this is basically a slightly unrolled loop to make it a little faster
if rank(m) == 3:
- for i in xrange(sampleix):
+ for i in range(sampleix):
dk[i] = norm(m[sampleix,:,:]-m[i,:,:])
if dk[i] in d_inv:
# ensure we find a unique distance for dictionary key
@@ -294,7 +293,7 @@
d_inv[u[0]] = i
else:
d_inv[dk[i]] = i
- for i in xrange(sampleix+1, npts):
+ for i in range(sampleix+1, npts):
ki = i-1
dk[ki] = norm(m[sampleix,:,:]-m[i,:,:])
if dk[ki] in d_inv:
@@ -322,7 +321,7 @@
else:
d_inv[dk[ki]] = i
elif rank(m) == 2:
- for i in xrange(sampleix):
+ for i in range(sampleix):
dk[i] = norm(m[sampleix,:]-m[i,:])
if dk[i] in d_inv:
# ensure we find a unique distance for dictionary key
@@ -348,7 +347,7 @@
d_inv[u[0]] = i
else:
d_inv[dk[i]] = i
- for i in xrange(sampleix+1, npts):
+ for i in range(sampleix+1, npts):
ki = i-1
dk[ki] = norm(m[sampleix,:]-m[i,:])
if dk[ki] in d_inv:
@@ -389,7 +388,7 @@
d.sort()
logd = log(d).ravel()
if logv is None:
- logv = log(range(1,len(d)+1))
+ logv = log(list(range(1,len(d)+1)))
nan_ixs = isfinite(logd) # mask, not a list of indices
logd = extract(nan_ixs, logd)
logv = extract(nan_ixs, logv)
@@ -463,7 +462,7 @@
else:
raise ValueError("Invalid low and high fit limits")
if not quiet:
- print "lo ix %d, hi ix %d, max ix %d"%(loix, hiix, lendat-1)
+ print("lo ix %d, hi ix %d, max ix %d"%(loix, hiix, lendat-1))
pfit = polyfit(x[loix:hiix],y[loix:hiix],1)
# print pfit
if doplot:
@@ -499,7 +498,7 @@
self.num_bins = len(bin_ords)-1
assert self.num_bins > 0, "Must be more than 2 ordinates to define bins"
self.bin_ords = array(bin_ords)
- self.bins = dict(zip(range(self.num_bins),[0]*self.num_bins))
+ self.bins = dict(list(zip(list(range(self.num_bins)),[0]*self.num_bins)))
self.coordinate = coordinate
self.tolerance = tolerance
self.intervals = [Interval('bin_%s'%i, float,
@@ -507,7 +506,7 @@
abseps=tolerance) for i in range(self.num_bins)]
self.midpoints = (self.bin_ords[1:]+self.bin_ords[:-1])/2.
if valuedict is not None:
- for k, v in valuedict.iteritems():
+ for k, v in valuedict.items():
self[self.resolve_bin_index(k)] = v
def resolve_bin_index(self, ordinate):
@@ -576,7 +575,7 @@
def clear(self):
"""Reset all bins to have zero contents."""
- self.bins = dict(zip(range(self.num_bins),[0]*self.num_bins))
+ self.bins = dict(list(zip(list(range(self.num_bins)),[0]*self.num_bins)))
def __str__(self):
return "Binned data with intervals %s:\n By bin number: %s"%(str([i.get() \
@@ -586,8 +585,8 @@
def to_pointset(self):
"""Convert to a pointset"""
- bin_ixs = xrange(self.num_bins)
- return Pointset(indepvararray=range(self.num_bins),
+ bin_ixs = range(self.num_bins)
+ return Pointset(indepvararray=list(range(self.num_bins)),
coorddict={self.coordinate: [self.bins[ix] \
for ix in bin_ixs],
'bin_limit_lo': [self.intervals[ix][0] \
@@ -635,11 +634,11 @@
nearby = []
refpt = data[refix]
if include_ref:
- for i in xrange(size(data,0)):
+ for i in range(size(data,0)):
if norm(refpt-data[i], which_norm) <= r:
nearby.append(i)
else:
- for i in xrange(size(data,0)):
+ for i in range(size(data,0)):
if i != refix:
if norm(refpt-data[i], which_norm) <= r:
nearby.append(i)
@@ -651,7 +650,7 @@
"""
assert rlo > 0 and rhi > rlo
nearby = []
- for i in xrange(size(data,0)):
+ for i in range(size(data,0)):
if i != refix:
d = norm(data[refix]-data[i], which_norm)
if d > rlo and d < rhi:
@@ -834,11 +833,11 @@
except ZeroDivisionError:
frac = Inf
if verbose:
- print i, data[i], frac
+ print(i, data[i], frac)
if frac > tol and frac < Inf:
knee_ixs.append((i,frac))
if verbose:
- print "High second derivatives at: ", knee_ixs, "\n"
+ print("High second derivatives at: ", knee_ixs, "\n")
knees = []
found = False # in a contiguous segment of high second derivatives
curr_kixs = []
@@ -847,7 +846,7 @@
process = False
kix, frac = knee_ixs[i]
if verbose:
- print "Processing knee at index", kix
+ print("Processing knee at index", kix)
if kix-1 == old_kix:
if i == len(knee_ixs)-1:
# this is the last index so have to process
@@ -860,13 +859,13 @@
else:
process = old_kix is not None
if verbose:
- print old_kix, found, curr_kixs
+ print(old_kix, found, curr_kixs)
if process:
if found:
found = False
if verbose:
- print "Current knee indices:", curr_kixs,
- print [knee_ixs[k] for k in curr_kixs]
+ print("Current knee indices:", curr_kixs, end=' ')
+ print([knee_ixs[k] for k in curr_kixs])
all_d2 = array([knee_ixs[k][1] for k in curr_kixs])
ixs_sort = argsort(all_d2)
max_ix = ixs_sort[-1]
@@ -874,13 +873,13 @@
curr_kixs = []
else:
if verbose:
- print "Appending knee index", old_kix
+ print("Appending knee index", old_kix)
knees.append(old_kix)
old_kix = kix
# add final singleton index of high derivative, if any
if not found and old_kix not in knees:
if verbose:
- print "Appending knee indeRefactoringTool: Refactored ./PyDSTool/Toolbox/adjointPRC.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/__init__.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/PySCes_SBML.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/ParamEst.py
x", old_kix
+ print("Appending knee index", old_kix)
knees.append(old_kix)
return knees
--- ./PyDSTool/Toolbox/adjointPRC.py (original)
+++ ./PyDSTool/Toolbox/adjointPRC.py (refactored)
@@ -31,7 +31,7 @@
try:
MDCont = ContClass(model)
except:
- print "Problem with model argument"
+ print("Problem with model argument")
raise
# If given an LC, use it for continuation
@@ -52,10 +52,10 @@
PCargs.verbosity = 2
MDCont.newCurve(PCargs)
- print 'Computing curve...'
+ print('Computing curve...')
start = clock()
MDCont['EQ1'].forward()
- print 'done in %.3f seconds!' % (clock()-start)
+ print('done in %.3f seconds!' % (clock()-start))
#PCargs.name = 'LC1'
#PCargs.type = 'LC-C'
@@ -137,13 +137,13 @@
MDCont['LC1'].forward()
pt = MDCont['LC1'].getSpecialPoint('RG1')
if verbosity > 1:
- print "\nRegular point chosen:", pt, "\n"
+ print("\nRegular point chosen:", pt, "\n")
J = getFlowJac(pt, verbose=verbosity>1)
# n = dimension of system
n = J.shape[0]
if verbosity > 1:
- print "Computing flow maps..."
+ print("Computing flow maps...")
maps, ntst = getFlowMaps(n, pt, 'RG', method=method)
cycle_true = pt.labels['RG']['cycle']
@@ -158,8 +158,8 @@
cycle_true[idxs]])
if verbosity > 1:
- print "Computing left eigenvetors corresponding to the unit ", \
- "eigenvalue along flow"
+ print("Computing left eigenvetors corresponding to the unit ", \
+ "eigenvalue along flow")
evec1 = getLeftEvecs(n, ntst, maps, flow_vecs, method=method,
verbose=verbosity>1)
t = cycle_true['t'][idxs]
@@ -180,9 +180,9 @@
PRC = rotate_phase(PRC, phase0_ix)
phase0_t = PRC['t'][phase0_ix]*t[-1]
if verbosity > 1:
- print "spike_est_ix =", spike_est_ix
- print "phase0_ix =", phase0_ix
- print "phase0_t =", phase0_t
+ print("spike_est_ix =", spike_est_ix)
+ print("phase0_ix =", phase0_ix)
+ print("phase0_t =", phase0_t)
# PRC pointset used a uniform sampling of
# cycle's time mesh points, so get ix in cycle by
# multiplying up phase0_ix by the sampling rate
@@ -220,7 +220,7 @@
saveObjects(objlist=save_objs, filename=savefile, force=force)
except ValueError:
- print "File already exists -- not saving return objects"
+ print("File already exists -- not saving return objects")
return_objs = save_objs
return_objs['PyCont'] = MDCont
--- ./PyDSTool/Toolbox/PySCes_SBML.py (original)
+++ ./PyDSTool/Toolbox/PySCes_SBML.py (refactored)
@@ -5,7 +5,7 @@
R. Clewley, 2012
"""
-from __future__ import division
+
from PyDSTool import Generator
from PyDSTool.common import args, remain
@@ -82,11 +82,11 @@
max_t = np.Inf
parlist = m.__fixed_species__ + m.__parameters__
- pardict = dict([(pname, p['initial']) for pname, p in m.__pDict__.items()])
+ pardict = dict([(pname, p['initial']) for pname, p in list(m.__pDict__.items())])
varlist = m.__species__ # list ['s0', 's1', 's2']
- icdict = dict([(vname, v['initial']) for vname, v in m.__sDict__.items() if not v['fixed']])
- fixed_species = dict([(pname, p['initial']) for pname, p in m.__sDict__.items() if p['fixed']])
+ icdict = dict([(vname, v['initial']) for vname, v in list(m.__sDict__.items()) if not v['fixed']])
+ fixed_species = dict([(pname, p['initial']) for pname, p in list(m.__sDict__.items()) if p['fixed']])
pardict.update(fixed_species)
fnspecs = {}
@@ -104,7 +104,7 @@
varspecs = make_varspecs(m, fnspecs)
- for fname, fspec in m.__userfuncs__.items():
+ for fname, fspec in list(m.__userfuncs__.items()):
# Don't know how these are implemented yet
fnspec[fname] = fspec
--- ./PyDSTool/Toolbox/ParamEst.py (original)
+++ ./PyDSTool/Toolbox/ParamEst.py (refactored)
@@ -3,7 +3,7 @@
Robert Clewley.
"""
-from __future__ import division
+
# PyDSTool imports
from PyDSTool.Points import Point, Pointset
@@ -104,19 +104,19 @@
orig_dirn corresponds to direction of positive dirn, in case when
re-calculating gradient the sign flips"""
record = {}
- print "Recalculating gradient"
+ print("Recalculating gradient")
grad = fun.gradient(p)
neut = np.array([grad[1], -grad[0]])
neut = neut/norm(neut)
if np.sign(dot(neut, orig_dirn)) != 1:
- print "(neut was flipped for consistency with direction)"
+ print("(neut was flipped for consistency with direction)")
neut = -neut
- print "Neutral direction:", neut
+ print("Neutral direction:", neut)
record['grad'] = grad
record['neut'] = neut
residuals = []
# inner loop - assumes curvature will be low (no adaptive step size)
- print "\n****** INNER LOOP"
+ print("\n****** INNER LOOP")
new_pars = copy(p)
i = 0
while True:
@@ -133,11 +133,11 @@
r = (copy(new_pars), res)
residuals.append(r)
all_records[i0+dirn*i] = r
- num_dirn_steps = len([k for k in all_records.keys() if \
+ num_dirn_steps = len([k for k in list(all_records.keys()) if \
k*dirn >= abs(i0)])
i += 1
- print len(all_records), "total steps taken, ", num_dirn_steps, \
- "in since grad re-calc: pars =", new_pars, " res=", res
+ print(len(all_records), "total steps taken, ", num_dirn_steps, \
+ "in since grad re-calc: pars =", new_pars, " res=", res)
else:
# re-calc gradient
break
@@ -159,7 +159,7 @@
space, given by dirn = +1/-1 from point p0.
maxsteps is *per* direction"""
- print "\nStarting direction:", dirn
+ print("\nStarting direction:", dirn)
dirn_rec = []
p = p0
if dirn == 1:
@@ -170,7 +170,7 @@
i = -1
done = False
while not done:
- print "Steps from i =", i
+ print("Steps from i =", i)
r = do_step(fun, p, dirn, maxsteps, stepsize, atol, i, orig_res,
orig_dirn, all_records)
if r['n'] == 0:
@@ -227,16 +227,16 @@
raise
except:
exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
- print "******************************************"
- print "Problem evaluating residual function"
- print " ", exceptionType, exceptionValue
+ print("******************************************")
+ print("Problem evaluating residual function")
+ print(" ", exceptionType, exceptionValue)
for line in traceback.format_exc().splitlines()[-4:-1]:
- print " " + line
- print " originally on line:", traceback.tb_lineno(exceptionTraceback)
+ print(" " + line)
+ print(" originally on line:", traceback.tb_lineno(exceptionTraceback))
if self.pest.verbose_level > 1:
raise
else:
- print "(Proceeding with penalty values)\n"
+ print("(Proceeding with penalty values)\n")
return 10*ones(pest.context.res_len)
class residual_fn_context_1D(helpers.ForwardFiniteDifferencesCache):
@@ -251,16 +251,16 @@
raise
except:
exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
- print "******************************************"
- print "Problem evaluating residual function"
- print " ", exceptionType, exceptionValue
+ print("******************************************")
+ print("Problem evaluating residual function")
+ print(" ", exceptionType, exceptionValue)
for line in traceback.format_exc().splitlines()[-4:-1]:
- print " " + line
- print " originally on line:", traceback.tb_lineno(exceptionTraceback)
+ print(" " + line)
+ print(" originally on line:", traceback.tb_lineno(exceptionTraceback))
if self.pest.verbose_level > 1:
raise
else:
- print "(Proceeding with penalty value)\n"
+ print("(Proceeding with penalty value)\n")
return 100
@@ -272,9 +272,9 @@
def grad_from_psens(psens, pest):
pd2a = pest.pars_dict_to_array
pd = {}
- for pname, fsens_dict in psens.items():
+ for pname, fsens_dict in list(psens.items()):
res_list = []
- for feat, sens_array in fsens_dict.items():
+ for feat, sens_array in list(fsens_dict.items()):
res_list.extend(list(sens_array))
pd[pname] = sum()
return pd2a(pd)
@@ -303,8 +303,8 @@
incr = []
decr = []
neut = []
- for mi, fdict in feat_sens[parname].iteritems():
- for f, sens in fdict.iteritems():
+ for mi, fdict in feat_sens[parname].items():
+ for f, sens in fdict.items():
sum_sens = sum(sens)
sign_ss = np.sign(sum_sens)
abs_ss = abs(sum_sens)
@@ -336,7 +336,7 @@
incr = []
decr = []
neut = []
- for pname, fdict in feat_sens.iteritems():
+ for pname, fdict in feat_sens.items():
sens = fdict[mi][feat]
sum_sens = sum(sens)
sign_ss = np.sign(sum_sens)
@@ -408,15 +408,15 @@
seen[x] = (s, f)
else:
seen[x] = (s, f)
- Lu = [(x,pair[0], pair[1]) for x, pair in seen.items()]
+ Lu = [(x,pair[0], pair[1]) for x, pair in list(seen.items())]
return sorted(Lu, reverse=True, key=operator.itemgetter(1))
def pp(l):
"""List pretty printer"""
- print "[",
+ print("[", end=' ')
for x in l:
- print x, ","
- print "]"
+ print(x, ",")
+ print("]")
# ---------------------------------
@@ -433,16 +433,16 @@
try:
solver = solver_lookup[method]
except KeyError:
- print "Specified solver not found. Will try recursive backtracking solver"
+ print("Specified solver not found. Will try recursive backtracking solver")
solver = RecursiveBacktrackingSolver
try:
problem = Problem(solver(forwardCheck))
except TypeError:
- print "Install constraint package from http://labix.org/python-constraint"
+ print("Install constraint package from http://labix.org/python-constraint")
raise ImportError("Must have constraint package installed to use this feature")
global D, feat_name_lookup, pars, par_deltas
par_deltas = deltas
- pars = feat_sens.keys()
+ pars = list(feat_sens.keys())
pars.sort()
num_pars = len(pars)
assert len(par_deltas) == num_pars
@@ -451,8 +451,8 @@
max_val = 0
for par in pars:
- for mi, fdict in feat_sens[par].iteritems():
- for f, ra in fdict.iteritems():
+ for mi, fdict in feat_sens[par].items():
+ for f, ra in fdict.items():
val = sum(ra)
if norm(val) > max_val:
max_val = val
@@ -465,11 +465,11 @@
problem.addVariables(pars, values)
feat_name_lookup = {}
- for f in D.keys():
+ for f in list(D.keys()):
feat_name_lookup[f.name] = f
constraint_funcs = []
- for f in D.keys():
+ for f in list(D.keys()):
if f in desired_feats:
op = 'operator.le'
this_tol = neg_tol
@@ -484,13 +484,13 @@
if verbose:
code += " print sum(prods)\n"
code += " return %s(sum(prods), %f)\n"%(op,this_tol)
- exec code
+ exec(code)
constraint_funcs.append(locals()['D'+f.name])
for func in constraint_funcs:
problem.addConstraint(FunctionConstraint(func), pars)
- print "Use problem.getSolution() to find a solution"
+ print("Use problem.getSolution() to find a solution")
return problem, D
@@ -500,16 +500,16 @@
For unweighted feature sensitivities, or else it
unweights weighted ones."""
D_n = {}
- for feat, pD in D_sum.items():
- pD_min_abs = min(abs(array(pD.values())))
+ for feat, pD in list(D_sum.items()):
+ pD_min_abs = min(abs(array(list(pD.values()))))
D_n[feat] = {}
- for pname, pD_val in pD.items():
+ for pname, pD_val in list(pD.items()):
D_n[feat][pname] = pD_val/pD_min_abs
return D_n
def filter_iface(psens, iface):
ws = {}
- for parname, wdict in psens.items():
+ for parname, wdict in list(psens.items()):
ws[parname] = {iface: wdict[iface]}
return ws
@@ -518,7 +518,7 @@
# between related MIs
if discrete_feats is None:
discrete_feats = []
- pars = feat_sens.keys()
+ pars = list(feat_sens.keys())
pars.sort()
D_sum = {}
@@ -526,8 +526,8 @@
max_val = 0
for par in pars:
- for mi, fdict in feat_sens[par].iteritems():
- for f, ra in fdict.iteritems():
+ for mi, fdict in feat_sens[par].items():
+ for f, ra in fdict.items():
val = sum(ra)
if norm(val) > max_val:
max_val = val
@@ -592,7 +592,7 @@
parseps = {}.fromkeys(parnames, 1e-7)
if parscales is None:
parscales = parseps.copy()
- for k, v in parscales.iteritems():
+ for k, v in parscales.items():
parscales[k] = 10*v
pest = ParamEst(freeParams=freepars,
testModel=model,
@@ -727,7 +727,7 @@
self.parScales = dict.fromkeys(self.freeParNames, 1)
else:
self.parScales = kw['freeParams']
- self.freeParNames = self.parScales.keys()
+ self.freeParNames = list(self.parScales.keys())
self.numFreePars = len(self.freeParNames)
self.freeParNames.sort()
self.testModel = kw['testModel']
@@ -781,7 +781,7 @@
def resetParArgs(self):
self.parTypeStr = []
- for i in xrange(self.numFreePars):
+ for i in range(self.numFreePars):
if self.freeParNames[i] in self.testModel.obsvars:
# for varying initial conditions
self.parTypeStr.append('ics')
@@ -889,16 +889,16 @@
entry = self.log[i]
except IndexError:
raise ValueError("No such call %i recorded"%i)
- print "\n **** Call %i"%i, "Residual norm: %f"%entry.residual_norm
+ print("\n **** Call %i"%i, "Residual norm: %f"%entry.residual_norm)
if entry.ics != {}:
- print "Ics:", entry.ics
+ print("Ics:", entry.ics)
if entry.pars != {}:
- print "Pars:", entry.pars
+ print("Pars:", entry.pars)
if full:
- print "Res:\n"
+ print("Res:\n")
self.context.show_res_info(entry.residual_vec)
else:
- print "Res:", entry.residual_vec
+ print("Res:", entry.residual_vec)
def pars_to_ixs(self):
all_pars = sortedDictKeys(self.testModel.pars)
@@ -907,7 +907,7 @@
return inv_ixs
def pars_array_to_dict(self, parray):
- return dict(zip(self.freeParNames, parray))
+ return dict(list(zip(self.freeParNames, parray)))
def pars_dict_to_array(self, pdict):
return array(sortedDictValues(filteredDict(pdict, self.freeParNames)))
@@ -982,11 +982,11 @@
"""
ws = self.context.feat_weights
wfeat_sens = {}
- for pn, sensdict in feat_sens.iteritems():
+ for pn, sensdict in feat_sens.items():
pd = wfeat_sens[pn] = {}
- for mi, fdict in sensdict.iteritems():
+ for mi, fdict in sensdict.items():
md = pd[mi] = {}
- for f, sens in fdict.iteritems():
+ for f, sens in fdict.items():
md[f] = sens*ws[(mi,f)]
return wfeat_sens
@@ -1070,7 +1070,7 @@
parsOrig = []
self.numFreePars = len(self.freeParNames)
self.resetParArgs()
- for i in xrange(self.numFreePars):
+ for i in range(self.numFreePars):
val = self.testModel.query(self.parTypeStr[i])\
[self.freeParNames[i]]
self.parsOrig[self.freeParNames[i]] = val
@@ -1111,8 +1111,8 @@
if not verbose:
out = rout.stop()
err = rerr.stop()
- print "Calculating residual failed for pars:", \
- parsOrig
+ print("Calculating residual failed for pars:", \
+ parsOrig)
raise
if not verbose:
out = rout.stop()
@@ -1130,10 +1130,10 @@
alg_results['message'] = results[3]
self.pestResult = {'success': success,
'cov': results[1],
- 'pars_sol': dict(zip(self.freeParNames,
- res_par_list)),
- 'pars_orig': dict(zip(self.freeParNames,
- orig_par_list)),
+ 'pars_sol': dict(list(zip(self.freeParNames,
+ res_par_list))),
+ 'pars_orig': dict(list(zip(self.freeParNames,
+ orig_par_list))),
'alg_results': alg_results,
'sys_sol': self.testModel
}
@@ -1144,20 +1144,20 @@
# because it converged.
if success or results[3].find('at most') != -1:
if success:
- print 'Solution of ', self.freeParNames, ' = ', results[0]
+ print('Solution of ', self.freeParNames, ' = ', results[0])
else:
## parvals = [self.testModel.pars[p] for p in \
## self.freeParNames]
- print 'Closest values of ', self.freeParNames, ' = ', \
- results[0]
+ print('Closest values of ', self.freeParNames, ' = ', \
+ results[0])
## parvals
- print 'Original values = ', parsOrig
- print 'Number of fn evals = ', results[2]["nfev"], \
- '(# iterations)'
+ print('Original values = ', parsOrig)
+ print('Number of fn evals = ', results[2]["nfev"], \
+ '(# iterations)')
if not success:
- print 'Solution not found: '+results[3]
+ print('Solution not found: '+results[3])
else:
- print 'Solution not found: '+results[3]
+ print('Solution not found: '+results[3])
return copy(self.pestResult)
@@ -1294,13 +1294,13 @@
if verbose:
if success:
- print 'Solution of ', self.freeParNames[0], ' = ', results[0]
- print 'Original value = ', parsOrig
- print 'Number of fn evals = ', results[3], "(# iterations)"
- print 'Error tolerance = ', xtol
+ print('Solution of ', self.freeParNames[0], ' = ', results[0])
+ print('Original value = ', parsOrig)
+ print('Number of fn evals = ', results[3], "(# iterations)")
+ print('Error tolerance = ', xtol)
else:
- print 'No convergence of BoundMin'
- print results
+ print('No convergence of BoundMin')
+ print(results)
return copy(self.pestResult)
@@ -1335,7 +1335,7 @@
s = zeros(shape(x), 'float')
else:
raise ValueError("Use default = 0 or 1 only")
- for i in xrange(len(x)-lookahead):
+ for i in range(len(x)-lookahead):
s[i,:] = [max(prec,val) for val in \
ravel((x[i+lookahead,:]-x[i,:]).toarray())]
return s
@@ -1405,7 +1405,7 @@
ival_ml = max([0, ival - lookahead])
ival_pl = min([max_ix, ival + lookahead])
if verbose:
- print "*********** t =", tval, " , ival =", ival
+ print("*********** t =", tval, " , ival =", ival)
v = slopes.coordarray[:,ival]
for ci, c in enumerate(coords):
for m in [0,1]:
@@ -1421,7 +1421,7 @@
if tval>(last_t[c][1-m]+halfper-detect_tol):
detect_on[ci][m] = True
if verbose:
- print " + %s detect (>half per of %s) for %s now True:"%(ms[m],ms[1-m],c), last_t[c][1-m], last_t[c][1-m]+halfper-detect_tol
+ print(" + %s detect (>half per of %s) for %s now True:"%(ms[m],ms[1-m],c), last_t[c][1-m], last_t[c][1-m]+halfper-detect_tol)
# The next segment allows consecutive local extrema of the
# same type without an intermediate of the other type.
# This is generally not desirable!
@@ -1438,8 +1438,8 @@
## print " + %s detect (>half per) for %s now True:"%(ms[1-m],c), last_t[c][1-m], last_t[c][m]+halfper-detect_tol
do_anything = detect_on[ci][0] or detect_on[ci][1]
if verbose:
- print "Detecting for %s? (min=%i) (max=%i)"%(c, int(detect_on[ci][0]), int(detect_on[ci][1]))
- print " v[ci] = %.4f, last_inc[ci] = %.4f"%(v[ci], last_inc[ci])
+ print("Detecting for %s? (min=%i) (max=%i)"%(c, int(detect_on[ci][0]), int(detect_on[ci][1])))
+ print(" v[ci] = %.4f, last_inc[ci] = %.4f"%(v[ci], last_inc[ci]))
if do_anything and v[ci] != last_inc[ci]:
# extremum if changed sign
if v[ci]>0:
@@ -1447,8 +1447,8 @@
if detect_on[ci][0]:
min_ival = argmin(x[c][ival:ival_pl])+ival
if verbose:
- print "Possible min:"
- print x[c][max([0,min_ival-lookahead])], x[c][min_ival], x[c][min([max_ix,min_ival+lookahead])]
+ print("Possible min:")
+ print(x[c][max([0,min_ival-lookahead])], x[c][min_ival], x[c][min([max_ix,min_ival+lookahead])])
if x[c][min([max_ix,min_ival+lookahead])] - x[c][min_ival] > lookahead_tol and \
x[c][max([0,min_ival-lookahead])] - x[c][min_ival] > lookahead_tol:
if do_fit:
@@ -1463,7 +1463,7 @@
min_tval = x['t'][min_ival]
min_xval = x[c][min_ival]
if verbose:
- print "found min for %s at "%c, min_tval
+ print("found min for %s at "%c, min_tval)
mins_t[c].append(min_tval)
mins_v[c].append(min_xval)
last_t[c][0]=min_tval
@@ -1477,8 +1477,8 @@
if detect_on[ci][1]:
max_ival = argmax(x[c][ival:ival_pl])+ival
if verbose:
- print "Possible max:"
- print x[c][max([0,max_ival-lookahead])], x[c][max_ival], x[c][min([max_ix,max_ival+lookahead])]
+ print("Possible max:")
+ print(x[c][max([0,max_ival-lookahead])], x[c][max_ival], x[c][min([max_ix,max_ival+lookahead])])
if x[c][max_ival] - x[c][min([max_ix,max_ival+lookahead])] > lookahead_tol and \
x[c][max_ival] - x[c][max([0,max_ival-lookahead])] > lookahead_tol:
if do_fit:
@@ -1493,7 +1493,7 @@
max_tval = x['t'][max_ival]
max_xval = x[c][max_ival]
if verbose:
- print "found max for %s at "%c, max_tval
+ print("found max for %s at "%c, max_tval)
maxs_t[c].append(max_tval)
maxs_v[c].append(max_xval)
last_t[c][1]=max_tval
@@ -1550,7 +1550,7 @@
if tval < tmin or tval > tmax:
continue
if verbose:
- print "******* t = ", tval
+ print("******* t = ", tval)
for ci, c in enumerate(coords):
for m in [0,1]:
if not detect_on[ci][m]:
@@ -1559,7 +1559,7 @@
if tval>(last_t[c][1-m]+halfper-detect_tol):
detect_on[ci][m] = True
if verbose:
- print " + %s detect (>half per of %s) for %s now True:"%(ms[m],ms[1-m],c), last_t[c][1-m], last_t[c][1-m]+halfper-detect_tol
+ print(" + %s detect (>half per of %s) for %s now True:"%(ms[m],ms[1-m],c), last_t[c][1-m], last_t[c][1-m]+halfper-detect_tol)
# The next segment allows consecutive local extrema of the
# same type without an intermediate of the other type.
# This is generally not desirable!
@@ -1573,13 +1573,13 @@
## print " + %s detect (>half per) for %s now True:"%(ms[1-m],c), last_t[c][m], last_t[c][m]+halfper-detect_tol
do_anything = detect_on[coord_ix][0] or detect_on[coord_ix][1]
if verbose:
- print "Detecting for %s? (min=%i) (max=%i)"%(c, int(detect_on[ci][0]), int(detect_on[ci][1]))
+ print("Detecting for %s? (min=%i) (max=%i)"%(c, int(detect_on[ci][0]), int(detect_on[ci][1])))
if do_anything:
if ex_type == 'min':
if detect_on[coord_ix][0]:
min_tval = tval
if verbose:
- print "... found min for %s at "%coord, min_tval
+ print("... found min for %s at "%coord, min_tval)
mins_t[coord].append(min_tval)
mins_v[coord].append(evdict['min_ev_'+coord][ei][coord])
last_t[coord][0]=min_tval
@@ -1590,7 +1590,7 @@
if detect_on[coord_ix][1]:
max_tval = tval
if verbose:
- print "... found max for %s at "%coord, max_tval
+ print("... found max for %s at "%coord, max_tval)
maxs_t[coord].append(max_tval)
maxs_v[coord].append(evdict['max_ev_'+coord][ei][coord])
last_t[coord][1]=max_tval
@@ -1611,11 +1611,11 @@
num_mins = [min([len(test_mins_t[c]), len(data_mins_t[c])]) for c in coords]
num_maxs = [min([len(test_maxs_t[c]), len(data_maxs_t[c])]) for c in coords]
except TypeError:
- print "Problem with mins and maxs in coords %s in generator %s"%(str(coords),gen.name)
- print "Number of events found =", len(gen.getEvents())
- print per, pertolfrac, tdetect
- print type(test_mins_t), type(test_maxs_t)
- print type(data_mins_t), type(data_maxs_t)
+ print("Problem with mins and maxs in coords %s in generator %s"%(str(coords),gen.name))
+ print("Number of events found =", len(gen.getEvents()))
+ print(per, pertolfrac, tdetect)
+ print(type(test_mins_t), type(test_maxs_t))
+ print(type(data_mins_t), type(data_maxs_t))
raise
res_mins_t = []
res_maxs_t = []
@@ -1624,8 +1624,8 @@
for ci,c in enumerate(coords):
nmin = num_mins[ci]
if len(data_mins_t[c]) != num_expected_mins or len(test_mins_t[c]) < num_expected_mins:
- print "Wrong number of minima for %s (expected %i)"%(c, num_expected_mins)
- print data_mins_t[c], test_mins_t[c]
+ print("Wrong number of minima for %s (expected %i)"%(c, num_expected_mins))
+ print(data_minRefactoringTool: Refactored ./PyDSTool/Toolbox/PRCtools.py
s_t[c], test_mins_t[c])
raise RuntimeError("Wrong number of minima")
# assume 0:num_expected is good
t1 = array(data_mins_t[c])-array(test_mins_t[c])[:num_expected_mins]
@@ -1635,8 +1635,8 @@
# max
nmax = num_maxs[ci]
if len(data_maxs_t[c]) != num_expected_maxs or len(test_maxs_t[c]) < num_expected_maxs:
- print "Wrong number of maxima for %s (expected %i)"%(c, num_expected_maxs)
- print data_maxs_t[c], test_maxs_t[c]
+ print("Wrong number of maxima for %s (expected %i)"%(c, num_expected_maxs))
+ print(data_maxs_t[c], test_maxs_t[c])
raise RuntimeError("Wrong number of maxima")
# assume 0:num_expected is good
t1 = array(data_maxs_t[c])-array(test_maxs_t[c])[:num_expected_maxs]
--- ./PyDSTool/Toolbox/PRCtools.py (original)
+++ ./PyDSTool/Toolbox/PRCtools.py (refactored)
@@ -52,9 +52,9 @@
t_check = 10000*np.ones((tries,),float)
norm_check = 10000*np.ones((tries,),float)
T = np.zeros((tries,),float)
- look_range = range(1, min((tries+1, len(evts))))
- if verbose:
- print "\n Tries: ", tries, "\n"
+ look_range = list(range(1, min((tries+1, len(evts)))))
+ if verbose:
+ print("\n Tries: ", tries, "\n")
for lookback in look_range:
try:
d_evts = [evts[i]-evts[i-lookback] for i in \
@@ -73,8 +73,8 @@
ix1 = min((t_ix, n_ix))
ix2 = max((t_ix, n_ix))
if verbose:
- print t_check, norm_check, T
- print ix1, ix2
+ print(t_check, norm_check, T)
+ print(ix1, ix2)
if t_check[ix1] < ev_t_tol and norm_check[ix1] < ev_norm_tol:
success = True
T_final = T[ix1]
@@ -101,8 +101,8 @@
model.set(algparams={'poly_interp': old_interp_setting})
return ref_traj, ref_pts, T_final
else:
- print "norm check was", norm_check
- print "t check was", t_check
+ print("norm check was", norm_check)
+ print("t check was", t_check)
raise RuntimeError("Failure to converge after 80 iterations")
@@ -143,7 +143,7 @@
model = embed(model)
if keep_trajs:
tag_pts = True
- print "Note: model object will be stored in PRC attribute _model"
+ print("Note: model object will be stored in PRC attribute _model")
try:
all_pts = ref_traj_period.sample()
ref_pts = all_pts[::skip]
@@ -167,14 +167,14 @@
PRCvals = []
t_off = 0
if verbose:
- print "Period T =", T
+ print("Period T =", T)
for i, t0 in enumerate(ref_ts):
if t0 > stop_at_t:
break
ic = do_pert(model, ref_pts[i], pertcoord, pertsize, t0)
if verbose:
- print i, "of", len(ref_ts), ": t0 = ", t0, "of", T, " t_end", settle*T+t0
- print " ", ic
+ print(i, "of", len(ref_ts), ": t0 = ", t0, "of", T, " t_end", settle*T+t0)
+ print(" ", ic)
model.set(ics=ic.copy(), tdata=[0, (settle+1)*T+t0])
if keep_trajs:
model.compute(trajname='pert_%i'%i, force=True)
@@ -183,7 +183,7 @@
model.compute(trajname='pert', force=True)
evts = model.getTrajEventTimes('pert', evname)
if verbose:
- print " Last event:", evts[-1]
+ print(" Last event:", evts[-1])
if i == 0:
# make sure to always use the same event number
evnum = max(0,len(evts)-2)
@@ -195,7 +195,7 @@
m = np.argmin(abs(PRCvals[-1] - test_vals))
val = test_vals[m]
if verbose and abs(PRCvals[-1] - val) > 0.05:
- print "\nCorrected value", i, PRCvals, val
+ print("\nCorrected value", i, PRCvals, val)
else:
# i = 0. Check that value is adjusted to be closest to zero,
# given that we assume the minimum will be at the beginning of the run.
@@ -236,7 +236,7 RefactoringTool: Refactored ./PyDSTool/Toolbox/NineML.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/ModelHelper.py
@@
PRC_val = -np.mod(evts[-1]+t0, T)/T
if abs(PRC_val) > 0.5:
PRC_val += 1
- print "t0 = %.6f, PRC value = %f" % (t0, PRC_val)
+ print("t0 = %.6f, PRC value = %f" % (t0, PRC_val))
if fignum is not None:
figure(fignum)
--- ./PyDSTool/Toolbox/NineML.py (original)
+++ ./PyDSTool/Toolbox/NineML.py (refactored)
@@ -5,7 +5,7 @@
R. Clewley, 2012
"""
-from __future__ import division
+
from PyDSTool import *
from PyDSTool.common import _seq_types, _num_types
@@ -57,8 +57,8 @@
# lists
pars = [p.name for p in c.parameters]
- vars = dyn.state_variables_map.keys()
- fns = c.aliases_map.keys()
+ vars = list(dyn.state_variables_map.keys())
+ fns = list(c.aliases_map.keys())
# Turn aliases into function defs:
# multiple passes until all dependencies resolved
@@ -116,7 +116,7 @@
reg_info_list = []
reg_models = {}
- all_reg_names = c.regimes_map.keys()
+ all_reg_names = list(c.regimes_map.keys())
num_regs = len(c.regimes_map)
if num_regs > 1:
is_hybrid = True
@@ -125,7 +125,7 @@
# This is the default value, updated to True if there are any
# state assignments for events (even for only one regime)
# r is a singleton regime
- r = c.regimes.next()
+ r = next(c.regimes)
for e in r.on_conditions:
for s in e.state_assignments:
is_hybrid = True
@@ -268,14 +268,14 @@
reg_MI = intModelInterface(reg_model)
reg_info_list.append(makeModelInfoEntry(reg_MI, all_reg_names,
- epmaps.values()))
+ list(epmaps.values())))
if is_hybrid:
# build MIs, map events, etc.
the_model = Model.HybridModel({'name': model_name,
'modelInfo': makeModelInfo(reg_info_list)})
else:
- the_model = reg_models.values()[0]
+ the_model = list(reg_models.values())[0]
return the_model
--- ./PyDSTool/Toolbox/ModelHelper.py (original)
+++ ./PyDSTool/Toolbox/ModelHelper.py (refactored)
@@ -110,60 +110,60 @@
if targetGen not in allODEgens:
# Print a list of the valid targets
- print 'Valid target ODE solvers: ' + ", ".join(allODEgens)
+ print('Valid target ODE solvers: ' + ", ".join(allODEgens))
raise ValueError('Invalid target ODE solver')
# Empty model spec to be populated with the information in modelDict
theModelSpec = SpiffyODEModel(modelName, compatibleGens=allODEgens)
if not silent:
- print "Building model: '%s'"%modelName
+ print("Building model: '%s'"%modelName)
# Build the ODE RHS, save list of ODEs
varnames = []
- if 'odes' in modelDict.keys():
- for odeName, expr in modelDict['odes'].iteritems():
+ if 'odes' in list(modelDict.keys()):
+ for odeName, expr in modelDict['odes'].items():
theModelSpec.add(Var(expr, odeName, specType='RHSfuncSpec'))
varnames.append(odeName)
if not silent:
- print 'Added ODE: ', odeName
+ print('Added ODE: ', odeName)
# Build the aux variables, save list of them
auxvarnames = []
- if 'auxs' in modelDict.keys():
- for auxName, expr in modelDict['auxs'].iteritems():
+ if 'auxs' in list(modelDict.keys()):
+ for auxName, expr in modelDict['auxs'].items():
theModelSpec.add(Var(expr, auxName, specType='ExpFuncSpec'))
auxvarnames.append(auxName)
if not silent:
- print 'Added aux variable: ', auxName
+ print('Added aux variable: ', auxName)
# Build the list of RHS specific parameters, save list of them
parnames = []
- if 'params' in modelDict.keys():
- for parName, val in modelDict['params'].iteritems():
+ if 'params' in list(modelDict.keys()):
+ for parName, val in modelDict['params'].items():
theModelSpec.add(Par(str(val), parName))
parnames.append(parName)
RefactoringTool: Refactored ./PyDSTool/Toolbox/ModelEst.py
RefactoringTool: No changes to ./PyDSTool/Toolbox/InputProfile.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/FSM.py
RefactoringTool: Refactored ./PyDSTool/Toolbox/FR.py
if not silent:
- print 'Added parameter: ', parName, "=", val
+ print('Added parameter: ', parName, "=", val)
# Build the inputs, save list of them
inputnames = []
inputdict = {}
- if 'inputs' in modelDict.keys():
- for inputName, val in modelDict['inputs'].iteritems():
+ if 'inputs' in list(modelDict.keys()):
+ for inputName, val in modelDict['inputs'].items():
theModelSpec.add(Input(str(inputName)))
inputnames.append(inputName)
#if not silent:
# print val.variables.keys()
inputdict[inputName] = val.variables[inputName]
if not silent:
- print 'Added input: ', inputName, "=", val
+ print('Added input: ', inputName, "=", val)
# Build the dict of extra functions, save list of them
auxfndict = {}
- if 'functions' in modelDict.keys():
- for funSig, expr in modelDict['functions'].iteritems():
+ if 'functions' in list(modelDict.keys()):
+ for funSig, expr in modelDict['functions'].items():
# check syntax; this could be taken care of by Lex-built
# syntax checking function
assert ')' == funSig[-1]
@@ -181,22 +181,22 @@
if name == 'Jacobian_pars':
makeJacP = False
if not silent:
- print 'Added function: ', name, " of arguments: ", args
+ print('Added function: ', name, " of arguments: ", args)
# Make symbolic jacobian if requested
if makeJac:
- if 'Jacobian' not in modelDict.keys():
+ if 'Jacobian' not in list(modelDict.keys()):
varnames.sort()
dotlist = [modelDict['odes'][x] for x in varnames]
F = Fun(dotlist, varnames, 'F')
Jac = Fun(Diff(F, varnames), ['t'] + varnames, 'Jacobian')
theModelSpec.add(Jac)
if not silent:
- print "Added jacobian"
+ print("Added jacobian")
if makeJacP:
- if 'Jacobian_pars' not in modelDict.keys():
+ if 'Jacobian_pars' not in list(modelDict.keys()):
varnames.sort()
parnames.sort()
dotlist = [modelDict['odes'][x] for x in varnames]
@@ -204,7 +204,7 @@
JacP = Fun(Diff(G, varnames + parnames), ['t'] + varnames + parnames, 'Jacobian_pars')
theModelSpec.add(JacP)
if not silent:
- print "Added jacobian w.r.t parameters"
+ print("Added jacobian w.r.t parameters")
# Construct the model
--- ./PyDSTool/Toolbox/ModelEst.py (original)
+++ ./PyDSTool/Toolbox/ModelEst.py (refactored)
@@ -60,8 +60,8 @@
# dict of par -> sensitivity
#sens = param_sensitivity(model, self.context, free_pars)
- print "Get pre-defined tols from features somehow"
- print "Establish parameter estimation class and run it"
+ print("Get pre-defined tols from features somehow")
+ print("Establish parameter estimation class and run it")
#pest = LMpest(freeParams=free_pars,
# testModel=model,
# context=self.context,
--- ./PyDSTool/Toolbox/FSM.py (original)
+++ ./PyDSTool/Toolbox/FSM.py (refactored)
@@ -78,7 +78,7 @@
self.value = value
def __str__(self):
- return `self.value`
+ return repr(self.value)
class FSM(object):
@@ -200,9 +200,9 @@
4. No transition was defined. If we get here then raise an exception.
"""
- if self.state_transitions.has_key((input_symbol, state)):
+ if (input_symbol, state) in self.state_transitions:
return self.state_transitions[(input_symbol, state)]
- elif self.state_transitions_any.has_key (state):
+ elif state in self.state_transitions_any:
return self.state_transitions_any[state]
elif self.default_transition is not None:
return self.default_transition
--- ./PyDSTool/Toolbox/FR.py (originalRefactoringTool: Refactored ./PyDSTool/Toolbox/DSSRT_tools.py
)
+++ ./PyDSTool/Toolbox/FR.py (refactored)
@@ -1,7 +1,7 @@
# Fruchterman-Reingold graph drawing algorithm in Python
# R. Clewley, November 2005
-from __future__ import division
+
from numpy import array, alltrue, arange, sign
from numpy.linalg import norm
import math
@@ -60,7 +60,7 @@
def itercool(t, t0, n=30):
cooler = cool(t0, tarray)
for i in range(n+1):
- print t
+ print(t)
t=cooler(t)
@@ -75,9 +75,9 @@
def in_degree(V, E):
ind = {}
- for vn, vv in V.iteritems():
+ for vn, vv in V.items():
count = 0
- for vert in V.keys():
+ for vert in list(V.keys()):
try:
es = E[vert]
except KeyError:
@@ -104,7 +104,7 @@
return k*k/x
od = out_degree(V, E)
- fixedverts = fixed.values()
+ fixedverts = list(fixed.values())
# initial temperature
t = t0 = max([W[1]-W[0], L[1]-L[0]])/3.5
@@ -115,12 +115,12 @@
for i in range(num_its):
# print "t = %.4f"%t
# calculate repulsive forces (with weak Gaussian noise)
- for vname, v in V.iteritems():
+ for vname, v in V.items():
# each vertex has two vectors: .pos and .disp
v.disp = array([0., 0.])
if vname in fixed:
continue
- for uname, u in V.iteritems():
+ for uname, u in V.items():
if u != v:
D = v.pos - u.pos
aD = norm(D)
@@ -141,7 +141,7 @@
aD = norm(D)
v.disp = v.disp + (D/aD) * fr(aD) \
+ array([normal(0, t), normal(0, t)])
- for vname, v in V.iteritems():
+ for vname, v in V.items():
# penalize edges from common vertex that are very close to
# eachother in angle
if od[vname] > 2:
@@ -188,7 +188,7 @@
# angles are close enough that use same direction for other vertex
angles_sorted[ni].u.disp = angles_sorted[ni].u.disp - c*vd
# calculate attractive forces along edges
- for vname, elist in E.iteritems():
+ for vname, elist in E.items():
if od[vname] > 3:
att_scale = 1.75
else:
@@ -205,7 +205,7 @@
# limit the maximum displacement to the temperature t
# and then prevent vertex being displaced outside frame
- for v in V.itervalues():
+ for v in V.values():
if v in fixedverts:
continue
v.pos = v.pos + (v.disp/norm(v.disp)) * min([norm(v.disp), t])
--- ./PyDSTool/Toolbox/DSSRT_tools.py (original)
+++ ./PyDSTool/Toolbox/DSSRT_tools.py (refactored)
@@ -12,7 +12,7 @@
from PyDSTool import *
from PyDSTool.parseUtils import symbolMapClass
-from FR import *
+from .FR import *
import os
from copy import copy
from random import uniform, gauss
@@ -71,7 +71,7 @@
inputs[mi].append(mo)
except AttributeError:
inputs[mi] = [mo]
- for k, v in inputs.iteritems():
+ for k, v in inputs.items():
if v is None:
inputs[k] = []
self.inputs = inputs
@@ -88,7 +88,7 @@
if remain(self.varsext, vars) != []:
raise NotImplementedError("Can only make network graph with all "
"external variables at this time")
- print "Finding graph layout for network..."
+ print("Finding graph layout for network...")
V = {}
E = {}
# prepare vertices
@@ -101,7 +101,7 @@
domX = [0.08, 0.96]
# override position initial conditions for specially selected variables
if ics is not None:
- for var, ic in ics.items():
+ for var, ic in list(ics.items()):
if ic[0] < domX[0] or ic[0] > domX[1]:
raise ValueError("X initial condition for %s out of "%var \
+ "bounds [%.3f, %.3f]"%(domX[0], domX[1]))
@@ -134,7 +134,7 @@
for v in vars:
if in_d[v] + out_d[v] == 0:
info(in_d, 'in-degrees')
- print "\n"
+ print("\n")
info(out_d, 'out-degrees')
raise ValueError("Variable %s had no associated edges"%v)
self._V = V
@@ -142,7 +142,7 @@
if ics is None:
fixedICs = {}
else:
- fixedICs = dict(zip(ics.keys(),[V[k] for k in ics.keys()]))
+ fixedICs = dict(list(zip(list(ics.keys()),[V[k] for k in list(ics.keys())])))
# call the Fruchtermann-Reingold algorithm to determine graph
FR(V, E, domX, domY, fixed=fixedICs)
self.nodes = []
@@ -215,8 +215,8 @@
bd0 = 0
bd1 = 1
else:
- print "Warning: variable %s has not been given bounds"%var
- print " (assuming +/- 'infty_val' attribute)"
+ print("Warning: variable %s has not been given bounds"%var)
+ print(" (assuming +/- 'infty_val' attribute)")
bd0 = -self._infty_val
bd1 = self._infty_val
magopt = int(bd0 == 0 and bd1 == 1)
@@ -232,8 +232,8 @@
bd0 = 0
bd1 = 1
else:
- print "Warning: variable %s has not been given bounds"%var
- print " (assuming +/- 'infty_val' attribute)"
+ print("Warning: variable %s has not been given bounds"%var)
+ print(" (assuming +/- 'infty_val' attribute)")
bd0 = -self._infty_val
bd1 = self._infty_val
# these variables still need vbars
@@ -317,7 +317,7 @@
try:
voltname = model._FScompatibleNames(model.searchForVars(parts[0]+'.'+'V')[0])
except:
- print "Problem finding membrane voltage name in model spec"
+ print("Problem finding membrane voltage name in model spec")
raise
self.cfac[voltname] = model._FScompatibleNames(fullname)
# need to take out function-specific parameters from depars --
@@ -328,40 +328,40 @@
# prepare DEpars
alldepars = model._FScompatibleNames(model.query('parameters')) # full list of pars
depar_names = remain(alldepars, not_depars)
- self.depars = dict(zip(depar_names, [mspec.flatSpec['pars'][p] for p in depar_names]))
+ self.depars = dict(list(zip(depar_names, [mspec.flatSpec['pars'][p] for p in depar_names])))
# perform the textual subs for non-tau or inf function calls with > 1 argument
raise NotImplementedError("This function is incomplete!")
# do something with subsFnDef
# work out gam1terms and gam2terms
# validate CFG
self.prepCFG()
- print "Finished preparing CFG information. Call outputCFG(filename) to output .cfg file"
+ print("Finished preparing CFG information. Call outputCFG(filename) to output .cfg file")
def prepCFG(self):
"""Prepare .cfg file (at least a pre-cursor for later editing by hand)"""
# Set remaining bounds to default limits
- bd_overlap = intersect(self.bounds.keys(), self.unitbounds)
+ bd_overlap = intersect(list(self.bounds.keys()), self.unitbounds)
if bd_overlap != []:
- print bd_overlap
+ print(bd_overlap)
raise ValueError("Clash between variables with explicitly declared"
"bounds and those with unit bounds")
- for v in remain(self.varsall, self.bounds.keys()+self.unitbounds):
+ for v in remain(self.varsall, list(self.bounds.keys())+self.unitbounds):
self.bounds[v] = [-self._infty_val, self._infty_val]
self._CFG['VARSEXT'] = [" ".join(self.varsext)]
self._CFG['VARSINT'] = [" ".join(self.varsint)]
- self._CFG['INPUTS'] = [ename + " " + " ".joinRefactoringTool: Refactored ./PyDSTool/Symbolic.py
(inlist) for ename, inlist in self.inputs.items()]
- self._CFG['BOUNDS'] = [ename + " %f %f"%(bd[0],bd[1]) for ename, bd in self.bounds.items()]
+ self._CFG['INPUTS'] = [ename + " " + " ".join(inlist) for ename, inlist in list(self.inputs.items())]
+ self._CFG['BOUNDS'] = [ename + " %f %f"%(bd[0],bd[1]) for ename, bd in list(self.bounds.items())]
self._CFG['UNITBOUNDS'] = [" ".join(self.unitbounds)]
self._CFG['DEQNS'] = [" ".join(self.deqns)]
- self._CFG['CFAC'] = [vname + " " + cname for (vname, cname) in self.cfac.items()]
+ self._CFG['CFAC'] = [vname + " " + cname for (vname, cname) in list(self.cfac.items())]
self._CFG['GAM1TERM'] = []
- for vname, termlists in self.gam1terms.iteritems():
+ for vname, termlists in self.gam1terms.items():
self._CFG['GAM1TERM'].extend([vname + " " + " ".join(termlist) for termlist in termlists])
self._CFG['GAM2TERM'] = []
- for vname, termlists in self.gam2terms.iteritems():
+ for vname, termlists in self.gam2terms.items():
self._CFG['GAM2TERM'].extend([vname + " " + " ".join(termlist) for termlist in termlists])
- deparnames = self.depars.keys()
+ deparnames = list(self.depars.keys())
deparnames.sort()
self._CFG['DEPAR'] = []
for parname in deparnames:
@@ -415,13 +415,13 @@
def prepDEpars(self):
updates = {}
- for par, parval in self.depars.iteritems():
+ for par, parval in self.depars.items():
try:
if par[-3:]=="tau":
updates[par] = (par+"_recip", 1/parval)
except IndexError:
pass
- for par, (newpar, newval) in updates.iteritems():
+ for par, (newpar, newval) in updates.items():
del self.depars[par]
self.depars[newpar] = newval
@@ -436,14 +436,14 @@
subsFnDef=[]
not_depars=[]
mfiles = {}
- allpars = pardict.keys()
- for fname, (fsig, fdef) in auxfndict.iteritems():
+ allpars = list(pardict.keys())
+ for fname, (fsig, fdef) in auxfndict.items():
if len(fsig) == 1 and fname[-3:] in ['tau', 'inf']:
fdefQS = QuantSpec("__fdefQS__", fdef)
# fpars are the parameters used in the function -- we fetch
# their values and subs them directly into the M file function.
fpars = intersect(fdefQS.freeSymbols, allpars)
- fpar_defs = dict(zip(fpars,[pardict[p] for p in fpars]))
+ fpar_defs = dict(list(zip(fpars,[pardict[p] for p in fpars])))
not_depars.extend(remain(fpars, not_depars))
if fname[-3:] == 'tau':
fname += "_recip"
@@ -457,7 +457,7 @@
subsFnDef.append(fname)
# make m files if nofiles==False
if makeMfiles:
- for fname, finfo in mfiles.iteritems():
+ for fname, finfo in mfiles.items():
makeMfileFunction(fname, finfo[0], finfo[1])
return subsFnDef, not_depars
@@ -481,9 +481,9 @@
except AttributeError:
raise TypeError("Invalid DSSRT_info object for plotNetworkGraph")
plt.figure()
- for v in V.itervalues():
+ for v in V.values():
plt.plot([v.pos[0]],[v.pos[1]],'ko')
- for elist in E.itervalues():
+ for elist in E.values():
for e in elist:
plt.plot([e.u.pos[0],e.v.pos[0]],
[e.u.pos[1],e.v.pos[1]],
--- ./PyDSTool/Symbolic.py (original)
+++ ./PyDSTool/Symbolic.py (refactored)
@@ -56,16 +56,16 @@
# ----------------------------------------------------------------------------
-from __future__ import division
-import os, sys, types, cPickle
-from Interval import Interval
-from common import *
-from utils import info as utils_info
-from parseUtils import *
-from errors import *
+
+import os, sys, types, pickle
+from .Interval import Interval
+from .common import *
+from .utils import info as utils_info
+from .parseUtils import *
+from .errors import *
#from math import *
-from utils import *
+from .utils import *
from numpy import array, Inf, NaN, isfinite, mod, sum, float64, int32
from numpy import sometrue, alltrue
# replacements of math functions so that expr2fun etc. produce vectorizable math functions
@@ -94,7 +94,7 @@
### Constants
# determine what "globals" will be for math evaluations in _eval method
math_dir = dir(math)
-math_globals = dict(zip(math_dir,[getattr(math, m) for m in math_dir]))
+math_globals = dict(list(zip(math_dir,[getattr(math, m) for m in math_dir])))
math_globals['Inf'] = Inf
math_globals['NaN'] = NaN
@@ -104,8 +104,8 @@
allmathnames_symbolic = [a.title() for a in allmathnames]
# the definitions for the math names are made lower down in this file
-mathNameMap = dict(zip(allmathnames_symbolic, allmathnames))
-inverseMathNameMap = dict(zip(allmathnames, allmathnames_symbolic))
+mathNameMap = dict(list(zip(allmathnames_symbolic, allmathnames)))
+inverseMathNameMap = dict(list(zip(allmathnames, allmathnames_symbolic)))
specTypes = ('RHSfuncSpec', 'ImpFuncSpec', 'ExpFuncSpec')
@@ -183,8 +183,8 @@
allnonnumbers = [n for n in symbs if isNameToken(n)]
if len(allnonnumbers) > 0 \
and alltrue([n in allmathnames for n in allnonnumbers]):
- namemap = dict(zip(allnonnumbers,
- [a.lower() for a in allnonnumbers]))
+ namemap = dict(list(zip(allnonnumbers,
+ [a.lower() for a in allnonnumbers])))
args[i].mapNames(namemap)
args[i] = eval(args[i]())
else:
@@ -195,9 +195,9 @@
argstr = ", ".join(map(str,args))
if convert:
try:
- return apply(eval(self.name.lower()), args)
+ return eval(self.name.lower())(*args)
except TypeError:
- print "Failed to evaluate function %s on args:"%self.name.lower(), argstr
+ print("Failed to evaluate function %s on args:"%self.name.lower(), argstr)
raise
else:
return QuantSpec("__result__", self.name + "(" + argstr +")")
@@ -209,12 +209,12 @@
else:
arglist.append(a)
try:
- return float(apply(eval(self.name.lower()), arglist))
+ return float(eval(self.name.lower())(*arglist))
except NameError:
argstr = ", ".join(map(str,args))
return QuantSpec("__result__", self.name + "(" + argstr +")")
except TypeError:
- print "Error evaluating %s on args:"%self.name.lower(), args
+ print("Error evaluating %s on args:"%self.name.lower(), args)
raise
def __str__(self):
@@ -264,7 +264,7 @@
that sequence, otherwise return the argument untouched."""
if isinstance(x, _seq_types):
if len(x) > 0:
- xstrlist = map(str,x)
+ xstrlist = list(map(str,x))
return '['+",".join(xstrlist)+']'
else:
return x
@@ -291,7 +291,7 @@
o = {}
try:
# d is a Point or dictionary
- for k, v in d.iteritems():
+ for k, v in d.items():
if isinstance(v, tuple):
if alltrue([isinstance(x, str) for x in v[0]]):
o[str(k)] = (v[0], str(v[1]))
@@ -326,8 +326,8 @@
o[d.subjectToken] = d.specStr
else:
raise TypeError("Invalid type %s"%str(type(d)))
- except TypeError, err:
- print "Argument was:\n", d
+ except TypeError as err:
+ print("Argument was:\n", d)
raise TypeError("Invalid argument type: %s "%str(err) + \
"or argument's values cannot be converted to key:value" + \
"strings")
@@ -341,9 +341,9 @@
qstr = str(q)
try:
val = eval(qstr, math_globals, local_free)
- except NameError, err:
+ except NameError as err:
raise ValueError("Invalid input.\nProblem was: %s"%str(err))
- except TypeError, err:
+ except TypeError as err:
# trap getitem or call error for string version of object
# try without runtime components, if any
if eval_at_runtime != []:
@@ -357,7 +357,7 @@
except KeyboardInterrupt:
raise
except:
- print "Internal error evaluating function spec"
+ print("Internal error evaluating function spec")
info(local_free, " ** Local free dict was")
info(math_globals, " ** Math globals dict was")
raise
@@ -420,7 +420,7 @@
"""
# put in local namespace for sake of final class method's
# alt_call use of filteredDict
- from common import filteredDict
+ from .common import filteredDict
# convert values into a dictionary of strings where possible
valDict = {}
# functions that will end up as methods in the wrapper
@@ -430,7 +430,7 @@
eval_at_runtime = []
free = []
h_map = symbolMapClass()
- for k, v in values.iteritems():
+ for k, v in values.items():
if isinstance(v, str):
vs = v
elif isinstance(v, _num_types):
@@ -475,25 +475,25 @@
# now make a Var from the QuantSpec
try:
qvar = Var(qexpr, 'q')
- except TypeError, e:
+ except TypeError as e:
raise TypeError("Invalid qexpr argument type: " + str(e))
fspec = qvar.eval(**valDict)
dyn_map = symbolMapClass()
temp_dynamic = {}
if ensure_dynamic is not None:
- dyn_keys = ensure_dynamic.keys()
+ dyn_keys = list(ensure_dynamic.keys())
dyn_vals = ["self._pardict['%s']" %d for d in dyn_keys]
- dyn_map.update(dict(zip(dyn_keys, dyn_vals)))
+ dyn_map.update(dict(list(zip(dyn_keys, dyn_vals))))
eval_at_runtime.extend(dyn_keys)
for k in dyn_keys:
temp_dynamic[k] = Var(k)
else:
dyn_keys = []
- for fname, (fnsig, fndef) in embed_funcs.iteritems():
+ for fname, (fnsig, fndef) in embed_funcs.items():
qtemp = QuantSpec('q', fndef)
- for emb_fname in embed_funcs.keys():
+ for emb_fname in list(embed_funcs.keys()):
# check for embedded function names in these definitions that need
# prefix 'self.' for later function creation
if emb_fname in qtemp:
@@ -504,13 +504,13 @@
embed_funcs[fname] = (fnsig, new_fndef)
free.extend(remain(fspec.freeSymbols,
- math_globals.keys()+local_free.keys()+embed_funcs.keys()+dyn_keys))
+ list(math_globals.keys())+list(local_free.keys())+list(embed_funcs.keys())+dyn_keys))
# hack to exclude object references which will be taken care of at runtime
# or string literals that aren't supposed to be free symbols
free = [sym for sym in free if not \
("'%s'"%sym in qexpr or '"%s"'%sym in qexpr)]
- mapnames = local_free.keys() + embed_funcs.keys()
- for k in local_free.keys():
+ mapnames = list(local_free.keys()) + list(embed_funcs.keys())
+ for k in list(local_free.keys()):
for sym in free:
if '.' in sym and sym[:sym.index('.')] == k:
mapnames.append(sym)
@@ -523,11 +523,11 @@
# they are objects!
free_h = [symb.replace('.', '_') for symb in free]
free_h_nonFS = [symb.replace('_', '.') for symb in free]
- h_map.update(dict(zip(free_h_nonFS, free_h)))
+ h_map.update(dict(list(zip(free_h_nonFS, free_h))))
free = free_h
- defs = filteredDict(local_free, [k for k, v in local_free.iteritems() if v is not None])
- local_free.update(dict(zip(free, [QuantSpec(symb) for symb in free])))
- scope = filteredDict(local_free, [k for k, v in local_free.iteritems() if v is not None])
+ defs = filteredDict(local_free, [k for k, v in local_free.items() if v is not None])
+ local_free.update(dict(list(zip(free, [QuantSpec(symb) for symb in free]))))
+ scope = filteredDict(local_free, [k for k, v in local_free.items() if v is not None])
scope.update(local_funcs)
scope.update(temp_dynamic)
fspec.mapNames(h_map)
@@ -543,8 +543,8 @@
for q in fspec.fromvector()]) + "]"
fspec_eval = QuantSpec('__temp__', temp_str).renderForCode()
if eval_at_runtime != []:
- fspec_eval.mapNames(dict(zip(mapnames,
- ['self.'+k for k in mapnames])))
+ fspec_eval.mapNames(dict(list(zip(mapnames,
+ ['self.'+k for k in mapnames]))))
fspec_eval.mapNames(dyn_map)
fspec_str = str(fspec_eval)
else:
@@ -564,16 +564,16 @@
return ''
if isinstance(fspec_eval, _num_types):
if eval_at_runtime != []:
- fspec.mapNames(dict(zip(mapnames,
- ['self.'+k+append_call_parens(k) for k in mapnames])))
+ fspec.mapNames(dict(list(zip(mapnames,
+ ['self.'+k+append_call_parens(k) for k in mapnames]))))
fspec_str = str(fspec)
else:
fspec_str = repr(fspec_eval)
elif not fspec.isvector():
# already found fspec_str using eval_at_runtime for isvector case
if eval_at_runtime != []:
- fspec.mapNames(dict(zip(mapnames,
- ['self.'+k+append_call_parens(k) for k in mapnames])))
+ fspec.mapNames(dict(list(zip(mapnames,
+ ['self.'+k+append_call_parens(k) for k in mapnames]))))
fspec_str = str(fspec)
else:
fspec_str = str(fspec_eval.renderForCode())
@@ -600,15 +600,15 @@
return self.__call__(**filteredDict(self._namemap(keyed_arg), self._args))
"""
if len(embed_funcs) > 0:
- for fname, (fnsig, fndef) in embed_funcs.iteritems():
+ for fname, (fnsig, fndef) in embed_funcs.items():
def_str += "\n def " + fname + "(self"
if len(fnsig) > 0:
def_str += ", " + ", ".join(fnsig)
def_str += "):\n return " + fndef
try:
- exec def_str in locals(), globals()
+ exec(def_str, locals(), globals())
except:
- print "Problem defining function:"
+ print("Problem defining function:")
raise
evalfunc = fn_wrapper()
evalfunc.__dict__.update(defs)
@@ -643,7 +643,7 @@
elif isinstance(b, Par):
valDict[str(b)] = str(b.eval())
elif isinstance(b, dict):
- for k, v in b.iteritems():
+ for k, v in b.items():
if k in valDict:
raise ValueError("Value for %s already bound"%k)
valDict[k] = str(v)
@@ -681,7 +681,7 @@
"""Internal utility for prepJacobian"""
add_fnspecs = {}
new_free = []
- math_globals_keys = math_globals.keys()
+ math_globals_keys = list(math_globals.keys())
for symb in symbols:
# derivatives of an unknown function f(x,y,z) will be marked
# f_0, f_1, or f_2 depending on which variable was selected
@@ -756,8 +756,8 @@
frame = frame.f_back
objdict = frame.f_globals
typelist = [Quantity, QuantSpec]
- for objname, obj in objdict.iteritems():
- if type(obj) not in [type, types.ClassType, types.ModuleType]:
+ for objname, obj in objdict.items():
+ if type(obj) not in [type, type, types.ModuleType]:
if compareClassAndBases(obj, typelist):
objdict_out[objname] = obj
elif deepSearch:
@@ -767,7 +767,7 @@
objdict_out[objname] = obj
elif isinstance(obj, dict):
if sometrue([compareClassAndBases(x, typelist) \
- for x in obj.values()]):
+ for x in list(obj.values())]):
objdict_out[objname] = obj
return objdict_out # original 'returnlevel=2'
@@ -792,7 +792,7 @@
## else:
self.subjectToken = token
else:
- print "Found:",subjectToken
+ print("Found:",subjectToken)
raise ValueError("Invalid subject token")
if specStr != "" and specStr[0] == '+':
if len(specStr) > 1:
@@ -1198,13 +1198,13 @@
other.specStr.replace(" ",""))
results.append(self.specType == other.specType)
results.append(self.parser() == other.parser())
- except AttributeError, err:
+ except AttributeError as err:
if diff:
- print "Type:", className(self), results
- print " " + str(err)
+ print("Type:", className(self), results)
+ print(" " + str(err))
return False
if diff:
- print "Type:", className(self), results
+ print("Type:", className(self), results)
return alltrue(results)
@@ -1307,7 +1307,7 @@
scope[self.subjectToken] = strval
scopeobjs = {}
# process scope objects
- for key, obj in scopeobjs.iteritems():
+ for key, obj in scopeobjs.items():
if isinstance(obj, Quantity):
if obj.name != self.subjectToken:
strval = str(obj.spec._eval(eval_type, {}))
@@ -1350,7 +1350,7 @@
# process scope objects, avoiding identity mappings of
# tokens that could lead to infinite loops
scope = {}
- for key, obj in scopeobjs.iteritems():
+ for key, obj in scopeobjs.items():
if key == '__result__':
# not a valid key
continue
@@ -1399,7 +1399,7 @@
scopeobjs = copy(defs)
# process scope objects
scope = {}
- for key, obj in scopeobjs.iteritems():
+ for key, obj in scopeobjs.items():
if key == '__result__':
continue
if isinstance(obj, Quantity):
@@ -1452,10 +1452,10 @@
'['+','.join([r() for r in res_eval])+']',
self.specType)
# apply definitions in scope
- arglist = scope.keys()
+ arglist = list(scope.keys())
arglist.sort()
# convert any numeric substitutions into strings
- for k, v in defs.iteritems():
+ for k, v in defs.items():
if not isinstance(v, str) and k not in [str(v), "__result__"]:
scope[k] = str(v)
else:
@@ -1540,7 +1540,7 @@
# but only use keys that weren't present before, to avoid circular
# mapping: e.g. s->t then t->s
if scope != {}:
- qtemp.mapNames(filteredDict(scope,remain(toks,scope.keys())))
+ qtemp.mapNames(filteredDict(scope,remain(toks,list(scope.keys()))))
# references to builtin aux functions or macros require temp
# definitions of those as Fun objects
qtoks = qtemp.parser.tokenized
@@ -1574,7 +1574,7 @@
# Would like to make this cleaner...
defstr = sq
except TypeError:
- print self.specStr, sq
+ print(self.specStr, sq)
raise
else:
# HACK: fix simplify_str()'s return of vector arg with round braces
@@ -1621,7 +1621,7 @@
if not num_qtemp:
freenamelist = remain(qtemp.freeSymbols,
allmathnames_symbolic + localfuncs)
- local_scope = dict(zip(freenamelist,[QuantSpec(symb) for symb in freenamelist]))
+ local_scope = dict(list(zip(freenamelist,[QuantSpec(symb) for symb in freenamelist])))
local_scope.update(local_fndef)
local_scope_feval = copy(local_scope)
if eval_type == 1:
@@ -1713,7 +1713,7 @@
isHierarchicalName(newsubj, treatMultiRefs=True)):
self.subjectToken = newsubj
else:
- print "Attempted to rename %s with object of type %s, value:"%(self.subjectToken,str(type(newsubj))), newsubj
+ print("Attempted to rename %s with object of type %s, value:"%(self.subjectToken,str(type(newsubj))), newsubj)
raise TypeError("Cannot rename a QuantSpec with a non-name string")
toks = [namemap(t) for t in self.parser.tokenized]
# strip() in case spaces were preserved and there were trailing spaces
@@ -1775,7 +1775,7 @@
# Also, any zXX refs present in the mrefs, where XX is not in
# the range [i1,i2], are free symbols of this Quantity
# because they aren't being defined here
- defrange = xrange(i1,i2+1)
+ defrange = range(i1,i2+1)
# Quantity subject token is 'z[<ixname>]'
# and future 'name' attribute
token = rootname + "[" + ixname + "]"
@@ -1807,10 +1807,10 @@
try:
temp_qspec = QuantSpec(surrogateToken, surrogateSpec,
specType, treatMultiRefs=True)
- except ValueError, e:
+ except ValueError as e:
# replace temp name __z__ with actual token name z[i]
new_e = (e[0].replace(surrogateToken, token))
- raise ValueError, new_e
+ raise ValueError(new_e)
for f in temp_qspec.freeSymbols:
try:
is_int = f[-1] in num_chars
@@ -1950,7 +1950,7 @@
# an integer, where expr is everything between the square brackets
original_tokenlist = temp.tokenized[2:-1]
ixname_occs = []
- for i in xrange(len(original_tokenlist)):
+ for i in range(len(original_tokenlist)):
if original_tokenlist[i] == ixname:
ixname_occs.append(i)
# make a list of all referenced integers by this expression, over this
@@ -2020,11 +2020,11 @@
return False
obj_rootname = obj.name[:p]
obj_ix = int(obj.name[p:]) # known to be ok integer
- for rootname, infotuple in multiDefRefs.iteritems():
+ for rootname, infotuple in multiDefRefs.items():
if obj_rootname == rootname:
# root of the name is present
# so check if the number falls in the subject range
- if obj_ix in xrange(infotuple[3], infotuple[4]+1):
+ if obj_ix in range(infotuple[3], infotuple[4]+1):
result = True
break
return result
@@ -2081,7 +2081,7 @@
token = name
self.multiDefInfo = (True, rootname, ixname, i1, i2)
else:
- print "Token name argument was:", name
+ print("Token name argument was:", name)
raise ValueError("Invalid Quantity token name")
elif isinstance(spec, QuantSpec):
actual_spec = copy(spec)
@@ -2109,7 +2109,7 @@
token = name
self.multiDefInfo = (True, rootname, ixname, i1, i2)
else:
- print "Token name argument was:", name
+ print("Token name argument was:", name)
raise TypeError("Invalid type for Quantity token name")
else:
token = spec.subjectToken
@@ -2251,7 +2251,7 @@
ixname = m[2]
i1 = m[3]
i2 = m[4]
- if x in xrange(i1,i2+1):
+ if x in range(i1,i2+1):
tokenized = []
for t in self.spec.parser.tokenized:
# can trust that t starting with '[' is a valid mref
@@ -2313,7 +2313,7 @@
try:
r1 = QuantSpec("__result__", otherstr, other_specType)
except TypeError:
- print "Failed to compile: '" + otherstr + "'"
+ print("Failed to compile: '" + otherstr + "'")
raise
r2 = QuantSpec("__result__", self.name, self.specType)
if reverseorder:
@@ -2408,7 +2408,7 @@
def eval(self, *scopearg, **defs):
"""eval does not require all free symbols to be resolved, but any
signature arguments (for a function) must be resolved."""
- arglist = defs.keys()
+ arglist = list(defs.keys())
if hasattr(self, 'signature'):
if not alltrue([s in arglist for s in self.signature]):
raise ValueError("All function signature arguments are "
@@ -2436,7 +2436,7 @@
assert self.spec.specType in specTypes, "specType invalid"
bad_tls = remain(self.targetLangs, targetLangs)
if len(bad_tls)>0:
- print "Invalid target languages:", bad_tls
+ print("Invalid target languages:", bad_tls)
raise ValueError("Invalid target language specified")
if self.typestr != 'var' and self.specType != 'ExpFuncSpec':
raise TypeError("Invalid spec type specified for %s"%className(self))
@@ -2448,11 +2448,11 @@
self.validate()
if not self.spec.isDefined(verbose) and self.typestr != 'par':
if verbose:
- print "'%s' ill defined: bound spec string is required"%self.name
+ print("'%s' ill defined: bound spec string is required"%self.name)
return False
if len(self.compatibleGens) == 0:
if verbose:
- print "'%s' ill defined: compatibleGens is empty"%self.name
+ print("'%s' ill defined: compatibleGens is empty"%self.name)
return False
return True
@@ -2481,7 +2481,7 @@
utils_info(self.__dict__, "ModelSpec " + self.name,
recurseDepthLimit=1+verboselevel)
else:
- print self.__repr__()
+ print(self.__repr__())
def __hash__(self):
h = (hash(type(self)), hash(self.name), hash(str(self.spec)),
@@ -2497,13 +2497,13 @@
results.extend([str(self.domain[i]) == str(other.domain[i]) \
for i in [0,1,2]])
results.append(self.spec == other.spec)
- except AttributeError, e:
+ except AttributeError as e:
if diff:
- print "Type:", className(self), results
- print " " + e
+ print("Type:", className(self), results)
+ print(" " + e)
return False
if diff:
- print "Type:", className(self), results
+ print("Type:", className(self), results)
return alltrue(results)
def __ne__(self, other):
@@ -2587,7 +2587,7 @@
for name in isection:
# dummy arg name
newname = "__"+name+"__"
- while newname in argNameMapInv.keys() + \
+ while newname in list(argNameMapInv.keys()) + \
self.signature+self.freeSymbols:
# ensure unique name
newname += "_"
@@ -2599,14 +2599,14 @@
for name in isection:
# dummy arg name
newname = "__"+name+"__"
- while newname in argNameMapInv.keys() + \
+ while newname in list(argNameMapInv.keys()) + \
self.signature+self.freeSymbols:
# ensure unique name
newname += "_"
argNameMapInv[newname] = name
qtemp.mapNames({name:newname})
args[i] = str(qtemp)
- res = self.spec._eval(1, **dict(zip(self.signature,args)))
+ res = self.spec._eval(1, **dict(list(zip(self.signature,args))))
res.mapNames(argNameMapInv)
return res
@@ -2622,7 +2622,7 @@
# references to builtin aux functions or macros require RefactoringTool: No changes to ./PyDSTool/Redirector.py
RefactoringTool: Refactored ./PyDSTool/PyCont/misc.py
temp defs of those
# as Fun objects
local_fndef = {}
-for fname in builtinFnSigInfo.keys():
+for fname in list(builtinFnSigInfo.keys()):
# function will not have to return anything in order to be eval'd
# but need a return value. we use '0'.
# final underscore is to avoid name clash with actual Python names
@@ -2741,7 +2741,7 @@
ostr = "[" + ",".join([str(Diff(o,a)) for o in t]) + "]"
return QuantSpec("__result__", ostr)
else:
- print "Found:", t, "type (%s)"%type(t)
+ print("Found:", t, "type (%s)"%type(t))
raise TypeError("Invalid type for t")
# deal with a -----------------------------------------
if compareClassAndBases(a, qtypes):
@@ -2752,7 +2752,7 @@
elif isinstance(a, str):
a_arg = a
else:
- print "Found:", a, "type (%s)"%type(a)
+ print("Found:", a, "type (%s)"%type(a))
raise TypeError("Invalid type for a")
# if didn't already recurse then fully reduced to strings
# ... attempt to simplify string using eval() method call
@@ -2762,7 +2762,7 @@
res.simplify()
return res
except:
- print "Tried to diff '%s' w.r.t. '%s'"%(t_arg,a_arg)
+ print("Tried to diff '%s' w.r.t. '%s'"%(t_arg,a_arg))
raise
@@ -2814,8 +2814,7 @@
return simplify(string2ast(o))
if t[0]=='term':
ttemp = ensureparen_div(t)
- lft,dlft,rt,drt=map(lambda x: ast2string(simplify(x)),
- getlftrtD(ttemp,a))
+ lft,dlft,rt,drt=[ast2string(simplify(x)) for x in getlftrtD(ttemp,a)]
if ttemp[2][0]=='STAR':
return simplify(string2ast(doadd(domul(dlft,rt),domul(lft,drt))))
if ttemp[2][0]=='SLASH':
@@ -2852,8 +2851,7 @@
ts.append(o)
dts.append(DiffStr(o,a))
if t[2][0]=='DOUBLESTAR':
- st,lft,dlft,rt,drt=map(lambda x: ast2string(simplify(x)),
- [t,ts[0],dts[0],ts[1],dts[1]])
+ st,lft,dlft,rt,drt=[ast2string(simplify(x)) for x in [t,ts[0],dts[0],ts[1],dts[1]]]
rt1=trysimple('%s-1'%rt)
if drt=='0':
return toPowSyntax(string2ast(domul(domul(rt,dlft),dopower(lft,rt1))))
@@ -2876,7 +2874,7 @@
ll=splitargs(ast2string(DiffStr(aa,a)))
ii=0;o='0'
for i in ll:
- o=doadd(o,domul(i,dofun(t[0][1]+'_'+`ii`,ast2string(aa))))
+ o=doadd(o,domul(i,dofun(t[0][1]+'_'+repr(ii),ast2string(aa))))
ii=ii+1
return simplify(string2ast(o))
return t
--- ./PyDSTool/PyCont/misc.py (original)
+++ ./PyDSTool/PyCont/misc.py (refactored)
@@ -75,11 +75,11 @@
in 'x' if num < 0.
"""
if num is None:
- ind = range(len(x)-1)
+ ind = list(range(len(x)-1))
elif num > 1:
- ind = range(num-1)
+ ind = list(range(num-1))
elif num < -1:
- ind = range(num, -1)
+ ind = list(range(num, -1))
else:
raise 'Number of indices must be larger than 1.'
@@ -93,7 +93,7 @@
def todict(C, X):
# Variables
- VARS = dict(zip(C.varslist,array(X)[C.coords]))
+ VARS = dict(list(zip(C.varslist,array(X)[C.coords])))
# Free parameters
for i, par in enumerate(C.freepars):
@@ -195,12 +195,12 @@
def testindij(n):
bn = n*(n-1)/2
- print "Testing %d..." % n
+ print("Testing %d..." % n)
for ind in range(bn):
i, j = indtoij(ind)
ind2 = ijtoind(i, j)
if ind != ind2:
- print "DAMNIT!\n"
+ print("DAMNIT!\n")
#print " %d ---> (%d,%d) ---> %d" % (ind,i,j,ind2)
def wedge(u, v):
@@ -282,12 +282,12 @@
p = direc*p
if check:
- print 'Checking...'
- print ' |q| = %f' % linalg.norm(q)
+ print('Checking...')
+ print(' |q| = %f' % linalg.norm(q))
temp = matrixmultiply(conjugate(p),q)
- print ' |<p,q> - 1| = ', abs(temp-1)
- print ' |Aq - iwq| = %f' % linalg.norm(matrixmultiply(J_coords,q) - 1j*w*q)
- RefactoringTool: No changes to ./PyDSTool/PyCont/auto/dev/setup.py
RefactoringTool: Refactored ./PyDSTool/PyCont/__init__.py
RefactoringTool: Refactored ./PyDSTool/PyCont/TestFunc.py
print ' |A*p + iwp| = %f\n' % linalg.norm(matrixmultiply(transpose(J_coords),p) + 1j*w*p)
+ print(' |<p,q> - 1| = ', abs(temp-1))
+ print(' |Aq - iwq| = %f' % linalg.norm(matrixmultiply(J_coords,q) - 1j*w*q))
+ print(' |A*p + iwp| = %f\n' % linalg.norm(matrixmultiply(transpose(J_coords),p) + 1j*w*p))
# Compute first lyapunov coefficient
B = F.hess(X, F.coords, F.coords)
@@ -365,7 +365,7 @@
except TypeError:
del u # move on to the next method
else:
- return u.keys()
+ return list(u.keys())
# We can't hash all the elements. Second fastest is to sort,
# which brings the equal elements together; then duplicates are
@@ -433,7 +433,7 @@
def negate(x):
if isinstance(x, dict):
- for k, v in x.iteritems():
+ for k, v in x.items():
x[k] = -1*v
elif isinstance(x, Point):
for i in range(len(x)):
@@ -445,7 +445,7 @@
elif isinstance(x, ndarray):
x = -1*x
elif isinstance(x, args):
- for k, v in x.iteritems():
+ for k, v in x.items():
x[k] = negate(x[k])
else:
raise TypeError("Invalid argument type given")
@@ -462,15 +462,15 @@
J = linalg.solve(jac1, jac0)
if verbose:
- print "Jacobian J*x"
- print "------------\n"
- print J
- print "\n"
-
- print "Check Jacobian"
- print "--------------\n"
- print " eigs = ", linalg.eig(J)[0]
- print " eigs = ", pt.labels['LC']['data'].evals
+ print("Jacobian J*x")
+ print("------------\n")
+ print(J)
+ print("\n")
+
+ print("Check Jacobian")
+ print("--------------\n")
+ print(" eigs = ", linalg.eig(J)[0])
+ print(" eigs = ", pt.labels['LC']['data'].evals)
return J
@@ -514,10 +514,10 @@
evals.append(w)
levecs.append(vl)
revecs.append(vr) # unused unless verbose (for debugging)
- idxs = range(ntst)
+ idxs = list(range(ntst))
if verbose:
- print "Eigenvalues:", [evals[i] for i in idxs]
+ print("Eigenvalues:", [evals[i] for i in idxs])
check1 = linalg.norm(matrixmultiply(maps[i], revecs[i][:,ind]) - \
evals[i][ind]*revecs[i][:,ind])
check2 = linalg.norm(matrixmultiply(transpose(levecs[i][:,ind]),
--- ./PyDSTool/PyCont/__init__.py (original)
+++ ./PyDSTool/PyCont/__init__.py (refactored)
@@ -1 +1 @@
-from ContClass import ContClass
+from .ContClass import ContClass
--- ./PyDSTool/PyCont/TestFunc.py (original)
+++ ./PyDSTool/PyCont/TestFunc.py (refactored)
@@ -19,7 +19,7 @@
#
# ----------------------------------------------------------------------------
-from misc import *
+from .misc import *
from PyDSTool.common import args, copy
from scipy import optimize, linalg
@@ -48,7 +48,8 @@
the function as acting on a 1 dimensional array, i.e. reference x[0] NOT x. This is so numjac works
without having to test cases (most generality)."""
- def __init__(self, (n, m), func=None, save=False, numpoints=None):
+ def __init__(self, xxx_todo_changeme, func=None, save=False, numpoints=None):
+ (n, m) = xxx_todo_changeme
if not hasattr(self, 'data'):
self.data = None
@@ -89,7 +90,7 @@
n = len(ind)
except:
n = self.n
- ind = range(n)
+ ind = list(range(n))
J = zeros((self.m, n), float)
for i in range(n):
@@ -110,13 +111,13 @@
n1 = len(ind1)
except:
n1 = self.n
- ind1 = range(n1)
+ ind1 = list(range(n1))
try:
n2 = len(ind2)
except:
n2 = self.n
- ind2 = range(n2)
+ ind2 = list(range(n2))
H = zeros((self.m,n1,n2), float)
for i in range(n1):
@@ -136,7 +137,8 @@
class TestFunc(Function):
"""You need to define the function yourself within an inherited class."""
- def __init__(self, (n, m), F, C, save=False, numpoints=None):
+ def __init__(self, xxx_todo_changeme1, F, C, save=False, numpoints=None):
+ (n, m) = xxx_todo_changeme1
Function.__init__(self, (n, m), func=None, save=save, numpoints=numpoints)
if not hasattr(self, "F"):
@@ -189,7 +191,7 @@
T1 = T
if self.C.verbosity >= 2 and i == self.C.MaxTestIters-1:
- print 'Maximum test function iterations reached.\n'
+ print('Maximum test function iterations reached.\n')
return X, V
@@ -202,7 +204,7 @@
n = len(ind)
except:
n = self.n
- ind = range(n)
+ ind = list(range(n))
J = zeros((self.m, n), float)
for i in range(n):
@@ -259,13 +261,14 @@
"""
- def __init__(self, (a,b), (n,m), F, C, r=1, update=False, corr=False, save=False, numpoints=None):
+ def __init__(self, xxx_todo_changeme2, xxx_todo_changeme3, F, C, r=1, update=False, corr=False, save=False, numpoints=None):
"""F: R^a --> R^b
Note: I did not assign b automatically (although I could - it would just be b = p*q) since
you may not want to use all of the entries of S. Some bordering methods are not
minimally augmented systems and thus only require certain entries of S."""
-
+ (a,b) = xxx_todo_changeme2
+ (n,m) = xxx_todo_changeme3
TestFunc.__init__(self, (a,b), F, C, save=save, numpoints=numpoints)
self.update = update
@@ -312,7 +315,7 @@
B = BC[:,0:self.data.p]
except:
if self.C.verbosity >= 1:
- print 'Warning: Problem updating border vectors. Using svd...'
+ print('Warning: Problem updating border vectors. Using svd...')
U, S, Vh = linalg.svd(A)
B = U[:,-1*self.data.p:]
C = transpose(Vh)[:,-1*self.data.q:]
@@ -346,7 +349,8 @@
return V, W
class BiAltMethod(TestFunc):
- def __init__(self, (n,m), F, C, save=False, numpoints=None):
+ def __init__(self, xxx_todo_changeme4, F, C, save=False, numpoints=None):
+ (n,m) = xxx_todo_changeme4
TestFunc.__init__(self, (n,m), F, C, save=save, numpoints=numpoints)
if self.data is None:
@@ -446,7 +450,7 @@
n = len(ind)
except:
n = self.n
- ind = range(n)
+ ind = list(range(n))
F_n = zeros((self.period, self.n), float)
F_n[0] = X
@@ -478,7 +482,7 @@
n = len(ind)
except:
n = self.n
- ind = range(n)
+ ind = list(range(n))
return self.F.jac(X, ind) - eye(self.F.m, self.F.n)[:,ind[0]:ind[-1]+1]
@@ -497,7 +501,7 @@
upper = {}
for par in C.freepars:
if C.curvetype == 'UD-C':
- if hasattr(C, '_userdomain') and par in C._userdomain.keys():
+ if hasattr(C, '_userdomain') and par in list(C._userdomain.keys()):
domain = C._userdomain[par]
else:
domain = [-1*Inf, Inf]
@@ -508,7 +512,7 @@
for par in C.varslist:
if C.curvetype == 'UD-C':
- if hasattr(C, '_userdomain') and par in C._userdomain.keys():
+ if hasattr(C, '_userdomain') and par in list(C._userdomain.keys()):
domain = C._userdomain[par]
else:
domain = [-1*Inf, Inf]
@@ -585,7 +589,7 @@
n = len(ind)
except:
n = self.n
- ind = range(n)
+ ind = list(range(n))
V, W = self.getVW(self.F.jac(X, self.F.coords))
H = self.F.hess(X, self.F.coords, ind)
@@ -621,7 +625,7 @@
n = len(ind)
except:
n = self.n
- ind = range(n)
+ ind = list(range(n))
self.bialtprodeye(2*self.F.jac(X, self.F.coords))
V, W = self.getVW(self.data.P)
@@ -690,7 +694,7 RefactoringTool: Refactored ./PyDSTool/PyCont/Plotting.py
@@
B = BC[:,:1]
except:
if self.C.verbosity >= 1:
- print 'Warning: Problem updating border vectors. Using svd...'
+ print('Warning: Problem updating border vectors. Using svd...')
U, S, Vh = linalg.svd(A)
B = U[:,-1:]
C = transpose(Vh)[:,-1:]
@@ -880,7 +884,8 @@
# Test function for UserDefinedCurve
class UserDefinedTestFunc(TestFunc):
- def __init__(self, (n, m), C, tfunc, save=False, numpoints=None):
+ def __init__(self, xxx_todo_changeme5, C, tfunc, save=False, numpoints=None):
+ (n, m) = xxx_todo_changeme5
TestFunc.__init__(self, (n, m), C.sysfunc, C, save=save, numpoints=numpoints)
self.tfunc = tfunc
--- ./PyDSTool/PyCont/Plotting.py (original)
+++ ./PyDSTool/PyCont/Plotting.py (refactored)
@@ -5,6 +5,7 @@
from PyDSTool.common import args
from PyDSTool.matplotlib_import import *
+from functools import reduce
# THESE ARE REPEATS FROM CONTINUATION! MAKE SURE AND UPDATE!!!
all_point_types = ['P', 'RG', 'LP', 'BP', 'H', 'BT', 'ZH', 'CP', 'GH', 'DH', 'LPC', 'PD',
@@ -34,9 +35,9 @@
# This is so I can make things alphabetical
all_pargs = []
all_args = []
- deleted = self.has_key('deleted') and self.deleted
+ deleted = 'deleted' in self and self.deleted
if not deleted:
- for k, v in self.iteritems():
+ for k, v in self.items():
if k in ['point', 'curve', 'cycle']:
if v[0].get_label() != '_nolegend_':
all_args.append(('Legend', v[0].get_label()))
@@ -49,7 +50,7 @@
all_pargs.append((k, v))
if len(all_args) == 0 and len(all_pargs) == 0:
- if self.has_key('deleted'):
+ if 'deleted' in self:
res.append(ct*4*' ' + 'Deleted\n')
else:
res.append(ct*4*' ' + 'Empty\n')
@@ -73,11 +74,11 @@
def fromLabel(self, label, key=None):
point = None
- if self.has_key('text') and self.text.get_text().lstrip(' ') == label or \
- self.has_key('point') and self.point[0].get_label() == label or \
- self.has_key('curve') and self.curve[0].get_label() == label:
+ if 'text' in self and self.text.get_text().lstrip(' ') == label or \
+ 'point' in self and self.point[0].get_label() == label or \
+ 'curve' in self and self.curve[0].get_label() == label:
return (key, self)
- for k, v in self.iteritems():
+ for k, v in self.items():
if isinstance(v, pargs):
point = v.fromLabel(label, key=k)
if point is not None:
@@ -105,13 +106,13 @@
bytype = all_point_types
elif objtype == 'curve':
bytype = all_curve_types
- for k, v in self.iteritems():
+ for k, v in self.items():
if isinstance(v, pargs):
- if v.has_key(objtype):
- if bylabel is not None and v.has_key('text') and v.text.get_text().lstrip(' ') in bylabel or \
+ if objtype in v:
+ if bylabel is not None and 'text' in v and v.text.get_text().lstrip(' ') in bylabel or \
byname is not None and k in byname or \
bytype is not None and k.strip('0123456789') in bytype or \
- bylegend is not None and ((v.has_key('curve') and v.curve[0].get_label() in bylegend) or (v.has_key('cycle') and v.cycle[0].get_label() in bylegend)):
+ bylegend is not None and (('curve' in v and v.curve[0].get_label() in bylegend) or ('cycle' in v and v.cycle[0].get_label() in bylegend)):
obj.append((k,v[objtype]))
v.get(objtype, bylabel=bylabel, byname=byname, bytype=bytype, bylegend=bylegend, obj=obj, ct=ct)
@@ -119,7 +120,7 @@
return obj
def toggleLabel(self, visible='on', refresh=True):
- if self.has_key('text'):
+ if 'text' in self:
self.text.set_visible(visible == 'on')
if refresh:
@@ -136,10 +137,10 @@
if bylabel is None and byname is None and bytype is None:
bytype = all_point_types # Turn off all points
- for k, v in self.iteritems():
+ for k, v in self.items():
if bytype is not None and k.strip('0123456789') in bytype or \
byname is not None and k in byname or \
- bylabel is not None and isinstance(v, pargs) and v.has_key('text') and v.text.get_text().lstrip(' ') in bylabel:
+ bylabel is not None and isinstance(v, pargs) and 'text' in v and v.text.get_text().lstrip(' ') in bylabel:
v.toggleLabel(visible=visible, refresh=False)
elif isinstance(v, pargs):
v.toggleLabels(visible=visible, bylabel=bylabel, byname=byname, bytype=bytype, ct=ct)
@@ -148,7 +149,7 @@
self.refresh()
def togglePoint(self, visible='on', refresh=True):
- if self.has_key('point'):
+ if 'point' in self:
self.point[0].set_visible(visible == 'on')
if refresh:
@@ -165,10 +166,10 @@
if bylabel is None and byname is None and bytype is None:
bytype = all_point_types # Turn off all points
- for k, v in self.iteritems():
+ for k, v in self.items():
if bytype is not None and k.strip('0123456789') in bytype or \
byname is not None and k in byname or \
- bylabel is not None and isinstance(v, pargs) and v.has_key('text') and v.text.get_text().lstrip(' ') in bylabel:
+ bylabel is not None and isinstance(v, pargs) and 'text' in v and v.text.get_text().lstrip(' ') in bylabel:
v.togglePoint(visible=visible, refresh=False)
elif isinstance(v, pargs):
v.togglePoints(visible=visible, bylabel=bylabel, byname=byname, bytype=bytype, ct=ct)
@@ -177,8 +178,8 @@
self.refresh()
def toggleCurve(self, visible='on', refresh=True):
- if self.has_key('curve'):
- for k, v in self.iteritems():
+ if 'curve' in self:
+ for k, v in self.items():
if isinstance(v, pargs):
v.toggleLabel(visible=visible, refresh=False)
v.togglePoint(visible=visible, refresh=False)
@@ -199,10 +200,10 @@
if bylegend is None and byname is None and bytype is None:
bytype = all_curve_types
- for k, v in self.iteritems():
- if bytype is not None and isinstance(v, pargs) and v.has_key('type') and v.type in bytype or \
+ for k, v in self.items():
+ if bytype is not None and isinstance(v, pargs) and 'type' in v and v.type in bytype or \
byname is not None and k in byname or \
- bylegend is not None and isinstance(v, pargs) and v.has_key('curve') and v.curve[0].get_label() in bylegend:
+ bylegend is not None and isinstance(v, pargs) and 'curve' in v and v.curve[0].get_label() in bylegend:
v.toggleCurve(visible=visible, refresh=False)
elif isinstance(v, pargs):
v.toggleCurves(visible=visible, bylegend=bylegend, byname=byname, bytype=bytype, ct=ct)
@@ -211,7 +212,7 @@
self.refresh()
def toggleCycle(self, visible='on', refresh=True):
- if self.has_key('cycle'):
+ if 'cycle' in self:
for line in self.cycle:
line.set_visible(visible == 'on')
@@ -229,10 +230,10 @@
if bylegend is None and byname is None and bytype is None:
bytype = all_point_types
- for k, v in self.iteritems():
+ for k, v in self.items():
if bytype is not None and k.strip('0123456789') in bytype or \
byname is not None and k in byname or \
- bylegend is not None and isinstance(v, pargs) and v.has_key('cycle') and v.cycle[0].get_label() in bylegend:
+ bylegend is not None and isinstance(v, pargs) and 'cycle' in v and v.cycle[0].get_label() in bylegend:
v.toggleCycle(visible=visible, refresh=False)
elif isinstance(v, pargs):
v.toggleCycles(visible=visible, bylegend=bylegend, byname=byname, bytype=bytype, ct=ct)
@@ -251,10 +252,10 @@
if bylabel is None and byname is None and bytype is None:
bytype = all_point_types
- for k, v in self.iteritems():
+ for k, v in self.items():
if bytype is not None and k.strip('0123456789') in bytype or \
byname is not None and k in byname or \
- bylabel is not None and isinstance(v, pargs) and ((v.has_key('text') and v.text.get_text().lstrip(' ') in bylabel) or (v.has_key('curve') and v.curve[0].get_label() in bylabel) or (v.has_key('cycle') and v.cycle[0].get_label() in bylabel)):
+ bylabel is not None and isinstance(v, pargs) and (('text' in v and v.text.get_text().lstrip(' ') in bylabel) or ('curve' in v and v.curve[0].get_label() in bylabel) or ('cycle' in v and v.cycle[0].get_label() in bylabel)):
v.toggleLabel(visible=visible, refresh=False)
v.togglePoint(visible=visible, refresh=False)
v.toggleCycle(visible=visible, refresh=False)
@@ -265,7 +266,7 @@
self.refresh()
def setLabel(self, label, refresh=True):
- if self.has_key('text'):
+ if 'text' in self:
self.text.set_text(' '+label)
if refresh:
@@ -282,10 +283,10 @@
if bylabel is None and byname is None and bytype is None:
bytype = all_point_types # Turn off all points
- for k, v in self.iteritems():
+ for k, v in self.items():
if bytype is not None and k.strip('0123456789') in bytype or \
byname is not None and k in byname or \
- bylabel is not None and isinstance(v, pargs) and v.has_key('text') and v.text.get_text().lstrip(' ') in bylabel:
+ bylabel is not None and isinstance(v, pargs) and 'text' in v and v.text.get_text().lstrip(' ') in bylabel:
v.setLabel(label, refresh=False)
elif isinstance(v, pargs):
v.setLabels(label, bylabel=bylabel, byname=byname, bytype=bytype, ct=ct)
@@ -294,10 +295,10 @@
self.refresh()
def setLegend(self, legend, refresh=True):
- if self.has_key('curve'):
+ if 'curve' in self:
for piece in self.curve:
piece.set_label(legend)
- elif self.has_key('cycle'):
+ elif 'cycle' in self:
for piece in self.cycle:
piece.set_label(legend)
@@ -314,14 +315,14 @@
bytype = [bytype]
if bylegend is None and byname is None and bytype is None:
- if v.has_key('curve'):
+ if 'curve' in v:
bytype = all_curve_types
else:
bytype = all_point_types # Turn off all points
- for k, v in self.iteritems():
- if bytype is not None and isinstance(v, pargs) and ((v.has_key('curve') and v.type in bytype) or (v.has_key('cycle') and k.strip('0123456789') in bytype)) or \
+ for k, v in self.items():
+ if bytype is not None and isinstance(v, pargs) and (('curve' in v and v.type in bytype) or ('cycle' in v and k.strip('0123456789') in bytype)) or \
byname is not None and k in byname or \
- bylegend is not None and isinstance(v, pargs) and ((v.has_key('curve') and v.curve[0].get_label() in bylegend) or (v.has_key('cycle') and v.cycle[0].get_label() in bylegend)):
+ bylegend is not None and isinstance(v, pargs) and (('curve' in v and v.curve[0].get_label() in bylegend) or ('cycle' in v and v.cycle[0].get_label() in bylegend)):
v.setLegend(legend, refresh=False)
elif isinstance(v, pargs):
v.setLegends(legend, bylegend=bylegend, byname=byname, bytype=bytype, ct=ct)
@@ -332,26 +333,26 @@
def refresh(self):
fig = None # Used to save current figure (reset when done)
- if not self.has_key('deleted'):
- if 'fig' in self.keys():
+ if 'deleted' not in self:
+ if 'fig' in list(self.keys()):
plt.figure(self.fig.number)
plt.draw()
- elif 'axes' in self.keys():
+ elif 'axes' in list(self.keys()):
plt.figure(self.axes.figure.number)
#Would like to say: plt.axes(self.axes) Doesn't work, though.
plt.draw()
- elif 'curve' in self.keys():
+ elif 'curve' in list(self.keys()):
plt.figure(self.curve[0].figure.number)
plt.draw()
- elif 'point' in self.keys():
+ elif 'point' in list(self.keys()):
plt.figure(self.point[0].figure.number)
plt.draw()
- elif 'cycle' in self.keys():
+ elif 'cycle' in list(self.keys()):
plt.figure(self.cycle[0].figure.number)
plt.draw()
else: # Only here in plot structure
fig = plt.gcf()
- for k, v in self.iteritems():
+ for k, v in self.items():
if isinstance(v, pargs):
v.refresh()
@@ -363,19 +364,19 @@
if they've been deleted by an outside source. This method is a little clumsy since
it has to spawn a dummy plot if a plot has been deleted, but who cares, it works."""
deleted = []
- for k, v in self.iteritems():
+ for k, v in self.items():
recursive_clean = True
if isinstance(v, pargs):
- if v.has_key('deleted'):
+ if 'deleted' in v:
deleted.append(k)
recursive_clean = False
- elif v.has_key('fig'):
+ elif 'fig' in v:
fig_check = plt.figure(v.fig.number)
if fig_check != v.fig:
plt.close(fig_check)
deleted.append(k)
recursive_clean = False
- elif v.has_key('axes'):
+ elif 'axes' in v:
try:
fig_axes = plt.axes(v.axes)
except:
@@ -385,24 +386,24 @@
deleted.append(k)
recursive_clean = False
elif fig_axes not in v.axes.figure.axes:
- print 'Warning: Axes were deleted without using plt.delaxes().'
+ print('Warning: Axes were deleted without using plt.delaxes().')
v.axes.figure.axes.append(fig_axes)
plt.draw()
- elif v.has_key('curve'):
+ elif 'curve' in v:
for piece in v.curve:
if piece not in piece.axes.lines:
deleted.append(k)
v.delete() # Remove remaining pieces of curve in pyplot
recursive_clean = False
break
- elif v.has_key('cycle'):
+ elif 'cycle' in v:
for piece in v.cycle:
if piece not in piece.axes.lines:
deleted.append(k)
v.delete()
recursive_clean = False
break
- elif v.has_key('point'):
+ elif 'point' in v:
if v.point[0] not in v.point[0].axes.lines or v.text not in v.text.axes.texts:
deleted.append(k)
if v.text in v.text.axes.texts:
@@ -418,32 +419,32 @@
self.pop(k)
def clear(self, refresh=True):
- if not self.has_key('deleted'):
- if self.has_key('fig'):
+ if 'deleted' not in self:
+ if 'fig' in self:
plt.figure(self.fig.number)
plt.clf()
- remove = [k for k in self.keys() if k != 'fig']
- elif self.has_key('axes'):
+ remove = [k for k in list(self.keys()) if k != 'fig']
+ elif 'axes' in self:
title = self.axes.title.get_text()
self.axes.clear()
plt.axes(self.axes)
plt.title(title)
- remove = [k for k in self.keys() if k != 'axes']
+ remove = [k for k in list(self.keys()) if k != 'axes']
if refresh:
self.refresh()
- elif self.has_key('curve'):
- remove = [k for k in self.keys() if k != 'curve']
+ elif 'curve' in self:
+ remove = [k for k in list(self.keys()) if k != 'curve']
for k in remove:
if isinstance(self[k], pargs):
self[k].clear(refresh=False)
if refresh:
self.refresh()
- elif self.has_key('point'):
+ elif 'point' in self:
if self.point[0] in self.point[0].axes.lines:
self.point[0].axes.lines.remove(self.point[0])
if self.text in self.point[0].axes.texts:
self.point[0].axes.texts.remove(self.text)
- remove = [k for k in self.keys() if k != 'point']
+ remove = [k for k in list(self.keys()) if k != 'point']
if refresh:
self.refresh()
self.deleted = True
@@ -454,25 +455,25 @@
for k in remove:
self.pop(k)
else:
- print 'Object is deleted.'
+ print('Object is deleted.')
def clearall(self):
- for v in self.itervalues():
+ for v in self.values():
if isinstance(v, pargs):
v.clear(refresh=False)
self.refresh()
def delete(self, refresh=True):
- if not self.has_key('deleted'):
- if self.has_key('fig'):
+ if 'deleted' not in self:
+ if 'fig' in self:
self.clear(refresh=False)
plt.close()
self.deleted = True
- elif self.has_key('axes'):
+ elif 'axes' in self:
self.clear(refresh=False)
plt.delaxes()
self.deleted = True
- elif self.has_key('curve'):
+ elif 'curve' in self:
self.clear(refresh=False)
for curve in self.curve:
if curve in self.curve[0].axes.lines:
@@ -480,7 +481,7 @@
if refresh:
self.refresh()
self.deleted = True
- elif self.has_key('cycle'):
+ elif 'cycle' in self:
self.clear(refresh=False)
for cycle in self.cycle:
if cycle in self.cycle[0].axes.lines:
@@ -488,17 +489,17 @@
if refresh:
self.refresh()
self.deleted = True
- elif self.has_key('point'):
+ elif 'point' in self:
self.clear(refresh=refresh)
else:
- for v in self.itervalues():
+ for v in self.values():
if isinstance(v, pargs):
v.delete(refresh=refresh)
else:
- print 'Object is already deleted.'
+ print('Object is already deleted.')
def deleteall(self):
- for v in self.itervalues():
+ for v in self.values():
if isinstance(v, pargs):
v.delete(refresh=False)
self.refresh()
@@ -510,7 +511,7 @@
self.axes = paxes.axes
# Get list of cycles from pargs class axes
- cycles = [thing.cycle[0] for k, thing in paxes.iteritems() if isinstance(thing, pargs) and thing.has_key('cycle')]
+ cycles = [thing.cycle[0] for k, tRefactoringTool: Refactored ./PyDSTool/PyCont/Continuation.py
hing in paxes.items() if isinstance(thing, pargs) and 'cycle' in thing]
# Put in order as in axes.lines (this should be same as order along curve, or user
# specified in cycles when plot_cycles was called)
self.cycles = []
@@ -552,7 +553,7 @@
line.set(linewidth=self.bgd_lw)
plt.draw()
- print 'Background linewidth = %f' % self.bgd_lw
+ print('Background linewidth = %f' % self.bgd_lw)
def change_fgd(self, up):
if up == 1:
@@ -566,7 +567,7 @@
self.cycles[self.curr].set(linewidth=self.fgd_lw)
plt.draw()
- print 'Foreground linewidth = %f' % self.fgd_lw
+ print('Foreground linewidth = %f' % self.fgd_lw)
def change_curr(self, up):
self.cycles[self.curr].set(linewidth=self.bgd_lw)
@@ -596,7 +597,7 @@
cfl = None
if isinstance(figure, plt.Figure):
- for k, v in plot.iteritems():
+ for k, v in plot.items():
if isinstance(v, pargs) and v.fig == figure:
cfl = k
break
@@ -605,13 +606,13 @@
figure = plt.figure()
else:
cfl = figure
- if cfl not in plot.keys():
+ if cfl not in list(plot.keys()):
plot[cfl] = pargs()
plot[cfl].fig = plt.figure()
elif isinstance(figure, int):
fighandle = plt.figure(figure)
cfl = 'fig' + str(figure)
- if cfl not in plot.keys():
+ if cfl not in list(plot.keys()):
plot[cfl] = pargs()
plot[cfl].fig = fighandle
else:
@@ -620,7 +621,7 @@
if cfl is None:
cfl = 'fig1'
ct = 1
- while cfl in plot.keys():
+ while cfl in list(plot.keys()):
ct += 1
cfl = 'fig'+repr(ct)
plot[cfl] = pargs()
@@ -642,7 +643,7 @@
cal = None
if isinstance(axes, plt.Axes):
- for k, v in plot[cfl].iteritems():
+ for k, v in plot[cfl].items():
if isinstance(v, pargs) and v.axes == axes:
cal = k
break
@@ -650,7 +651,7 @@
if cal is None:
cal = 'axes1'
ct = 1
- while cal in plot[cfl].keys():
+ while cal in list(plot[cfl].keys()):
ct += 1
cal = 'axes'+repr(ct)
plot[cfl][cal] = pargs()
@@ -658,7 +659,7 @@
plot[cfl][cal].axes.set_title(cal)
elif isinstance(axes, str):
cal = axes
- if cal not in plot[cfl].keys():
+ if cal not in list(plot[cfl].keys()):
plot[cfl][cal] = pargs()
plot[cfl][cal].axes = plt.axes()
plot[cfl][cal].axes.set_title(cal)
--- ./PyDSTool/PyCont/Continuation.py (original)
+++ ./PyDSTool/PyCont/Continuation.py (refactored)
@@ -9,10 +9,10 @@
# -----------------------------------------------------------------------------------------
-from misc import *
-from TestFunc import *
-from BifPoint import *
-from Plotting import *
+from .misc import *
+from .TestFunc import *
+from .BifPoint import *
+from .Plotting import *
from PyDSTool import Point, Pointset, PointInfo, args
from PyDSTool.common import pickle, sortedDictValues, sortedDictKeys
@@ -22,8 +22,8 @@
from PyDSTool.matplotlib_import import *
except ImportError:
from PyDSTool.matplotlib_unavailable import *
- print "Warning: matplotlib failed to import properly and so is not"
- print " providing a graphing interface"
+ print("Warning: matplotlib failed to import properly and so is not")
+ print(" providing a graphing interface")
from numpy.random import random
from numpy import dot as matrixmultiply
@@ -88,7 +88,7 @@
6: 'BP', 7: 'PD', 8: 'NS', 9: 'P', -9: 'MX'}
solution_measures_list = ['max', 'min', 'avg', 'nm2'] # Ordering is important
-solution_measures = dict(zip(solution_measures_list,[0, 0, 1, 2]))
+solution_measures = dict(list(zip(solution_measures_list,[0, 0, 1, 2])))
all_args_list = unique(cont_args_list + equilibrium_args_list + fold_args_list +
hopf_args_list + fixedpoint_args_list +
@@ -179,14 +179,14 @@
else:
if len(self.freepars) == Jquant0.dim:
# Supplied Jac w.r.t. params is custom-made for only the free params in this continuation
- self.parsindices = arange(range(Jquant0.dim))
+ self.parsindices = arange(list(range(Jquant0.dim)))
else:
# Assume supplied Jac w.r.t. params is for all params in the original system
# therefore there should be fewer free params than # system parameters
assert len(self.freepars) < Jquant0.dim
- self.parsindices = array([self.parsdict.keys().index(p) for p in self.freepars])
+ self.parsindices = array([list(self.parsdict.keys()).index(p) for p in self.freepars])
else:
- self.parsindices = array([self.parsdict.keys().index(p) for p in self.freepars])
+ self.parsindices = array([list(self.parsdict.keys()).index(p) for p in self.freepars])
self.varsdim = len(self.varslist)
self.freeparsdim = len(self.freepars)
self.auxparsdim = len(self.auxpars)
@@ -223,7 +223,7 @@
# Initialize vars and pars based on initpoint
self.initpoint = self.model.query('ics')
- for k, v in args['initpoint'].iteritems():
+ for k, v in args['initpoint'].items():
if k in self.varslist or k in args['auxpars']:
self.initpoint[k] = v
elif k in self.model.query('pars'):
@@ -310,7 +310,7 @@
def update(self, args):
"""Update parameters for Continuation."""
if args is not None:
- for k, v in args.iteritems():
+ for k, v in args.items():
if k in cont_args_list:
if k == 'LocBifPoints':
if isinstance(v, str):
@@ -321,7 +321,7 @@
# Handle stopping points
w = []
- if args.has_key('StopAtPoints'):
+ if 'StopAtPoints' in args:
w = args['StopAtPoints']
if isinstance(w, str):
if w.lower() == 'all':
@@ -338,7 +338,7 @@
elif k != 'StopAtPoints':
exec('self.' + k + ' = ' + repr(v))
elif k not in all_args_list:
- print "Warning: " + k + " is either not a valid parameter or immutable."
+ print("Warning: " + k + " is either not a valid parameter or immutable.")
def _preTestFunc(self, X, V):
@@ -384,7 +384,7 @@
if self.SPOut is not None:
# add simple "user"-defined function to catch parameter values
# during continuation
- for par, par_vals in self.SPOut.items():
+ for par, par_vals in list(self.SPOut.items()):
try:
par_ix = self.params[self.freepars.index(par)]
except IndexError:
@@ -399,7 +399,7 @@
def _system(self, X):
- VARS = dict(zip(self.varslist, array(X)[self.coords]))
+ VARS = dict(list(zip(self.varslist, array(X)[self.coords])))
for i, par in enumerate(self.freepars):
self.parsdict[par] = X[self.params[i]]
try:
@@ -411,7 +411,7 @@
def _systemjac(self, x0, ind=None):
- VARS = dict(zip(self.varslist, array(x0)[self.coords]))
+ VARS = dict(list(zip(self.varslist, array(x0)[self.coords])))
for i, par in enumerate(self.freepars):
self.parsdict[par] = x0[self.params[i]]
try:
@@ -428,7 +428,7 @@
def _systemjac_withpars(self, x0, ind=None):
- VARS = dict(zip(self.varslist, array(x0)[self.coords]))
+ VARS = dict(list(zip(self.varslist, array(x0)[self.coords])))
for i, par in enumerate(self.freepars):
self.parsdict[par] = x0[self.params[i]]
try:
@@ -447,7 +447,7 @@
def _systemuser(self, X):
"""Calls self._userfunc, which is assumed to return an array of RHS
values for the relevant (possibly subset of) variables."""
- VARS = dict(zip(self.varslist, array(X)[self.coords]))
+ VARS = dict(list(zip(self.varslist, array(X)[self.coords])))
for i, par in enumerate(self.freepars):
self.parsdict[par] = X[self.params[i]]
return self._userfunc(self, VARS, self.parsdict)
@@ -456,7 +456,7 @@
def _systemjacuser(self, x0, ind=None):
"""Calls self._userjac, which is assumed to return an array of
[Jac_x, Jac_p]."""
- VARS = dict(zip(self.varslist, array(X)[self.coords]))
+ VARS = dict(list(zip(self.varslist, array(X)[self.coords])))
for i, par in enumerate(self.freepars):
self.parsdict[par] = X[self.params[i]]
return self._userjac(self, VARS, self.parsdict)
@@ -471,7 +471,7 @@
# store commonly referenced values for efficiency
V_loc = V[loc]
curve_loc = curve[loc]
- for bftype, bfinfo in self.BifPoints.iteritems():
+ for bftype, bfinfo in self.BifPoints.items():
flag_list = []
for i, testfunc in enumerate(bfinfo.testfuncs):
for k in range(testfunc.m):
@@ -605,11 +605,11 @@
X[n] = self.sol[coords[n]]
if origin is not None:
X[n] = X[n] - origin[coords[n]]
- elif coords[n] in self.parsdict.keys():
+ elif coords[n] in list(self.parsdict.keys()):
X[n] = array([self.parsdict[coords[n]]]*len(self.sol))
if origin is not None:
X[n] = X[n] - origin[coords[n]]
- elif dirs is not None and coords[n] in dirs.keys():
+ elif dirs is not None and coords[n] in list(dirs.keys()):
# Project curve onto plane spanned by coordinate directions
# spanning variables and free parameters
X[n] = array([matrixmultiply(x-aorigin, dirs[coords[n]]) \
@@ -628,7 +628,7 @@
name = self.name
if name in self.plot[cfl][cal]:
num = 0
- for k, v in self.plot[cfl][cal].iteritems():
+ for k, v in self.plot[cfl][cal].items():
if isinstance(v, pargs) and k.split('_')[0] == name:
num += 1
name = name + '_' + repr(num)
@@ -643,7 +643,7 @@
disp_args['label'] = '_nolegend_'
stabdict = partition([x.labels[label]['stab'] \
for x in self.sol],['S','U','N'])
- for stabtype, stablist in stabdict.iteritems():
+ for stabtype, stablist in stabdict.items():
for curve in stablist:
self.plot[cfl][cal][name].curve.extend(plt.plot(X[0][curve[0]:curve[1]], \
X[1][curve[0]:curve[1]], \
@@ -677,18 +677,18 @@
bflist = self.sol.bylabel(bftype)
if bflist is not None:
for point in bflist:
- if point.labels[bftype].has_key('name'):
+ if 'name' in point.labels[bftype]:
X = zeros(2, float)
for n in range(2):
if coords[n] in self.sol.coordnames:
X[n] = point[coords[n]]
if origin is not None:
X[n] = X[n] - origin[coords[n]]
- elif coords[n] in self.parsdict.keys():
+ elif coords[n] in list(self.parsdict.keys()):
X[n] = self.parsdict[coords[n]]
if origin is not None:
X[n] = X[n] - origin[coords[n]]
- elif dirs is not None and coords[n] in dirs.keys():
+ elif dirs is not None and coords[n] in list(dirs.keys()):
# Project point onto plane spanned by coordinate directions
# spanning variables and free parameters
X[n] = matrixmultiply(point-aorigin,
@@ -783,16 +783,16 @@
B = r_[A,[V]]
R = r_[matrixmultiply(A,V),0]
Q = r_[fun(X),0]
- if self.curvetype == 'UD-C' and self._userdata.has_key('problem') \
+ if self.curvetype == 'UD-C' and 'problem' in self._userdata \
and self._userdata.problem:
problem = 1
break
if self.verbosity >= 10:
- print " [%d]" % k
+ print(" [%d]" % k)
u, s, vh = linalg.svd(B)
cond = s[0]/s[-1]
diag.cond.append(cond)
- print " Log(Condition #) = %lf" % log10(cond)
+ print(" Log(Condition #) = %lf" % log10(cond))
WX = linalg.solve(B,mat([R,Q]).T)
subtract(V, WX[:,0], V)
divide(V, linalg.norm(V), V)
@@ -803,7 +803,7 @@
Vnrm = linalg.norm(WX[:,1])
converged = Fnrm < self.FuncTol and Vnrm < self.VarTol
if self.verbosity >= 10:
- print ' (Fnrm, Vnrm) = (%.12f,%.12f)' % (Fnrm, Vnrm)
+ print(' (Fnrm, Vnrm) = (%.12f,%.12f)' % (Fnrm, Vnrm))
x0 = x1
x1 = linalg.norm(X-Xold)
Xold = X.copy()
@@ -834,16 +834,16 @@
A = jac(X)
B = r_[A,[vi]]
Q = r_[fun(X), X[ind] - xi]
- if self.curvetype == 'UD-C' and self._userdata.has_key('problem') \
+ if self.curvetype == 'UD-C' and 'problem' in self._userdata \
and self._userdata.problem:
problem = 1
break
if self.verbosity >= 10:
- print " [%d]" % k
+ print(" [%d]" % k)
u, s, vh = linalg.svd(B)
cond = s[0]/s[-1]
diag.cond.append(cond)
- print " Log(Condition #) = %lf" % log10(cond)
+ print(" Log(Condition #) = %lf" % log10(cond))
W = linalg.solve(B, Q)
subtract(X, W, X)
@@ -852,7 +852,7 @@
Vnrm = linalg.norm(W)
converged = Fnrm < self.FuncTol and Vnrm < self.VarTol
if self.verbosity >= 10:
- print ' (Fnrm, Vnrm) = (%.12f,%.12f)' % (Fnrm, Vnrm)
+ print(' (Fnrm, Vnrm) = (%.12f,%.12f)' % (Fnrm, Vnrm))
x0 = x1
x1 = linalg.norm(X-Xold)
Xold = X.copy()
@@ -880,16 +880,16 @@
B = r_[A,[V]]
Q = r_[fun(X),
matrixmultiply(X-self.curve[self.loc-1],V)-self.StepSize]
- if self.curvetype == 'UD-C' and self._userdata.has_key('problem') \
+ if self.curvetype == 'UD-C' and 'problem' in self._userdata \
and self._userdata.problem:
problem = 1
break
if self.verbosity >= 10:
- print " [%d]" % k
+ print(" [%d]" % k)
u, s, vh = linalg.svd(B)
cond = s[0]/s[-1]
diag.cond.append(cond)
- print " Log(Condition #) = %lf" % log10(cond)
+ print(" Log(Condition #) = %lf" % log10(cond))
W = linalg.solve(B, Q)
subtract(X, W, X)
@@ -898,7 +898,7 @@
Vnrm = linalg.norm(W)
converged = Fnrm < self.FuncTol and Vnrm < self.VarTol
if self.verbosity >= 10:
- print ' (Fnrm, Vnrm) = (%.12f,%.12f)' % (Fnrm, Vnrm)
+ print(' (Fnrm, Vnrm) = (%.12f,%.12f)' % (Fnrm, Vnrm))
x0 = x1
x1 = linalg.norm(X-Xold)
Xold = X.copy()
@@ -942,7 +942,7 @@
elif isinstance(x0, Point):
x0 = x0.todict()
for p in self.freepars:
- if p not in x0.keys():
+ if p not in list(x0.keys()):
x0[p] = self.parsdict[p]
x0 = tocoords(self, x0)
@@ -1001,7 +1001,7 @@
k, converged, problem, diag = self.Corrector(curve[0], V[0])
except:
converged = False
- print "Error occurred in dynamical system computation"
+ print("Error occurred in dynamical system computation")
else:
val = linalg.norm(self.CorrFunc(curve[0]))
attempts += 1
@@ -1011,7 +1011,7 @@
# Initialize index location on curve data set
self.loc = 0
if self.verbosity >= 3:
- print ' Found initial point on curve.'
+ print(' Found initial point on curve.')
# Initialize test functions
self._createTestFuncs()
@@ -1040,12 +1040,12 @@
SSC_c, SSC_C = 0.8, 1.2
if self.verbosity >= 3:
- print ' Beginning continuation...'
+ print(' Beginning continuation...')
# Continuation loop
closed = False
stop = False
problem = False
- if self.curvetype == 'UD-C' and self._userdata.has_key('problem'):
+ if self.curvetype == 'UD-C' and 'problem' in self._userdata:
self._userdata.problem = False
# de-references to improve efficiency
@@ -1066,9 +1066,9 @@
# self._userdata.problem = False
# problem = False
if self.verbosity >= 10:
- print "Step #%d:" % loc
- print " Corrector steps: %d/%d" % (k, self.MaxCorrIters)
- print " Converged: %d" % (converged and not problem)
+ print("Step #%d:" % loc)
+ print(" Corrector steps: %d/%d" % (k, self.MaxCorrIters))
+ print(" Converged: %d" % (converged and not problem))
if problem:
stop = True
@@ -1077,11 +1077,11 @@
if self.StepSize > self.MinStepSize:
# Reduce stepsize and try again
if self.verbosity >= 3:
- print "Trouble converging. Reducing stepsize. (ds=%lf)" % self.StepSize
+ print("Trouble converging. Reducing stepsize. (ds=%lf)" % self.StepSize)
self.StepSize = max(self.MinStepSize, self.StepSize*SSC_c)
else:
# Stop continuation
- print "Did not converge. Stopping continuation. Reduce MinStepSize to continue."
+ print("Did not converge. Stopping continuation. Reduce MinStepSize to continue.")
raise PyDSTool_ExistError("Did not converge. Stopping continuation. Reduce MinStepSize to continue")
else:
# Increase stepsize for fast convergence
@@ -1120,8 +1120,8 @@
# Print information
if self.verbosity >= 4:
- print "Loc = %4d %s = %lf" % (loc, self.freepars[0],
- curve[loc][-1])
+ print("Loc = %4d %s = %lf" % (loc, self.freepars[0],
+ curve[loc][-1]))
# Save information
self._savePointInfo(loc)
@@ -1134,7 +1134,7 @@
# V[self.loc]), ds=self.StepSize)})
self.CurveInfo[loc] = ('MX', {'data': args(V = todict(self,
V[loc]), ds=self.StepSize)})
- elif not closed and not self.CurveInfo[loc].has_key('P'):
+ elif not closed and 'P' not in self.CurveInfo[loc]:
self.CurveInfo[loc] = ('P', {'data': args(V = todict(self,
V[loc])), 'plot': args()})
@@ -1160,7 +1160,7 @@
pt.labels[pttype]['name'] = pttype + repr(num)
else:
pt.labels[pttype] = {'name': pttype + repr(num)}
- if pt.labels[pttype].has_key('cycle'):
+ if 'cycle' in pt.labels[pttype]:
pt.labels[pttype]['cycle'].name = pttype + repr(num)
num += 1
self.new_sol_segment = copy(self.sol)
@@ -1182,7 +1182,7 @@
i -= 1
# Set start point (if bif point, set to startx)
- if sol1.labels[pt_type].has_key('startx'):
+ if 'startx' in sol1.labels[pt_type]:
x0 = sol1.labels[pt_type]['startx']
else:
x0 = sol1
@@ -1192,7 +1192,7 @@
except:
v0 = None
- if sol1.labels[self.curvetype.split('-')[0]]['data'].has_key('ds'):
+ if 'ds' in sol1.labels[self.curvetype.split('-')[0]]['data']:
self.StepSize = min(self.StepSize,
sol1.labels[self.curvetype.split('-')[0]]['data'].ds)
@@ -1222,7 +1222,7 @@
pt.labels[pttype]['name'] = pttype + repr(num)
else:
pt.labels[pttype] = {'name': pttype + repr(num)}
- if pt.labels[pttype].has_key('cycle'):
+ if 'cycle' in pt.labels[pttype]:
pt.labels[pttype]['cycle'].name = pttype + repr(num)
num += 1
@@ -1249,11 +1249,11 @@
sol0 = self.sol[0]
# Type of end point
- if sol0.labels.has_key('P'):
+ if 'P' in sol0.labels:
etype0 = 'P'
else:
etype0 = 'MX'
- if self.sol[-1].labels.has_key('P'):
+ if 'P' in self.sol[-1].labels:
etype1 = 'P'
else:
etype1 = 'MX'
@@ -1261,16 +1261,16 @@
# Turn tangent vectors around (for non auto only)
if not self.UseAuto:
# Turn tangent vectors at end point type around
- for k, v in sol0.labels[etype0]['data'].V.iteritems():
+ for k, v in sol0.labels[etype0]['data'].V.items():
sol0.labels[etype0]['data'].V[k] = -1*v
- for k, v in self.sol[-1].labels[etype1]['data'].V.iteritems():
+ for k, v in self.sol[-1].labels[etype1]['data'].V.items():
self.sol[-1].labels[etype1]['data'].V[k] = -1*v
# Turn tangent vectors at curve type around
ctype = self.curvetype.split('-')[0]
for pt in self.sol:
- for k, v in pt.labels[ctype]['data'].V.iteritems():
+ for k, v in pt.labels[ctype]['data'].V.items():
pt.labels[ctype]['data'].V[k] = -1*v
for pttype in self.LocBifPoints + other_special_points:
@@ -1282,14 +1282,14 @@
pt.labels[pttype]['name'] = pttype + repr(num)
else:
pt.labels[pttype] = {'name': pttype + repr(num)}
- if pt.labels[pttype].has_key('cycle'):
+ if 'cycle' in pt.labels[pttype]:
pt.labels[pttype]['cycle'].name = pttype + repr(num)
num += 1
self.new_sol_segment = copy(self.sol)
else:
sol0 = self.sol[0]
# Set start point (if bif point, set to startx)
- if sol0.labels['P'].has_key('startx'):
+ if 'startx' in sol0.labels['P']:
x0 = sol0.labels['P']['startx']
else:
x0 = sol0
@@ -1307,7 +1307,7 @@
# self.StepSize = self.sol[0].labels[ctype]['data'].ds
#except:
# pass
- if sol0.labels[self.curvetype.split('-')[0]]['data'].has_key('ds'):
+ if 'ds' in sol0.labels[self.curvetype.split('-')[0]]['data']:
self.StepSize = min(self.StepSize,
sol0.labels[self.curvetype.split('-')[0]]['data'].ds)
@@ -1319,24 +1319,24 @@
sol0 = sol[0]
# Type of end point
- etype = sol0.labels.has_key('P') and 'P' or 'MX'
+ etype = 'P' in sol0.labels and 'P' or 'MX'
if etype in sol0.labels:
sol0.labels[etype]['name'] = etype+'1'
else:
sol0.labels[etype] = {'name': etype+'1'}
- if sol0.labels[etype].has_key('cycle'):
+ if 'cycle' in sol0.labels[etype]:
sol0.labels[etype]['cycle'].name = etype+'1'
# Turn tangent vectors around (for non auto only)
if not self.UseAuto:
# Turn tangent vector around at point type endtype and change name
- for k, v in sol0.labels[etype]['data'].V.iteritems():
+ for k, v in sol0.labels[etype]['data'].V.items():
sol0.labels[etype]['data'].V[k] = -1*v
# Turn tangent vectors at curve type around
for pt in sol:
- for k, v in pt.labels[ctype]['data'].V.iteritems():
+ for k, v in pt.labels[ctype]['data'].V.items():
pt.labels[ctype]['data'].V[k] = -1*v
# Fix labels
@@ -1358,7 +1358,7 @@
pt.labels[pttype]['name'] = pttype + repr(num)
else:
pt.labels[pttype] = {'name': pttype + repr(num)}
- if pt.labels[pttype].has_key('cycle'):
+ if 'cycle' in pt.labels[pttype]:
pt.labels[pttype]['cycle'].name = pttype + repr(num)
num += 1
@@ -1374,7 +1374,7 @@
x0 = ic.copy()
x0 = x0.todict()
for p in self.freepars:
- if p not in x0.keys():
+ if p not in list(x0.keys()):
x0[p] = self.parsdict[p]
x0 = tocoords(self, x0)
@@ -1392,7 +1392,7 @@
if icv is None:
# Get Jacobian information
- print "Creating vector...\n"
+ print("Creating vector...\n")
J_coords = self.CorrFunc.jac(x0, self.coords)
J_params = self.CorrFunc.jac(x0, self.params)
@@ -1411,26 +1411,26 @@
#while (abs(x0[ind] - ic[ind]) < 1.0):
out = []
while (dy >= 1e-4):
- print "%s = %lf" % (self.varslist[ind], x0[ind])
+ print("%s = %lf" % (self.varslist[ind], x0[ind]))
# Get Jacobian information
#J_coords = self.CorrFunc.jac(x0, self.coords)
#J_params = self.CorrFunc.jac(x0, self.params)
k, converged, problem, diag = self.Corrector(x0, v0)
- print 'x0 = ', x0
+ print('x0 = ', x0)
if not converged:
- print " Did not converge."
+ print(" Did not converge.")
if (Dy >= dy):
- print " Changing stepsize."
+ print(" Changing stepsize.")
Dy -= dy
dy *= 0.5
else:
- print " Minimum reached. Stopping simulation."
+ print(" Minimum reached. Stopping simulation.")
raise PyDSTool_ExistError("Failed to converge")
else:
out.append((Dy, diag))
#print " Converged. Avg. cond. # = %lf" % (csum/k)
- print " Converged. Avg. cond. # = %lf" % (sum(diag.cond)/len(diag.cond))
+ print(" Converged. Avg. cond. # = %lf" % (sum(diag.cond)/len(diag.cond)))
# Takes care of "infinite" domains
if (Dy >= 5.0):
@@ -1457,7 +1457,7 @@
x0 = ic.copy()
x0 = x0.todict()
for p in self.freepars:
- if p not in x0.keys():
+ if p not in list(x0.keys()):
x0[p] = self.parsdict[p]
x0 = tocoords(self, x0)
@@ -1473,7 +1473,7 @@
if icv is None:
# Get Jacobian information
- print "Creating vector...\n"
+ print("Creating vector...\n")
J_coords = self.CorrFunc.jac(x0, self.coords)
J_params = self.CorrFunc.jac(x0, self.params)
@@ -1518,7 +1518,7 @@
x0[ind[0]] = xmin + j*dx
x0[ind[1]] = ymax - i*dy
ix0 = x0.copy()
- print "(%d, %d) -- (%s, %s) = (%lf, %lf)" % (i, j, key[ind[0]], key[ind[1]], x0[ind[0]], x0[ind[1]])
+ print("(%d, %d) -- (%s, %s) = (%lf, %lf)" % (i, j, key[ind[0]], key[ind[1]], x0[ind[0]], x0[ind[1]]))
# Get Jacobian information
#J_coords = self.CorrFunc.jac(x0, self.coords)
@@ -1532,11 +1532,11 @@
k, converged, problem, diag = self.Corrector(x0, v0)
- print 'x0 = ', x0
+ print('x0 = ', x0)
if not converged:
- print " Did not converge."
+ print(" Did not converge.")
if len(diag.cond) > 0:
- print " Avg. cond. # = %lf" % (sum(diag.cond)/len(diag.cond))
+ print(" Avg. cond. # = %lf" % (sum(diag.cond)/len(diag.cond)))
if problem:
# Did not converge due to failure in backward integration
out[i].append(('XB', ix0, x0, diag))
@@ -1549,7 +1549,7 @@
# Did not converge for unknown reason
out[i].append(('X', ix0, x0, diag))
else:
- print " Converged. Avg. cond. # = %lf" % (sum(diag.cond)/len(diag.cond))
+ print(" Converged. Avg. cond. # = %lf" % (sum(diag.cond)/len(diag.cond)))
# Converged
out[i].append(('C', ix0, x0, diag))
@@ -1568,7 +1568,7 @@
x0 = ic.copy()
x0 = x0.todict()
for p in self.freepars:
- if p not in x0.keys():
+ if p not in list(x0.keys()):
x0[p] = self.parsdict[p]
x0 = tocoords(self, x0)
@@ -1584,7 +1584,7 @@
if icv is None:
# Get Jacobian information
- print "Creating vector...\n"
+ print("Creating vector...\n")
J_coords = self.CorrFunc.jac(x0, self.coords)
J_params = self.CorrFunc.jac(x0, self.params)
@@ -1602,34 +1602,34 @@
v1[2] = 1.0
v1 = v1 - v0[2]*v0
v1 = v1/linalg.norm(v1)
- print "Checking orthonormal..."
- print " |v0| = %lf" % linalg.norm(v0)
- print " |v1| = %lf" % linalg.norm(v1)
- print " <v0,v1> = %lf" % matrixmultiply(v0,v1)
+ print("Checking orthonormal...")
+ print(" |v0| = %lf" % linalg.norm(v0))
+ print(" |v1| = %lf" % linalg.norm(v1))
+ print(" <v0,v1> = %lf" % matrixmultiply(v0,v1))
out = []
d0 = Dx/(2*step)
d1 = Dy/(2*step)
- print "Start x = ", x0
+ print("Start x = ", x0)
for i in range(step, -1*(step+1), -1):
out.append([])
for j in range(-1*step, step+1):
x = x0 + j*d0*v0 + i*d1*v1
- print "(%d, %d) -- (y, theta, a) = (%lf, %lf, %lf)" % (i, j, x[0], x[1], x[2])
+ print("(%d, %d) -- (y, theta, a) = (%lf, %lf, %lf)" % (i, j, x[0], x[1], x[2]))
ix = x.copy()
v = v0.copy()
k, converged, problem, diag = self.Corrector(x, v)
- print 'x = ', x
+ print('x = ', x)
if not converged:
if len(diag.cond) > 0:
- print " Avg. cond. # = %lf" % (sum(diag.cond)/len(diag.cond))
+ print(" Avg. cond. # = %lf" % (sum(diag.cond)/len(diag.cond)))
if problem:
# Did not converge due to failure in backward integration
- print " Did not converge (XB)."
+ print(" Did not converge (XB).")
out[step-i].append(('XB', ix, x, diag))
elif k >= self.MaxCorrIters:
Fnm_flag = monotone([nm[0] for nm in diag.nrm], -3,
@@ -1639,14 +1639,14 @@
cond_flag = monotone(diag.cond, -3, direc=-1)
if Fnm_flag and Vnm_flag and cond_flag:
# Did not converge but may have converged with more time steps
- print " Did not converge (XC)."
+ print(" Did not converge (XC).")
out[step-i].append(('XC', ix, x, diag))
else:
# Did not converge for unknown reason
- print " Did not converge (X)."
+ print(" Did not converge (X).")
out[step-i].append(('X', ix, x, diag))
else:
- print " Converged. Avg. cond. # = %lf" % (sum(diag.cond)/len(diag.cond))
+ print(" Converged. Avg. cond. # = %lf" % (sum(diag.cond)/len(diag.cond)))
# Converged
out[step-i].append(('C', ix, x, diag))
@@ -1765,42 +1765,42 @@
num = 1;
for pt in self.sol.bylabel(pttype):
pt.labels[pttype]['name'] = pttype + repr(num)
- if pt.labels[pttype].has_key('cycle'):
+ if 'cycle' in pt.labels[pttype]:
pt.labels[pttype]['cycle'].name = pttype + repr(num)
num += 1
def info(self):
- print self.__repr__()
- print "Using model: %s\n"%self.model.name
+ print(self.__repr__())
+ print("Using model: %s\n"%self.model.name)
if self.description is not 'None':
- print 'Description'
- print '----------- \n'
- print self.description, '\n'
- print 'Model Info'
- print '---------- \n'
- print " Variables : %s"%', '.join(self.varslist)
- print " Parameters: %s\n"%', '.join(self.parsdict.keys())
- print 'Continuation Parameters'
- print '----------------------- \n'
+ print('Description')
+ print('----------- \n')
+ print(self.description, '\n')
+ print('Model Info')
+ print('---------- \n')
+ print(" Variables : %s"%', '.join(self.varslist))
+ print(" Parameters: %s\n"%', '.join(list(self.parsdict.keys())))
+ print('Continuation Parameters')
+ print('----------------------- \n')
args_list = cont_args_list[:]
exclude = ['description']
args_list.insert(2, 'auxpars')
for arg in args_list:
if hasattr(self, arg) and arg not in exclude:
- print arg, ' = ', eval('self.' + arg)
- print '\n'
+ print(arg, ' = ', eval('self.' + arg))
+ print('\n')
spts = ''
if self.sol is not None:
for pttype in all_point_types:
if self.sol.bylabel(pttype) is not None:
for pt in self.sol.bylabel(pttype):
- if pt.labels[pttype].has_key('name'):
+ if 'name' in pt.labels[pttype]:
spts = spts + pt.labels[pttype]['name'] + ', '
- print 'Special Points'
- print '-------------- \n'
- print spts[:-2]
+ print('Special Points')
+ print('-------------- \n')
+ print(spts[:-2])
def __repr__(self):
@@ -1843,7 +1843,7 @@
Continuation.update(self, args)
if args is not None:
- for k, v in args.iteritems():
+ for k, v in args.items():
if k in equilibrium_args_list:
if k == 'LocBifPoints':
if isinstance(v, str):
@@ -1854,7 +1854,7 @@
# Handle stopping points
w = []
- if args.has_key('StopAtPoints'):
+ if 'StopAtPoints' in args:
w = args['StopAtPoints']
if isinstance(w, str):
if w.lower() == 'all':
@@ -1866,10 +1866,10 @@
if bftype not in cont_bif_points and \
bftype not in equilibrium_bif_points:
if self.verbosity >= 1:
- print "Warning: Detection of " + bftype + " points not implemented for curve EP-C."
+ print("Warning: Detection of " + bftype + " points not implemented for curve EP-C.")
elif bftype == 'H' and self.varsdim == 1:
if self.verbosity >= 1:
- print "Warning: Variable dimension must be larger than 1 to detect Hopf points."
+ print("Warning: Variable dimension must be larger than 1 to detect Hopf points.")
else:
if bftype not in self.LocBifPoints:
self.LocBifPoints.append(bftype)
@@ -1906,7 +1906,7 @@
save=True, numpoints=self.MaxNumPoints+1)
#method1 = Fold_Det(self.CorrFunc, self, save=True, numpoints=self.MaxNumPoints+1)
self.TestFuncs.append(method1)
- if 'BP' not in self.BifPoints.keys():
+ if 'BP' not in list(self.BifPoints.keys()):
method2 = Branch_Det(self.CorrFunc, self, save=True,
numpoints=self.MaxNumPoints+1)
self.TestFuncs.append(method2)
@@ -1970,15 +1970,15 @@
"""Update parameters for FoldCurve."""
Continuation.update(self, args)
if 'BP' in self.LocBifPoints:
- print "BP point detection not implemented: ignoring this type of point"
+ print("BP point detection not implemented: ignoring this type of point")
self.LocBifPoints.remove('BP')
if 'BP' in self.StopAtPoints:
- print "BP point detection not implemented: ignoring this type of point"
+ print("BP point detection not implemented: ignoring this type of point")
self.StopAtPoints.remove('BP')
#self.LocBifPoints = [] # Temporary fix: Delete after branch point implementation for fold curve
if args is not None:
- for k, v in args.iteritems():
+ for k, v in args.items():
if k in fold_args_list:
if k == 'LocBifPoints':
if isinstance(v, str):
@@ -1989,7 +1989,7 @@
# Handle stopping points
w = []
- if args.has_key('StopAtPoints'):
+ if 'StopAtPoints' in args:
w = args['StopAtPoints']
if isinstance(w, str):
if w.lower() == 'all':
@@ -2001,7 +2001,7 @@
if bftype == 'BP' or bftype not in cont_bif_points \
and bftype not in fold_bif_points:
if self.verbosity >= 1:
- print "Warning: Detection of " + bftype + " points not implemented for curve LP-C."
+ print("Warning: Detection of " + bftype + " points not implemented for curve LP-C.")
else:
if bftype not in self.LocBifPoints:
self.LocBifPoints.append(bftype)
@@ -2041,7 +2041,7 @@
method1 = Hopf_Det(self.CorrFunc.sysfunc, self,
save=True, numpoints=self.MaxNumPoints+1)
self.TestFuncs.append(method1)
- if 'BT' not in self.BifPoints.keys():
+ if 'BT' not in list(self.BifPoints.keys()):
method2 = BT_Fold(self.CorrFunc, self, save=True,
numpoints=self.MaxNumPoints+1)
self.TestFuncs.append(method2)
@@ -2107,7 +2107,7 @@
#self.LocBifPoints = [] # Temporary fix: Delete after branch point implementation for hopf curve
if args is not None:
- for k, v in args.iteritems():
+ for k, v in args.items():
if k in hopf_args_list:
if k == 'LocBifPoints':
if isinstance(v, str):
@@ -2118,7 +2118,7 @@
# Handle stopping points
w = []
- if args.has_key('StopAtPoints'):
+ if 'StopAtPoints' in args:
w = args['StopAtPoints']
if isinstance(w, str):
if w.lower() == 'all':
@@ -2130,10 +2130,10 @@
if bftype == 'BP' or bftype not in cont_bif_points \
and bftype not in hopf_bif_points:
if self.verbosity >= 1:
- print "Warning: Detection of " + bftype + " points not implemented for curve H-C1."
+ print("Warning: Detection of " + bftype + " points not implemented for curve H-C1.")
elif bftype == 'DH' and self.varsdim <= 3:
if self.verbosity >= 1:
- print "Warning: Variable dimension must be larger than 3 to detect Double Hopf points."
+ print("Warning: Variable dimension must be larger than 3 to detect Double Hopf points.")
else:
if bftype not in self.LocBifPoints:
self.LocBifPoints.append(bftype)
@@ -2266,7 +2266,7 @@
#self.LocBifPoints = [] # Temporary fix: Delete after branch point implementation for hopf curve
if args is not None:
- for k, v in args.iteritems():
+ for k, v in args.items():
if k in hopf_args_list:
if k == 'LocBifPoints':
if isinstance(v, str):
@@ -2277,7 +2277,7 @@
# Handle stopping points
w = []
- if args.has_key('StopAtPoints'):
+ if 'StopAtPoints' in args:
w = args['StopAtPoints']
if isinstance(w, str):
if w.lower() == 'all':
@@ -2288,7 +2288,7 @@
for bftype in v:
if bftype in ['BP', 'DH'] or bftype not in cont_bif_points and bftype not in hopf_bif_points:
if self.verbosity >= 1:
- print "Warning: Detection of " + bftype + " points not implemented for curve H-C2."
+ print("Warning: Detection of " + bftype + " points not implemented for curve H-C2.")
else:
if bftype not in self.LocBifPoints:
self.LocBifPoints.append(bftype)
@@ -2380,7 +2380,7 @@
if bftype is 'LPC':
method1 = LPC_Det(self.sysfunc, self, save=True, numpoints=self.MaxNumPoints+1)
self.TestFuncs.append(method1)
- if 'BP' not in self.BifPoints.keys():
+ if 'BP' not in list(self.BifPoints.keys()):
method2 = Branch_Det(self.CorrFunc, self, save=True, numpoints=self.MaxNumPoints+1)
self.TestFuncs.append(method2)
else:
@@ -2404,7 +2404,7 @@
Continuation.update(self, args)
if args is not None:
- for k, v in args.iteritems():
+ for k, v in args.items():
if k in fixedpoint_args_list:
if k == 'LocBifPoints':
if isinstance(v, str):
@@ -2415,7 +2415,7 @@
# Handle stopping points
w = []
- if args.has_key('StopAtPoints'):
+ if 'StopAtPoints' in args:
w = args['StopAtPoints']
if isinstance(w, str):
if w.lower() == 'all':
@@ -2426,10 +2426,10 @@
for bftype in v:
if bftype not in cont_bif_points and bftype not in fixedpoint_bif_points:
if self.verbosity >= 1:
- print "Warning: Detection of " + bftype + " points not implemented for curve FP-C."
+ print("Warning: Detection of " + bftype + " points not implemented for curve FP-C.")
elif bftype == 'NS' and self.varsdim == 1:
if self.verbosity >= 1:
- print "Warning: Variable dimension must be larger than 1 to detect NS points."
+ print("Warning: Variable dimension must be larger than 1 to detect NS points.")
else:
if bftype not in self.LocBifPoints:
self.LocBifPoints.append(bftype)
@@ -2484,20 +2484,20 @@
"""Update parameters for LimitCycleCurve."""
Continuation.update(self, args)
if args is not None:
- for k, v in args.iteritems():
+ for k, v in args.items():
if k in limitcycle_args_list:
if k == 'SolutionMeasures':
self.SolutionMeasures = ['max', 'min']
if isinstance(v, str):
if v.lower() == 'all':
- v = solution_measures.keys()
+ v = list(solution_measures.keys())
else:
v = [v]
for smtype in v:
- if smtype not in solution_measures.keys():
+ if smtype not in list(solution_measures.keys()):
if self.verbosity >= 1:
- print "Warning: Solution measure " + smtype + " is not valid."
+ print("Warning: Solution measure " + smtype + " is not valid.")
elif smtype not in self.SolutionMeasures:
self.SolutionMeasures.append(smtype)
@@ -2513,7 +2513,7 @@
# Handle stopping points
w = []
- if args.has_key('StopAtPoints'):
+ if 'StopAtPoints' in args:
w = args['StopAtPoints']
if isinstance(w, str):
if w.lower() == 'all':
@@ -2525,8 +2525,8 @@
if bftype not in cont_bif_points \
and bftype not in limitcycle_bif_points:
if self.verbosity >= 1:
- print "Warning: Detection of %s"%bftype,
- print " points not implemented for curve LC-C."
+ print("Warning: Detection of %s"%bftype, end=' ')
+ print(" points not implemented for curve LC-C.")
else:
if bftype not in self.LocBifPoints:
self.LocBifPoints.append(bftype)
@@ -2551,8 +2551,8 @@
if cycles is None:
cycles = []
for pt in self.sol:
- for ptdata in pt.labels.itervalues():
- if ptdata.has_key('cycle'):
+ for ptdata in pt.labels.values():
+ if 'cycle' in ptdata:
cycles.append(ptdata['cycle'].name)
elif not isinstance(cycles, list):
cycles = [cycles]
@@ -2592,7 +2592,7 @@
elif isinstance(cyclename, Pointset):
pts.append(cyclename)
else:
- print 'Point must be type(str) or type(Pointset).'
+ print('Point must be type(str) or type(Pointset).')
cycles = pts
# Get maximal period
@@ -2842,7 +2842,7 @@
# CHECK ME (Moved from below)
parsdim = len(self.parsdict)
- ipar = range(min(parsdim,10)) + [10] + range(50,parsdim+40)
+ ipar = list(range(min(parsdim,10))) + [10] + list(range(50,parsdim+40))
parkeys = sortedDictKeys(self.parsdict)
# INSERT SPOut STUFF HERE
@@ -2853,7 +2853,7 @@
else:
iuz = []
vuz = []
- for k, v in self.SPOut.iteritems():
+ for k, v in self.SPOut.items():
pind = ipar[parkeys.index(k)]
iuz.extend(len(v)*[pind])
vuz.extend(v)
@@ -2903,7 +2903,7 @@
# FIX ME
x0n = x0.copy()
- for k, v in x0.iteritems():
+ for k, v in x0.items():
kn = k
for smtype in self.SolutionMeasures:
if k.rfind('_'+smtype) > 0:
@@ -2916,8 +2916,8 @@
elif isinstance(x0, Point):
# Check to see if point contains a cycle. If it does, assume
# we are starting at a cycle and save it in initcycle
- for v in x0.labels.itervalues():
- if v.has_key('cycle'):
+ for v in x0.labels.values():
+ if 'cycle' in v:
c0 = v # Dictionary w/ cycle, name, and tangent information
try:
T = x0['_T']
@@ -2925,12 +2925,12 @@
T = None
x0 = x0.todict()
for p in self.freepars:
- if p not in x0.keys():
+ if p not in list(x0.keys()):
x0[p] = self.parsdict[p]
# FIX ME
x0n = x0.copy()
- for k, v in x0.iteritems():
+ for k, v in x0.items():
kn = k
for smtype in self.SolutionMeasures:
if k.rfind('_'+smtype) > 0:
@@ -3073,8 +3073,8 @@
if sp_endpt < self.loc:
if self.verbosity > 0:
- print 'Warning: NaNs in solution from AUTO. ',
- print 'Reduce stepsize and try again.'
+ print('Warning: NaNs in solution from AUTO. ', end=' ')
+ print('Reduce stepsize and try again.')
self.loc = sp_endpt
self.curve = self.curve[0:self.loc+1]
self.CurveInfo[self.loc] = ('MX', \
@@ -3102,14 +3102,14 @@
def info(self):
Continuation.info(self)
- print '\nLimit Cycle Curve Parameters'
- print '------------------------------\n'
+ print('\nLimit Cycle Curve Parameters')
+ print('------------------------------\n')
args_list = limitcycle_args_list[:]
args_list.remove('LocBifPoints')
for arg in args_list:
iRefactoringTool: Refactored ./PyDSTool/PyCont/ContClass.py
f hasattr(self, arg):
- print arg, ' = ', eval('self.' + arg)
- print '\n'
+ print(arg, ' = ', eval('self.' + arg))
+ print('\n')
@@ -3125,15 +3125,15 @@
self.parsdict = initargs['userpars'].copy()
self._userfunc = initargs['userfunc']
self._userdata = args()
- if initargs.has_key('userjac'):
+ if 'userjac' in initargs:
self._userjac = initargs['userjac']
- if initargs.has_key('usertestfuncs'):
+ if 'usertestfuncs' in initargs:
self._usertestfuncs = initargs['usertestfuncs']
- if initargs.has_key('userbifpoints'):
+ if 'userbifpoints' in initargs:
self._userbifpoints = initargs['userbifpoints']
else:
self._userbifpoints = []
- if initargs.has_key('userdomain'):
+ if 'userdomain' in initargs:
self._userdomain = initargs['userdomain']
[initargs.pop(i) for i in ['uservars','userpars','userjac','userfunc',
@@ -3148,7 +3148,7 @@
Continuation.update(self, args)
if args is not None:
- for k, v in args.iteritems():
+ for k, v in args.items():
if k in userdefined_args_list:
exec('self.' + k + ' = ' + repr(v))
--- ./PyDSTool/PyCont/ContClass.py (original)
+++ ./PyDSTool/PyCont/ContClass.py (refactored)
@@ -3,10 +3,10 @@
Drew LaMar, March 2006
"""
-from Continuation import EquilibriumCurve, FoldCurve, HopfCurveOne, HopfCurveTwo, \
+from .Continuation import EquilibriumCurve, FoldCurve, HopfCurveOne, HopfCurveTwo, \
FixedPointCurve, LimitCycleCurve, UserDefinedCurve
-from misc import *
-from Plotting import pargs, initializeDisplay
+from .misc import *
+from .Plotting import pargs, initializeDisplay
from PyDSTool.Model import Model, findTrajInitiator
from PyDSTool.Generator import Generator
@@ -67,7 +67,7 @@
def __init__(self, model):
if isinstance(model, Generator):
self.model = embed(model, make_copy=False)
- self.gensys = self.model.registry.values()[0]
+ self.gensys = list(self.model.registry.values())[0]
else:
self.model = model
mi, swRules, globalConRules, nextModelName, reused, \
@@ -120,7 +120,7 @@
# Check parameters
if (curvetype != 'UD-C' and self.model.pars == {}) or \
- (curvetype == 'UD-C' and not initargs.has_key('userpars')):
+ (curvetype == 'UD-C' and 'userpars' not in initargs):
raise ValueError('No parameters defined for this system!')
# Process initial point
@@ -129,8 +129,8 @@
# Default to initial conditions for model
if self.model.icdict == {}:
raise ValueError('No initial point defined for this system!')
- elif initargs.has_key('uservars'):
- if remain(initargs['uservars'], self.model.icdict.keys()) == []:
+ elif 'uservars' in initargs:
+ if remain(initargs['uservars'], list(self.model.icdict.keys())) == []:
# uservars just used to select a subset of system's regular state vars
initargs['initpoint'] = filteredDict(self.model.icdict,
initargs['uservars'])
@@ -149,7 +149,7 @@
elif isinstance(initargs['initpoint'], str):
curvename, pointname = initargs['initpoint'].split(':')
pointtype = pointname.strip('0123456789')
- if not self.curves.has_key(curvename):
+ if curvename not in self.curves:
raise KeyError('No curve of name ' + curvename + ' exists.')
else:
point = self.curves[curvename].getSpecialPoint(pointtype, pointname)
@@ -162,8 +162,8 @@
if isinstance(initargs['initpoint'], Point):
# Check to see if point contains a cycle. If it does, assume
# we are starting at a cycle and save it in initcycle
- for v in initargs['initpoint'].labels.itervalues():
- if v.has_key('cycle'):
+ for v in initargs['initpoint'].labels.values():
+ if 'cycle' in v:
initargs['initcycle'] = v # Dictionary w/ cycle, name, and tangent information
# Save initial point information
@@ -206,11 +206,11 @@
savedict = {}
- print self.__dict__['curves'].keys()
+ print(list(self.__dict__['curves'].keys()))
# Save data for each curve with different prefix
- for name in self.__dict__['curves'].keys():
+ for name in list(self.__dict__['curves'].keys()):
if self[name].curvetype not in ['EP-C', 'LC-C']:
- print "Can't save curve type", self[name].curvetype, "yet. (", name, ")"
+ print("Can't save curve type", self[name].curvetype, "yet. (", name, ")")
continue
# Can save equilibrium curves
else:
@@ -228,7 +228,7 @@
savedict[name+'_'+key] = array(curve[key])
# Add stabilities
- if 'stab' in curve[0].labels[label].keys():
+ if 'stab' in list(curve[0].labels[label].keys()):
savedict[name+'_stab'] = [curve[x].labels[label]['stab'] for x in range(N)]
temp = zeros(N)
for x in range(N):
@@ -239,7 +239,7 @@
savedict[name+'_stab'] = array(temp)
# Add domain
- if 'domain' in curve[0].labels[label].keys():
+ if 'domain' in list(curve[0].labels[label].keys()):
savedict[name+'_domain'] = [curve[x].labels[label]['domain'] for x in range(N)]
temp = zeros(N)
for x in range(N):
@@ -250,9 +250,9 @@
savedict[name+'_domain'] = array(temp)
# Add data
- if 'data' in curve[0].labels[label].keys():
+ if 'data' in list(curve[0].labels[label].keys()):
# Add eigenvalues
- if 'evals' in curve[0].labels[label]['data'].keys():
+ if 'evals' in list(curve[0].labels[label]['data'].keys()):
dim = len(curve[0].labels[label]['data']['evals'])
evltmp = [[] for x in range(dim)]
for x in range(dim):
@@ -260,11 +260,11 @@
savedict[name+'_evals'] = array(evltmp)
# Add ds
- if 'ds' in curve[0].labels[label]['data'].keys():
+ if 'ds' in list(curve[0].labels[label]['data'].keys()):
savedict[name+'_ds'] = array([curve[y].labels[label]['data']['ds'] for y in range(N)])
# Add eigenvectors
- if 'evecs' in curve[0].labels[label]['data'].keys():
+ if 'evecs' in list(curve[0].labels[label]['data'].keys()):
#dim = len(curve.coordnames) - 1
dim = len(curve[0].labels[label]['data']['evecs'][0])
evectmp = []
@@ -274,8 +274,8 @@
savedict[name+'_evecs'] = array(evectmp)
# Add V
- if 'V' in curve[0].labels[label]['data'].keys():
- for key in curve[0].labels[label]['data']['V'].keys():
+ if 'V' in list(curve[0].labels[label]['data'].keys()):
+ for key in list(curve[0].labels[label]['data']['V'].keys()):
savedict[name+'_V_'+key] = array([curve[x].labels[label]['data']['V'][key] for x in range(N)])
# Save the dictionary in matlab format
@@ -285,13 +285,13 @@
def exportGeomview(self, coords=None, filename="geom.dat"):
if coords is not None and len(coords) == 3:
GeomviewOutput = "(progn (geometry " + self.model.name + " { LIST {: axes_" + self.model.name + "}"
- for cname, curve in self.curves.iteritems():
+ for cname, curve in self.curves.items():
GeomviewOutput += " {: " + cname + "}"
GeomviewOutput += "}))\n\n"
# Get axes limits
alim = [[Inf,-Inf],[Inf,-Inf],[Inf,-Inf]]
- for cname, curve in self.curves.iteritems():
+ for cname, curve in self.curves.items():
for n in range(len(coords)):
alim[n][0] = min(alim[n][0], min(curve.sol[coords[n]].toarray()))
alim[n][1] = max(alim[n][1], max(curve.sol[coords[n]].toarray()))
@@ -300,7 +300,7 @@
"0 0 0 1 0 0 0 1 0 0 0 1 " + \
"2 0 1 1 0 0 1 2 0 2 0 1 0 1 2 0 3 0 0 1 1})\n\n"
- for cname, curve in self.curves.iteritems():
+ for cname, curve in self.curves.items():
GeomviewOutput += "(hdefine geometry " + cname + " { LIST {: curve_" + cname + "} {: specpts_" + cname + "}})\n\n"
GeomviewOutput += "(hdefine geometry curve_" + cname + " { appearance { linewidth 2 } SKEL " + \
@@ -336,14 +336,14 @@
return
if curves is None:
- curves = self.curves.keys()
+ curves = list(self.curves.keys())
plot_curves = []
for curve in curves:
- if self.curves.has_key(curve):
+ if curve in self.curves:
plot_curves.append(curve)
else:
- print "Warning: Curve " + curve + " does not exist."
+ print("Warning: Curve " + curve + " does not exist.")
if len(plot_curves) > 0:
initializeDisplay(self.plot, figure=figure, axes=axes)
@@ -352,24 +352,24 @@
self.curves[curve].display(coords, figure=figure, axes=axes, stability=stability, domain=domain, init_display=False, **plot_args)
def computeEigen(self):
- for curve in self.curves.itervalues():
+ for curve in self.curves.values():
curve.computeEigen()
def info(self):
- print self.__repr__()
+ print(self.__repr__())
#print " Variables : %s"%', '.join(self.model.allvars)
#print " Parameters: %s\n"%', '.join(self.model.pars.keys())
- print "Containing curves: "
+ print("Containing curves: ")
for c in self.curves:
- print " " + c + " (type " + self.curves[c].curvetype + ")"
+ print(" " + c + " (type " + self.curves[c].curvetype + ")")
def update(self, args):
"""Update parameters for all curves."""
- for c in args.keys():
+ for c in list(args.keys()):
if c not in curve_args_list:
args.pop(c)
- for v in self.curves.values():
+ for v in list(self.curves.values()):
v.update(args)
def loadAutoMod(self):
@@ -379,9 +379,9 @@
elif thisplatform in ['Linux', 'IRIX', 'Solaris', 'SunOS', 'Darwin', 'FreeBSD']:
self._dllext = '.so'
else:
- print "Shared library extension not tested on this platform."
- print "If this process fails please report the errors to the"
- print "developers."
+ print("Shared library extension not tested on this platform.")
+ print("If this process fails please report the errors to the")
+ print("developers.")
self._dllext = '.so'
self._compilation_tempdir = os.path.join(os.getcwd(),
@@ -392,8 +392,8 @@
"A file already exists with the same name"
os.mkdir(self._compilation_tempdir)
except:
- print "Could not create compilation temp directory " + \
- self._compilation_tempdir
+ print("Could not create compilation temp directory " + \
+ self._compilation_tempdir)
raise
self._compilation_sourcedir = os.path.join(_pydstool_path,"PyCont/auto/module")
self._vf_file = self.gensys.name+"_vf.c"
@@ -407,13 +407,13 @@
self.makeAutoLibSource()
self.compileAutoLib()
else:
- print "Build the library using the makeLib method, or in "
- print "stages using the makeLibSource and compileLib methods."
+ print("Build the library using the makeLib method, or in ")
+ print("stages using the makeLibSource and compileLib methods.")
try:
self._autoMod = __import__("auto"+self._vf_filename_ext, globals())
except:
- print "Error loading auto module."
+ print("Error loading auto module.")
raise
def forceAutoLibRefresh(self):
@@ -433,9 +433,9 @@
if delfiles:
gc.collect()
# still not able to delete these files!!!!! Argh!
- print "Cannot rebuild library without restarting session. Sorry."
- print "Try asking the Python developers to make a working module"
- print "unimport function!"
+ print("Cannot rebuild library without restarting session. Sorry.")
+ print("Try asking the Python developers to make a working module")
+ print("unimport function!")
def makeAutoLib(self, libsources=[], libdirs=[], include=[]):
"""makeAutoLib calls makeAutoLibSource and then the compileAutoLib method.
@@ -457,7 +457,7 @@
('string.h', STDLIB), ('autovfield.h', USERLIB),
('auto_c.h', USERLIB)])
include_str = '#include "auto_f2c.h"\n' # This must come first
- for libstr, libtype in libinclude.iteritems():
+ for libstr, libtype in libinclude.items():
if libtype == STDLIB:
quoteleft = '<'
quoteright = '>'
@@ -470,8 +470,8 @@
for libstr in include:
if libstr in libinclude:
# don't repeat libraries
- print "Warning: library '" + libstr + "' already appears in list"\
- + " of imported libraries"
+ print("Warning: library '" + libstr + "' already appears in list"\
+ + " of imported libraries")
else:
include_str += "#include " + '"' + libstr + '"\n'
@@ -501,7 +501,7 @@
inames = self.funcspec.inputs
pnames.sort()
inames.sort()
- for i in xrange(self.gensys.numpars):
+ for i in range(self.gensys.numpars):
p = pnames[i]
# add to defines (WATCH OUT FOR PERIOD _T!!!)
if (i < 10):
@@ -510,13 +510,13 @@
pardefines += self.funcspec._defstr+" "+p+"\tp_["+str(i+40)+"]\n"
# add period _T
pardefines += self.funcspec._defstr+" _T\tp_[10]\n"
- for i in xrange(self.gensys.dimension):
+ for i in range(self.gensys.dimension):
v = vnames[i]
# add to defines
vardefines += self.funcspec._defstr+" "+v+"\tY_["+str(i)+"]\n"
## # add to undefines
## varundefines += self.funcspec._undefstr+" "+v+"\n"
- for i in xrange(len(self.funcspec.inputs)):
+ for i in range(len(self.funcspec.inputs)):
inp = inames[i]
# add to defines
inpdefines += self.funcspec._defstr+" "+inp+"\txv_["+str(i)+"]\n"
@@ -527,7 +527,7 @@
# add signature for auxiliary functions
if self.funcspec.auxfns:
allfilestr += "\n"
- for finfo in self.funcspec.auxfns.values():
+ for finfo in list(self.funcspec.auxfns.values()):
allfilestr += finfo[1] + ";\n"
allfilestr += "\nvoid auxvars(unsigned, unsigned, double, double*, double*, " \
+ "double*, unsigned, double*, unsigned, double*);\n" \
@@ -542,11 +542,11 @@
allfilestr += self.funcspec.spec[0] + "\n\n"
if self.funcspec.auxfns:
- for fname, finfo in self.funcspec.auxfns.iteritems():
+ for fname, finfo in self.funcspec.auxfns.items():
fbody = finfo[0]
# subs _p into auxfn-to-auxfn calls (but not to the signature)
fbody_parsed = addArgToCalls(fbody,
- self.funcspec.auxfns.keys(),
+ list(self.funcspec.auxfns.keys()),
"p_, wk_, xv_", notFirst=fname)
if 'initcond' in self.funcspec.auxfns:
# convert 'initcond(x)' to 'initcond("x")' for
@@ -578,9 +578,9 @@
#allfilestr = allfilestr.replace("double**","doublereal **")
file.write(allfilestr)
file.close()
- except IOError, e:
- print "Error opening file "+self._vf_file+" for writing"
- raise IOError, e
+ except IOError as e:
+ print("Error opening file "+self._vf_file+" for writing")
+ raise IOError(e)
def compileAutoLib(self, libsources=[], libdirs=[]):
"""compileAutoLib generates a python extension DLL with continuer and vector
@@ -595,21 +595,21 @@
# then DLL file already exists and we can't overwrite it at this
# time
proceed = False
- print "\n"
- print "-----------------------------------------------------------"
- print "Present limitation of Python: Cannot rebuild library"
- print "without exiting Python and deleting the shared library"
- print " " + str(os.path.join(os.getcwd(),
- "_auto"+self._vf_filename_ext+self._dllext))
- print "by hand! If you made any changes to the system you should"
- print "not proceed with running the integrator until you quit"
- print "and rebuild."
- print "-----------------------------------------------------------"
- print "\n"
+ print("\n")
+ print("-----------------------------------------------------------")
+ print("Present limitation of Python: Cannot rebuild library")
+ print("without exiting Python and deleting the shared library")
+ print(" " + str(os.path.join(os.getcwd(),
+ "_auto"+self._vf_filename_ext+self._dllext)))
+ print("by hand! If you made any changes to the system you should")
+ print("not proceed with running the integrator until you quit")
+ print("and rebuild.")
+ print("-----------------------------------------------------------")
+ print("\n")
else:
proceed = True
if not proceed:
- print "Did not compile shared library."
+ print("Did not compile shared library.")
return
if self._autoMod is not None:
self.forceAutoLibRefresh()
@@ -626,7 +626,7 @@
ifacefile_orig.close()
ifacefile_copy.close()
except IOError:
- print "automod.i copying error in auto compilation directory"
+ print("automod.i copying error in auto compilation directory")
raise
swigfile = os.path.join(self._compilation_tempdir,
@@ -688,8 +688,8 @@
library_dirs=libdirs+['./'],
libraries=libsources)])
except:
- print "\nError occurred in generating Auto system..."
- print sys.exc_info()[0], sys.exc_info()[1]
+ print("\nError occurred in generating Auto system...")
+ print(sys.exc_info()[0], sys.exc_info()[1])
raise RuntimeError
rout.stop() # restore stdout
try:
@@ -705,9 +705,9 @@
os.path.join(os.getcwd(),
"auto"+self._vf_filename_ext+".py"))
except:
- print "\nError occurred in generating Auto system"
- print "(while moving library extension modules to CWD)"
- print sys.exc_info()[0], sys.exc_info()[1]
+ prinRefactoringTool: Refactored ./PyDSTool/PyCont/BifPoint.py
t("\nError occurred in generating Auto system")
+ print("(while moving library extension modules to CWD)")
+ print(sys.exc_info()[0], sys.exc_info()[1])
raise RuntimeError
def __repr__(self):
--- ./PyDSTool/PyCont/BifPoint.py (original)
+++ ./PyDSTool/PyCont/BifPoint.py (refactored)
@@ -3,9 +3,9 @@
Drew LaMar, March 2006
"""
-from misc import *
+from .misc import *
from PyDSTool.common import args
-from TestFunc import DiscreteMap, FixedPointMap
+from .TestFunc import DiscreteMap, FixedPointMap
from numpy import Inf, NaN, isfinite, r_, c_, sign, mod, mat, \
subtract, divide, transpose, eye, real, imag, \
@@ -65,29 +65,29 @@
def info(self, C, ind=None, strlist=None):
if ind is None:
- ind = range(len(self.found))
+ ind = list(range(len(self.found)))
elif isinstance(ind, int):
ind = [ind]
if C.verbosity >= 1:
- print self.label + ' Point found '
+ print(self.label + ' Point found ')
if C.verbosity >= 2:
- print '========================== '
+ print('========================== ')
for n, i in enumerate(ind):
- print n, ': '
+ print(n, ': ')
Xd = self.found[i].X
- for k, j in Xd.iteritems():
- print k, ' = ', j
- print ''
+ for k, j in Xd.items():
+ print(k, ' = ', j)
+ print('')
if hasattr(self.found[i], 'eigs'):
- print 'Eigenvalues = \n'
+ print('Eigenvalues = \n')
for x in self.found[i].eigs:
- print ' (%f,%f)' % (x.real, x.imag)
- print '\n'
+ print(' (%f,%f)' % (x.real, x.imag))
+ print('\n')
if strlist is not None:
for string in strlist:
- print string
- print ''
+ print(string)
+ print('')
class SPoint(BifPoint):
@@ -131,7 +131,7 @@
def info(self, C, ind=None):
if ind is None:
- ind = range(len(self.found))
+ ind = list(range(len(self.found)))
elif isinstance(ind, int):
ind = [ind]
@@ -207,7 +207,7 @@
def info(self, C, ind=None):
if ind is None:
- ind = range(len(self.found))
+ ind = list(range(len(self.found)))
elif isinstance(ind, int):
ind = [ind]
@@ -244,29 +244,29 @@
numzero = len([eig for eig in W if abs(eig) < 1e-4])
if numzero > 1:
if C.verbosity >= 2:
- print 'Fold-Fold!\n'
+ print('Fold-Fold!\n')
del self.found[-1]
return False
elif numzero == 0:
if C.verbosity >= 2:
- print 'False positive!\n'
+ print('False positive!\n')
del self.found[-1]
return False
if C.verbosity >= 2:
- print '\nChecking...'
- print ' |q| = %f' % linalg.norm(q)
- print ' <p,q> = %f' % matrixmultiply(p,q)
- print ' |Aq| = %f' % linalg.norm(matrixmultiply(J_coords,q))
- print ' |transpose(A)p| = %f\n' % linalg.norm(matrixmultiply(transpose(J_coords),p))
-
- self.info(C, -1)
-
- return True
-
- def info(self, C, ind=None):
- if ind is None:
- ind = range(len(self.found))
+ print('\nChecking...')
+ print(' |q| = %f' % linalg.norm(q))
+ print(' <p,q> = %f' % matrixmultiply(p,q))
+ print(' |Aq| = %f' % linalg.norm(matrixmultiply(J_coords,q)))
+ print(' |transpose(A)p| = %f\n' % linalg.norm(matrixmultiply(transpose(J_coords),p)))
+
+ self.info(C, -1)
+
+ return True
+
+ def info(self, C, ind=None):
+ if ind is None:
+ ind = list(range(len(self.found)))
elif isinstance(ind, int):
ind = [ind]
@@ -296,9 +296,9 @@
for j in range(i+1,len(eigs)):
if C.verbosity >= 2:
if abs(eigs[i]) < 1e-5 and abs(eigs[j]) < 1e-5:
- print 'Fold-Fold point found in Hopf!\n'
+ print('Fold-Fold point found in Hopf!\n')
elif abs(imag(eigs[j])) < 1e-5 and abs(real(eigs[i]) + real(eigs[j])) < 1e-5:
- print 'Neutral saddle found!\n'
+ print('Neutral saddle found!\n')
elif abs(real(eigs[i])) < 1e-5:
for j in range(i+1, len(eigs)):
if abs(real(eigs[j])) < 1e-5 and abs(real(eigs[i]) - real(eigs[j])) < 1e-5:
@@ -333,7 +333,7 @@
def info(self, C, ind=None):
if ind is None:
- ind = range(len(self.found))
+ ind = list(range(len(self.found)))
elif isinstance(ind, int):
ind = [ind]
@@ -367,17 +367,17 @@
else:
b = C.CorrFunc.testfunc.data.w[:,0]
c = C.CorrFunc.testfunc.data.v[:,0]
- print '\nChecking...'
- print ' <b,c> = %f' % matrixmultiply(transpose(b), c)
- print '\n'
-
- self.info(C, -1)
-
- return True
-
- def info(self, C, ind=None):
- if ind is None:
- ind = range(len(self.found))
+ print('\nChecking...')
+ print(' <b,c> = %f' % matrixmultiply(transpose(b), c))
+ print('\n')
+
+ self.info(C, -1)
+
+ return True
+
+ def info(self, C, ind=None):
+ if ind is None:
+ ind = list(range(len(self.found)))
elif isinstance(ind, int):
ind = [ind]
@@ -404,7 +404,7 @@
def info(self, C, ind=None):
if ind is None:
- ind = range(len(self.found))
+ ind = list(range(len(self.found)))
elif isinstance(ind, int):
ind = [ind]
@@ -432,17 +432,17 @@
a = 0.5*matrixmultiply(transpose(p), reshape([bilinearform(B[i,:,:], q, q) \
for i in range(B.shape[0])],(B.shape[0],1)))[0][0]
if C.verbosity >= 2:
- print '\nChecking...'
- print ' |a| = %f' % a
- print '\n'
-
- self.info(C, -1)
-
- return True
-
- def info(self, C, ind=None):
- if ind is None:
- ind = range(len(self.found))
+ print('\nChecking...')
+ print(' |a| = %f' % a)
+ print('\n')
+
+ self.info(C, -1)
+
+ return True
+
+ def info(self, C, ind=None):
+ if ind is None:
+ ind = list(range(len(self.found)))
elif isinstance(ind, int):
ind = [ind]
@@ -468,7 +468,7 @@
def info(self, C, ind=None):
if ind is None:
- ind = range(len(self.found))
+ ind = list(range(len(self.found)))
elif isinstance(ind, int):
ind = [ind]
@@ -493,9 +493,9 @@
for j in range(i+1,len(eigs)):
if C.verbosity >= 2:
if abs(eigs[i]) < 1e-5 and abs(eigs[j]) < 1e-5:
- print 'Fold-Fold point found in Hopf!\n'
+ print('Fold-Fold point found in Hopf!\n')
elif abs(imag(eigs[j])) < 1e-5 and abs(real(eigs[i]) + real(eigs[j])) < 1e-5:
- print 'Neutral saddle found!\n'
+ print('Neutral saddle found!\n')
elif abs(real(eigs[i])) < 1e-5:
for j in range(i+1, len(eigs)):
if abs(real(eigs[j])) < 1e-5 and abs(real(eigs[i]) - real(eigs[j])) < 1e-5:
@@ -530,7 +530,7 @@
def info(self, C, ind=None):
if ind is None:
- ind = range(len(self.found))
+ ind = list(range(len(self.found)))
elif isinstance(ind, int):
ind = [ind]
@@ -564,7 +564,7 @@
dRefactoringTool: Refactored ./PyDSTool/Points.py
ef info(self, C, ind=None):
if ind is None:
- ind = range(len(self.found))
+ ind = list(range(len(self.found)))
elif isinstance(ind, int):
ind = [ind]
@@ -619,7 +619,7 @@
def info(self, C, ind=None):
if ind is None:
- ind = range(len(self.found))
+ ind = list(range(len(self.found)))
elif isinstance(ind, int):
ind = [ind]
@@ -662,7 +662,7 @@
def info(self, C, ind=None):
if ind is None:
- ind = range(len(self.found))
+ ind = list(range(len(self.found)))
elif isinstance(ind, int):
ind = [ind]
--- ./PyDSTool/Points.py (original)
+++ ./PyDSTool/Points.py (refactored)
@@ -7,13 +7,13 @@
# ----------------------------------------------------------------------------
-from __future__ import division
+
## PyDSTool imports
-from utils import *
-from common import *
-from errors import *
-from parseUtils import symbolMapClass, mapNames
+from .utils import *
+from .common import *
+from .errors import *
+from .parseUtils import symbolMapClass, mapNames
## Other imports
from numpy import Inf, NaN, isfinite, array2string, r_, c_, \
@@ -96,7 +96,7 @@
kw = kwd
self._parameterized = False
self.labels = {}
- if intersect(kw.keys(), point_keys) == []:
+ if intersect(list(kw.keys()), point_keys) == []:
temp_kw = {}
temp_kw['coorddict'] = copy(kw)
kw = copy(temp_kw)
@@ -118,7 +118,7 @@
coordvalues = []
if 'coorddict' in kw:
vals = []
- for n, v in kw['coorddict'].iteritems():
+ for n, v in kw['coorddict'].items():
# Add coord name with type checking
coordnames.append(n if isinstance(n, str) else repr(n))
@@ -237,16 +237,16 @@
def makeIxMaps(self):
- self._name_ix_map = dict(zip(self.coordnames, range(self.dimension)))
+ self._name_ix_map = dict(list(zip(self.coordnames, list(range(self.dimension)))))
self._ix_name_map = copy(self.coordnames)
def todict(self, aslist=False):
"""Convert Point to a dictionary of array values (or of list with aslist=True)."""
if aslist:
- return dict(zip(self._ix_name_map, self.coordarray.tolist()))
- else:
- return dict(zip(self._ix_name_map, self.coordarray))
+ return dict(list(zip(self._ix_name_map, self.coordarray.tolist())))
+ else:
+ return dict(list(zip(self._ix_name_map, self.coordarray)))
def __contains__(self, coord):
return coord in self.coordnames
@@ -261,11 +261,11 @@
return d
def update(self, d):
- for k, v in d.iteritems():
+ for k, v in d.items():
self.coordarray[self._map_names_to_ixs(k)] = v
def items(self):
- return zip(self._ix_name_map, self.coordarray)
+ return list(zip(self._ix_name_map, self.coordarray))
def iteritems(self):
return iter(zip(self._ix_name_map, self.coordarray))
@@ -294,7 +294,7 @@
except TypeError:
# list of strings
return [self._name_ix_map[n] for n in namelist]
- except KeyError, e:
+ except KeyError as e:
raise PyDSTool_KeyError("Name not found: "+str(e))
@@ -304,8 +304,8 @@
def _force_coords_to_ixlist(self, x):
if x is None:
- return range(self.dimension)
- elif x in xrange(self.dimension):
+ return list(range(self.dimension))
+ elif x in range(self.dimension):
# only used for recursive calls
return [x]
elif x in self.coordnames:
@@ -313,7 +313,7 @@
return [self._name_ix_map[x]]
elif isinstance(x, _seq_types):
if len(x) == 0:
- return range(self.dimension)
+ return list(range(self.dimension))
else:
return [self._force_coords_to_ixlist(el)[0] for el in x]
elif isinstance(x, slice):
@@ -321,14 +321,14 @@
s1, s2, s3 = x.indices(stop)
if s1 < 0 or s2 > self.dimension or s1 >= self.dimension:
raise ValueError("Slice index out of range")
- return range(s1, s2, s3)
+ return list(range(s1, s2, s3))
else:
raise ValueError("Invalid coordinate / index: %s"%str(x) + \
" -- coord names are: %s"%str(self.coordnames))
def __call__(self, coords):
- if coords in xrange(self.dimension+1):
+ if coords in range(self.dimension+1):
if coords == self.dimension:
# trap for when Point is used as an iterator, i.e. as
# for x in pt -- avoids writing an __iter__ method that
@@ -540,7 +540,7 @@
outputStr += c+': '+dvstr
if c != self.coordnames[-1]:
outputStr += "\n"
- for label, infodict in self.labels.iteritems():
+ for label, infodict in self.labels.items():
outputStr += "\nLabels: %s (%s)"%(label, str(infodict))
return outputStr
@@ -553,7 +553,7 @@
def info(self, verboselevel=1):
- print self._infostr(verboselevel)
+ print(self._infostr(verboselevel))
def __abs__(self):
@@ -595,7 +595,7 @@
if kw != {}:
raise ValueError("Cannot mix keyword dictionary and keywords")
kw = kwd
- if intersect(kw.keys(), point_keys) == []:
+ if intersect(list(kw.keys()), point_keys) == []:
# creating Pointset from dictionary
temp_kw = {}
temp_kw['coorddict'] = copy(kw)
@@ -612,8 +612,8 @@
self.indepvartype = _num_equivtype[it]
except KeyError:
raise TypeError('Independent variable type %s not valid'%str(it))
- vals = kw['indepvardict'].values()[0]
- self.indepvarname = kw['indepvardict'].keys()[0]
+ vals = list(kw['indepvardict'].values())[0]
+ self.indepvarname = list(kw['indepvardict'].keys())[0]
if isinstance(vals, _seq_types):
self.indepvararray = array(vals, self.indepvartype)
else:
@@ -696,7 +696,7 @@
self.coordtype = _num_equivtype[ct]
except KeyError:
raise TypeError('Coordinate type %s not valid for Point'%str(ct))
- for c, v in kw['coorddict'].iteritems():
+ for c, v in kw['coorddict'].items():
if isinstance(c, str):
c_key = c
else:
@@ -716,7 +716,7 @@
raise TypeError("Must pass arrays, lists, or numeric types")
else:
coorddict[c_key] = array([v], self.coordtype)
- self.coordnames = coorddict.keys()
+ self.coordnames = list(coorddict.keys())
# only way to order dictionary keys for array is to sort
self.coordnames.sort()
self.dimension = len(self.coordnames)
@@ -779,10 +779,10 @@
else:
coordnames = [str(cix) for cix in range(self.dimension)]
if len(coordnames) != self.dimension:
- print "Pointset initialization error:"
- print "Found Coordnames: ", coordnames, \
- "(dimension = %s)"%len(coordnames)
- print "vs. data dimension =", self.dimension
+ print("Pointset initialization error:")
+ print("Found Coordnames: ", coordnames, \
+ "(dimension = %s)"%len(coordnames))
+ print("vs. data dimension =", self.dimension)
raise ValueError("Mismatch between number of coordnames and "
"dimension of data")
cs = array(coordnames)
@@ -896,7 +896,7 @@
def reverse(self):
"""Reverse order of points *IN PLACE*."""
self.coordarray = self.coordarray[:,::-1]
- self.labels.mapIndices(dict(zip(range(0,len(self)),range(len(self)-1,-1,-1))))
+ self.labels.mapIndices(dict(list(zip(list(range(0,len(self))),list(range(len(self)-1,-1,-1))))))
def rename(self, coord, newcoord):
"""Rename a coordinate."""
@@ -908,7 +908,7 @@
self.makeIxMaps()
def makeIxMaps(self):
- self._name_ix_map = dict(zip(self.coordnames, range(self.dimension)))
+ self._name_ix_map = dict(list(zip(self.coordnames, list(range(self.dimension)))))
self._ix_name_map = copy(self.coordnames)
if self._parameterized:
self._indepvar_ix_map = makeArrayIxMap(self.indepvararray)
@@ -920,7 +920,7 @@
"""Add string label to indexed point. info dictionary is optional"""
if ix < 0:
ix = len(self)+ix
- if ix in xrange(len(self)):
+ if ix in range(len(self)):
self.labels.update(ix, label, info)
else:
raise ValueError("Index out of range")
@@ -1121,9 +1121,9 @@
s1, s2, s3 = ref1.indices(stop)
if s1 < 0 or s2 > ls or s1 >= ls:
raise ValueError("Slice index out of range")
- ca = take(self.coordarray, xrange(s1, s2, s3), axis=1)
+ ca = take(self.coordarray, range(s1, s2, s3), axis=1)
try:
- ci = take(self.indepvararray, xrange(s1, s2, s3),axis=0)
+ ci = take(self.indepvararray, range(s1, s2, s3),axis=0)
except (IndexError, AttributeError):
# non-parameterized pointset
pass
@@ -1134,12 +1134,12 @@
lowest_ix = len(self)+lowest_ix
new_cl_ixs = [i-lowest_ix for i in cl_ixs]
else:
- print "ref1 argument =", ref1
+ print("ref1 argument =", ref1)
raise TypeError("Type %s is invalid for Pointset indexing"%str(type(ref1)))
ixlist = self._force_coords_to_ixlist(ref2)
ca = take(ca, ixlist, axis=0)
try:
- cl.mapIndices(dict(zip(cl_ixs, new_cl_ixs)))
+ cl.mapIndices(dict(list(zip(cl_ixs, new_cl_ixs))))
except AttributeError:
pass
if self._parameterized:
@@ -1224,7 +1224,7 @@
elif isinstance(ix, (list, ndarray)):
new_cl_ixs = [ixmap[i] for i in cl_ixs]
try:
- labels.mapIndices(dict(zip(cl_ixs, new_cl_ixs)))
+ labels.mapIndices(dict(list(zip(cl_ixs, new_cl_ixs))))
except AttributeError:
# empty
pass
@@ -1250,7 +1250,7 @@
else:
labels = self.labels[ix]
try:
- labels.mapIndices(dict(zip(labels, [i-ix[0] for i in labels.getIndices()])))
+ labels.mapIndices(dict(list(zip(labels, [i-ix[0] for i in labels.getIndices()]))))
except AttributeError:
# empty
pass
@@ -1267,7 +1267,7 @@
def __contains__(self, other):
- for i in xrange(len(self)):
+ for i in range(len(self)):
if comparePointCoords(self.__getitem__(i), other):
return True
return False
@@ -1390,7 +1390,7 @@
lenp = len(p)
vd_p = p.todict()
try:
- s_ixs = [self.findIndex(iva_p[i])[1]+i for i in xrange(lenp)]
+ s_ixs = [self.findIndex(iva_p[i])[1]+i for i in range(lenp)]
except TypeError:
raise ValueError("Independent variable "
"values in Pointset already present")
@@ -1398,7 +1398,7 @@
s_label_ixs = self.labels.getIndices()
sLabelMap = {}
pLabelMap = {}
- for i in xrange(lenp):
+ for i in range(lenp):
s_ix = s_ixs[i]
if i in p_label_ixs:
pLabelMap[i] = s_ix
@@ -1406,7 +1406,7 @@
if s_label_ix >= s_ix-i:
sLabelMap[s_label_ix] = s_label_ix+i+1
# for each one, list-insert new point data
- for p_ix in xrange(lenp):
+ for p_ix in range(lenp):
s_ix = s_ixs[p_ix]
iva.insert(s_ix, iva_p[p_ix])
for k in self._ix_name_map:
@@ -1514,18 +1514,18 @@
self.coordarray.dtype)
if self._parameterized:
self.indepvararray.resize(new_len)
- tvals = tval[range(added_len)]
+ tvals = tval[list(range(added_len))]
self.indepvararray[old_len:] = tvals
- for tix in xrange(old_len):
+ for tix in range(old_len):
self.coordarray[:, tix] = old_coords[:, tix]
pdict = p.todict()
self.coordarray[:, old_len:] = r_[[pdict[c][start_ix:] for c in self._ix_name_map]]
p_labels = copy(p.labels)
pixs = p.labels.getIndices()
if start_ix == 1:
- p_labels.mapIndices(dict(zip(pixs, [i+old_len-1 for i in pixs])))
- else:
- p_labels.mapIndices(dict(zip(pixs, [i+old_len for i in pixs])))
+ p_labels.mapIndices(dict(list(zip(pixs, [i+old_len-1 for i in pixs]))))
+ else:
+ p_labels.mapIndices(dict(list(zip(pixs, [i+old_len for i in pixs]))))
self.labels.update(p_labels)
elif isinstance(p, Point):
# check p dimension and coordnames and type
@@ -1564,9 +1564,9 @@
self.indepvararray.resize(new_len)
self.indepvararray.resize(new_len)
self.indepvararray[new_len-1] = tval
- for tix in xrange(new_len-1):
+ for tix in range(new_len-1):
self.coordarray[:, tix] = old_coords[:, tix]
- for ix in xrange(self.dimension):
+ for ix in range(self.dimension):
self.coordarray[ix,new_len-1] = p(self._ix_name_map[ix])
if len(p.labels) > 0:
self.labels.update({new_len-1: p.labels})
@@ -1602,9 +1602,9 @@
def todict(self, aslist=False):
"""Convert Pointset to a dictionary of arrays (or of lists with aslist=True)."""
if aslist:
- d = dict(zip(self._ix_name_map, self.coordarray.tolist()))
- else:
- d = dict(zip(self._ix_name_map, self.coordarray))
+ d = dict(list(zip(self._ix_name_map, self.coordarray.tolist())))
+ else:
+ d = dict(list(zip(self._ix_name_map, self.coordarray)))
if self._parameterized:
d[self.indepvarname] = self.indepvararray
return d
@@ -1623,8 +1623,8 @@
precision = 8
lenv = len(self)
if lenv > 8:
- ixslo = range(0,2)
- ixshi = range(lenv-2,lenv)
+ ixslo = list(range(0,2))
+ ixshi = list(range(lenv-2,lenv))
outputStr += "\n"
if self._parameterized:
iv = self.indepvararray
@@ -1666,7 +1666,7 @@
def info(self, verboselevel=1):
- print self._infostr(verboselevel)
+ print(self._infostr(verboselevel))
def __copy__(self):
@@ -1715,8 +1715,8 @@
try:
if other._parameterized and self._parameterized:
if not all(self.indepvararray == other.indepvararray):
- print self.indepvararray
- print other.indepvararray
+ print(self.indepvararray)
+ print(other.indepvararray)
raise ValueError("Mismatched independent variable arrays")
except AttributeError:
pass
@@ -1808,7 +1808,7 @@
# always expect the dictionary to be based on index
self.by_label = DefaultDict({})
self.by_index = DefaultDict({})
- for k, v in ptlabels.iteritems():
+ for k, v in ptlabels.items():
if not isinstance(k, _int_types):
raise TypeError("Initialization dictionary must be keyed "
"by integer indices")
@@ -1816,7 +1816,7 @@
self.by_label[v][k] = {}
self.by_index[k][v] = {}
else:
- for label, infodict in v.iteritems():
+ for label, infodict in v.items():
self.by_label[label][k] = infodict
self.by_index[k][label] = infodict
else:
@@ -1826,7 +1826,7 @@
def mapIndices(self, ixMapDict):
by_index = {}
ixMap = symbolMapClass(ixMapDict)
- for ix, rest in self.by_index.iteritems():
+ for ix, rest in self.by_index.items():
by_index[ixMap(ix)] = rest
self.__init__(by_index)
@@ -1835,19 +1835,19 @@
"""Map labels, using a symbol map of class symbolMapClass."""
self.by_label = mapNames(themap, self.by_label)
new_by_index = {}
- for ix, labdict in self.by_index.iteritems():
+ for ix, labdict in self.by_index.items():
new_by_index[ix] = mapNames(themap, labdict)
self.by_index = new_by_index
def sortByIndex(self):
ixkeys = sortedDictKeys(self.by_index)
- return zip(ixkeys,[self.by_index[ix] for ix in ixkeys])
+ return list(zip(ixkeys,[self.by_index[ix] for ix in ixkeys]))
def sortByLabel(self):
labelkeys = sortedDictKeys(self.by_label)
- return zip(labelkeys,[self.by_label[label] for label in labelkeys])
+ return list(zip(labelkeys,[self.by_label[label] for label in labelkeys]))
def getIndices(self):
@@ -1880,7 +1880,7 @@
stop = key.stop or max_ixs+1
try:
s1, s2, s3 = key.indices(stop)
- ixs = xrange(s1, s2, s3)
+ ixs = range(s1, s2, s3)
key = intersect(ixs, self_ixs)
except TypeError:
key = self_ixs
@@ -1889,13 +1889,13 @@
keylabels = intersect(key, self.getLabels())
key = []
for l in keylabels:
- key.extend(self.by_label[l].keys())
+ key.extend(list(self.by_label[l].keys()))
key = makeSeqUnique(key)
elif all([isinstance(k, _int_types) for k in key]):
key = intersect(key, self.getIndices())
else:
raise TypeError("Invalid key type for PointInfo")
- return PointInfo(dict(zip(key,[self.by_index[i] for i in key])))
+ return PointInfo(dict(list(zip(key,[self.by_index[i] for i in key]))))
elif key in self.by_index:
return self.by_index[key]
elif key in self.by_label:
@@ -1968,9 +1968,9 @@
if key2 == ():
# remove all labels associated with index, or vice versa
if byix:
- key2 = self.by_index[key1].keys()
- else:
- key2 = self.by_label[key1].keys()
+ key2 = list(self.by_index[key1].keys())
+ else:
+ key2 = list(self.by_label[key1].keys())
if byix:
for k in key2:
# have to check k in dict otherwise DefaultDict creates entry!
@@ -2000,14 +2000,14 @@
def update(self, key1, key2=None, info=None):
if isinstance(key1, PointInfo):
if key2 is None and info is None:
- for k, v in key1.by_index.iteritems():
- for vk, vv in v.iteritems():
+ for k, v in key1.by_index.items():
+ for vk, vv in v.items():
self.update(k, vk, vv)
else:
raise TypeError("Invalid calling sequence to update")
elif isinstance(key1, dict):
if key2 is None and info is None:
- for k, v in key1.iteritems():
+ for k, v in key1.items():
if isinstance(k, _int_types):
if k < 0:
k = k + len(self.by_index)
@@ -2020,7 +2020,7 @@
k3 = v[1]
self.update(k, k2, k3)
elif isinstance(v, dict):
- for k2, k3 in v.iteritems():
+ for k2, k3 in v.items():
self.update(k, k2, k3)
else:
raise ValueError("Invalid data for update")
@@ -2054,14 +2054,14 @@
def __delitem__(self, key):
if key in self.by_index:
- labels = self.by_index[key].keys()
+ labels = list(self.by_index[key].keys())
del self.by_index[key]
for label in labels:
del self.by_label[label][key]
if self.by_label[label] == {}:
del self.by_label[label]
elif key in self.by_label:
- ixs = self.by_label[key].keys()
+ ixs = list(self.by_label[key].keys())
del self.by_label[key]
for ix in ixs:
del self.by_index[ix][key]
@@ -2073,8 +2073,8 @@
def __eq__(self, other):
try:
- return all(self.by_index.keys() == other.by_index.keys()) and \
- all(self.by_label.keys() == other.by_label.keys())
+ return all(list(self.by_index.keys()) == list(other.by_index.keys())) and \
+ all(list(self.by_label.keys()) == list(other.by_label.keys()))
except AttributeError:
raise TypeError("Invalid type for comparison to PointInfo")
@@ -2107,11 +2107,11 @@
def _pretty_print_label(d):
"""Internal utility to pretty print point label info."""
s = " %s: "%repr(d[0])
- entry_keys = d[1].keys()
+ entry_keys = list(d[1].keys())
ki = 0
kimax = len(entry_keys)
for k in entry_keys:
- keys = d[1][k].keys()
+ keys = list(d[1][k].keys())
if len(keys) == 0:
s += "{%s: {}}"%k
else:
@@ -2134,9 +2134,9 @@
"""
try:
p1d = dict(p1)
- p1dk = p1d.keys()
+ p1dk = list(p1d.keys())
p2d = dict(p2)
- p2dk = p2d.keys()
+ p2dk = list(p2d.keys())
except:
raise TypeError("Invalid Points, Pointsets, or dictionaries passed "
"to comparePointCoords")
@@ -2312,7 +2312,7 @@
raise TypeError("Must pass Pointset to this function: use "
"arrayToPointset first!")
infodict_usedkeys = []
- for key, info in infodict.iteritems():
+ for key, info in infodict.items():
if isinstance(info, str):
infodict_usedkeys += [info]
elif info == []:
@@ -2323,9 +2323,9 @@
allnames = copy(thepointset.coordnames)
if thepointset._parameterized:
allnames.append(thepointset.indepvarname)
- remlist = remain(infodict_usedkeys, allnames+range(len(allnames)))
+ remlist = remain(infodict_usedkeys, allnames+list(range(len(allnames))))
if remlist != []:
- print "Coords not found in pointset:", remlist
+ print("Coords not found in pointset:", remlist)
raise ValueError("invalid keys in infodict - some not present "
"in thepointset")
assert isinstance(ext, str), "'ext' extension argument must be a string"
@@ -2341,11 +2341,11 @@
totlen = len(thepointset)
if totlen == 0:
raise ValueError("Pointset is empty")
- for fname, tup in infodict.iteritems():
+ for fname, tup in infodict.items():
try:
f = open(fname+ext, modestr)
except IOError:
- RefactoringTool: Refactored ./PyDSTool/ModelSpec.py
print "There was a problem opening file "+fname+ext
+ print("There was a problem opening file "+fname+ext)
raise
try:
if isinstance(tup, str):
@@ -2386,7 +2386,7 @@
"tuples/lists of strings or integers")
except IOError:
f.close()
- print "Problem writing to file"+fname+ext
+ print("Problem writing to file"+fname+ext)
raise
except KeyError:
f.close()
@@ -2442,7 +2442,7 @@
if filelen <= 1:
raise ValueError("Only 1 data point found in variables datafile")
x_dummy_all = xFileStrList[preamblelines].rstrip("\n")
- x_dummy_vallist = filter(lambda s: s != '', x_dummy_all.split(sep))
+ x_dummy_vallist = [s for s in x_dummy_all.split(sep) if s != '']
if t is None:
get_t = 0
elif isinstance(t, str):
@@ -2467,10 +2467,10 @@
if indices == []:
if get_t == 2:
dim = len(x_dummy_vallist)-1
- indices = remain(range(0,dim+1),[t])
+ indices = remain(list(range(0,dim+1)),[t])
else:
dim = len(x_dummy_vallist)
- indices = range(0,dim)
+ indices = list(range(0,dim))
else:
dim = len(indices)
if get_t == 2:
@@ -2516,11 +2516,11 @@
tVals = zeros(filelen-start, float)
xVals = zeros([filelen-start, dim], float)
# read rest of file
- for i in xrange(filelen-start):
+ for i in range(filelen-start):
vLine = xFileStrList[i+start].rstrip("\n")
if vLine == '':
continue
- vLineVals = filter(lambda s: s != '', vLine.split(sep))
+ vLineVals = [s for s in vLine.split(sep) if s != '']
if get_t == 1:
# Additional left strip of space char in case sep is different
tLine = tFileStrList[i+start].rstrip("\n").lstrip(sep).lstrip(" ")
@@ -2535,7 +2535,7 @@
try:
xLineVals = [vLineVals[ix] for ix in indices]
except IndexError:
- print "Valid indices were: 0 -", len(vLineVals)-1
+ print("Valid indices were: 0 -", len(vLineVals)-1)
raise
if len(xLineVals) != dim:
raise ValueError("Exactly "+str(dim)+" values expected per "
@@ -2549,13 +2549,13 @@
return xVals
else:
# non-parameterized pointset
- return Pointset(dict(zip(varnames, xVals)))
+ return Pointset(dict(list(zip(varnames, xVals))))
else:
if varnames is None:
return {t_name: tVals, 'vararray': xVals.T}
else:
return Pointset(indepvardict={t_name: tVals},
- coorddict=dict(zip(varnames,xVals.T)))
+ coorddict=dict(list(zip(varnames,xVals.T))))
def export_pointset_to_CSV(filename, pts):
@@ -2578,10 +2578,10 @@
# data rows
if pts._parameterized:
- for i in xrange(len(pts)):
+ for i in range(len(pts)):
writer.writerow([pts.indepvararray[i]] + list(pts.coordarray[:,i]))
else:
- for i in xrange(len(pts)):
+ for i in range(len(pts)):
writer.writerow(pts.coordarray[:,i])
outfile.close()
@@ -2658,7 +2658,7 @@
tlo, thi = pinterval
ts = pts.indepvararray
all_dict = value_dict.copy()
- assert remain(value_dict.keys(), pts.coordnames) == []
+ assert remain(list(value_dict.keys()), pts.coordnames) == []
if eps is None:
eps = pts._abseps
if tlo < ts[0]:
--- ./PyDSTool/ModelSpec.py (original)
+++ ./PyDSTool/ModelSpec.py (refactored)
@@ -12,15 +12,15 @@
# ----------------------------------------------------------------------------
-from __future__ import division
-from common import *
-from utils import info as utils_info
-from parseUtils import *
-from errors import *
-from Symbolic import *
+
+from .common import *
+from .utils import info as utils_info
+from .parseUtils import *
+from .errors import *
+from .Symbolic import *
from math import *
-from utils import *
+from .utils import *
from numpy import Inf, NaN, isfinite, mod, sum
from numpy import sometrue, alltrue
from copy import copy, deepcopy
@@ -90,7 +90,7 @@
def rename(self, newName):
oldName = self.name
- for robj in self._registry.values():
+ for robj in list(self._registry.values()):
if robj.objParentName == oldName:
robj.objParentName = newName
self.name = newName
@@ -139,7 +139,7 @@
## if globalRefs is None:
## print "Unresolved symbols:", self.freeSymbols
## else:
- print "Unresolved symbols:", remain(self.freeSymbols, globalRefs)
+ print("Unresolved symbols:", remain(self.freeSymbols, globalRefs))
raise ValueError("Cannot flatten incomplete functional "
"specification")
if self.funcSpecDict == {} or force:
@@ -148,14 +148,14 @@
except KeyboardInterrupt:
raise
except:
- print "compileFuncSpec() failed"
+ print("compileFuncSpec() failed")
raise
fs = self.funcSpecDict
# name mappings to be compatible with FuncSpec.py and python variable
# naming rules: i.e. "a_name.b.x3" (ModelSpec) <-> "a_name_b_x3" (FuncSpec/python)
FScompatibleNames = {}
FScompatibleNamesInv = {}
- for name in self._registry.keys():
+ for name in list(self._registry.keys()):
FScompatibleNames[name] = replaceSep(name)
FScompatibleNamesInv[replaceSep(name)] = name
# store for later use
@@ -202,7 +202,7 @@
outfs['domains'] = {}
outfs['spectypes'] = {}
# mathNameMap maps title case math function names to all lower-case
- mathNameMap = dict(zip(allmathnames_symbolic,allmathnames))
+ mathNameMap = dict(list(zip(allmathnames_symbolic,allmathnames)))
# ----- start of add_to_fs function -----
def add_to_fs(k, name, carg, i=None):
# locally-defined because refers to outfs from scope of method
@@ -237,7 +237,7 @@
if multiDefUnravel:
# reconstruct list of full names for mrefs, e.g. 'z[i]' from 'z'
# otherwise just leave the dict empty
- for k, v in self.multiDefRefs.iteritems():
+ for k, v in self.multiDefRefs.items():
try:
ksubs = FScompatibleNames[k]
except KeyError:
@@ -252,14 +252,14 @@
FScompatibleNamesInv[ksubs+str(ix)] = k+str(ix)
full_mref_names[ksubs+"["+v[0]+","+str(v[1])+","+str(v[2])+"]"]\
= ksubs
- for k, v in fs.iteritems():
+ for k, v in fs.items():
if k in quants:
for c in v:
- if c.name in full_mref_names.keys():
+ if c.name in list(full_mref_names.keys()):
# unravel defs given by pairs p in unravelDict
root = full_mref_names[c.name]
for p in unravelDict[root]:
- for i in xrange(p[0],p[1]+1):
+ for i in range(p[0],p[1]+1):
name = root + str(i)
try:
if name not in outfs[k]:
@@ -292,36 +292,36 @@
defined = True # initial value
if len(self.compatibleGens) == 0:
if verbose:
- print "'%s' ill defined: empty compatibleGens"%self.name
+ print("'%s' ill defined: empty compatibleGens"%self.name)
return False
if len(self.targetLangs) == 0:
if verbose:
- print "'%s' ill defined: empty targetLangs"%self.name
+ print("'%s' ill defined: empty targetLangs"%self.name)
return False
if self.isEmpty():
if verbose:
- print "'%s' ill defined: empty contents"%self.name
+ print("'%s' ill defined: empty contents"%self.name)
return False
- for v in self.variables.values():
+ for v in list(self.variables.values()):
if not v.isDefined(verbose):
if verbose:
- print "... in '%s' (type %s)"%(self.name,str(self.__class__))
+ print("... in '%s' (type %s)"%(self.name,str(self.__class__)))
return False
- for p in self.pars.values():
+ for p in list(self.pars.values()):
if not p.isDefined(verbose):
if verbose:
- print "... in '%s' (type %s)"%(self.name,str(self.__class__))
+ print("... in '%s' (type %s)"%(self.name,str(self.__class__)))
return False
if not ignoreInputs:
- for i in self.inputs.values():
+ for i in list(self.inputs.values()):
if not i.isDefined(verbose):
if verbose:
- print "... in '%s' (type %s)"%(self.name,str(self.__class__))
+ print("... in '%s' (type %s)"%(self.name,str(self.__class__)))
return False
- for a in self.auxfns.values():
+ for a in list(self.auxfns.values()):
if not a.isDefined(verbose):
if verbose:
- print "... in '%s' (type %s)"%(self.name,str(self.__class__))
+ print("... in '%s' (type %s)"%(self.name,str(self.__class__)))
return False
return defined
@@ -373,13 +373,13 @@
results.append(type(self) == type(other))
results.append(self.name == other.name)
results.append(self._registry == other._registry)
- except AttributeError, e:
+ except AttributeError as e:
if diff:
- print "Type:", className(self), results
- print " " + e
+ print("Type:", className(self), results)
+ print(" " + e)
return False
if diff:
- print "Type:", className(self), results
+ print("Type:", className(self), results)
return alltrue(results)
@@ -398,26 +398,26 @@
"Invalid target language for '" + self.name + "'"
if hasattr(self, 'components'):
# leaf nodes do not have this
- for c in self.components.values():
+ for c in list(self.components.values()):
assert c in self._componentNameMap, "Component name map incomplete"
# assert remain(self._componentNameMap[c],
# self._registry.keys()) == []
- for v in self.flatSpec['FScompatibleNamesInv'](self.variables.values()):
+ for v in self.flatSpec['FScompatibleNamesInv'](list(self.variables.values())):
assert v in self._componentNameMap, "Variable name map incomplete"
- for p in self.flatSpec['FScompatibleNamesInv'](self.pars.values()):
+ for p in self.flatSpec['FScompatibleNamesInv'](list(self.pars.values())):
if p not in self._componentNameMap and p.name not in self.eventPars:
- print "\n", self.name, self
- print "Pars:", p
- print p.name in self.flatSpec['FScompatibleNames']
- print p.name in self.flatSpec['FScompatibleNamesInv']
- print self.eventPars
- print self.flatSpec['FScompatibleNamesInv'](p)
- print "Component name map:", self._componentNameMap
+ print("\n", self.name, self)
+ print("Pars:", p)
+ print(p.name in self.flatSpec['FScompatibleNames'])
+ print(p.name in self.flatSpec['FScompatibleNamesInv'])
+ print(self.eventPars)
+ print(self.flatSpec['FScompatibleNamesInv'](p))
+ print("Component name map:", self._componentNameMap)
raise AssertionError("Parameter name map incomplete")
i = None
- for i in self.flatSpec['FScompatibleNamesInv'](self.inputs.values()):
+ for i in self.flatSpec['FScompatibleNamesInv'](list(self.inputs.values())):
assert i in self._componentNameMap, "External input name map incomplete"
- for a in self.flatSpec['FScompatibleNamesInv'](self.auxfns.values()):
+ for a in self.flatSpec['FScompatibleNamesInv'](list(self.auxfns.values())):
assert a in self._componentNameMap, "Auxiliary function name map incomplete"
# !! check that compatibleGens point to known Generator types !!
# if get this far without raising exception, then valid
@@ -462,11 +462,11 @@
self.auxfns[objname] = obj
elif isinstance(obj, ModelSpec):
if not issubclass(self.__class__, obj.compatibleContainers):
- print "Component " + self.name + ": " + self.__class__.__name__
- print "Invalid sub-component " + objname \
- + " (type " + className(obj) + ") to add,"
- print " with compatible container types:", obj.compatibleContainers
- print "Compatible sub-component types: ", self._allSubcomponentTypes
+ print("Component " + self.name + ": " + self.__class__.__name__)
+ print("Invalid sub-component " + objname \
+ + " (type " + className(obj) + ") to add,")
+ print(" with compatible container types:", obj.compatibleContainers)
+ print("Compatible sub-component types: ", self._allSubcomponentTypes)
raise ValueError("Incompatible sub-component type"
" for object '" + objname + "'")
else:
@@ -487,21 +487,21 @@
# object inherits self's
obj.compatibleGens = self.compatibleGens
elif len(remain(obj.compatibleGens, self.compatibleGens)) > 0:
- print remain(obj.compatibleGens, self.compatibleGens)
+ print(remain(obj.compatibleGens, self.compatibleGens))
raise ValueError("Incompatible generators found in component"
" '" + obj.name + "'")
if len(obj.targetLangs) == 0:
# object inherits self's
obj.targetLangs = self.targetLangs
elif len(remain(obj.targetLangs, self.targetLangs)) > 0:
- print remain(obj.targetLangs, self.targetLangs)
+ print(remain(obj.targetLangs, self.targetLangs))
raise ValueError("Incompatible target language in component"
" '" + obj.name + "'")
if obj.name in protected_allnames:
raise ValueError("Name '" + obj.name + "' is a protected name")
if not compareClassAndBases(obj, self._allSubcomponentTypes):
- print "Valid sub-component types that have been declared:", \
- self._allSubcomponentTypes
+ print("Valid sub-component types that have been declared:", \
+ self._allSubcomponentTypes)
raise TypeError("Invalid type for object '" + obj.name + \
"' in component '" + self.name + "'")
if parent_obj is None:
@@ -526,7 +526,7 @@
# names that are to be added to the registry at this level.
namemap = {}
tracebacknames = []
- for sub_regObj in obj._registry.values():
+ for sub_regObj in list(obj._registry.values()):
subobj = sub_regObj.obj
subobjname = self._register(subobj, depth+1, obj)
# _register won't have created an entry yet
@@ -547,7 +547,7 @@
# First, take out symbols defined by obj (i.e. those appearing in
# its registry) from self.freeSymbols
mapper = symbolMapClass(namemap)
- globalized_newdefs = mapper(obj._registry.keys())
+ globalized_newdefs = mapper(list(obj._registry.keys()))
self.freeSymbols = remain(self.freeSymbols,
globalized_newdefs)
obj_freeSymbols = mapper(obj.freeSymbols)
@@ -559,7 +559,7 @@
# print "Obj free (orig):", obj.freeSymbols, "(mapped)", obj_freeSymbols
# the following never executes!
if obj_freeSymbols != obj.freeSymbols:
- print "mapped object free symbols not same as originals"
+ print("mapped object free symbols not same as originals")
# Test code introspection for HH_spectest.py
# if self.name == 'cell1' and obj.name == 'chan_s21':
# # this is None, so comment out namemap[s] = snew below!
@@ -575,7 +575,7 @@
# namemap[s] = snew
# # TEMP
# print self.name, obj.name, "namemap[%s] = %s"%(s,snew)
- for sub_regObj in obj._registry.values():
+ for sub_regObj in list(obj._registry.values()):
subobjname = namemap[sub_regObj.obj.name]
subsplit = subobjname.split(NAMESEP)
# resolve the first parent of objects brought up from deep
@@ -694,7 +694,7 @@
# print "new free symbols from obj:", obj_freeSymbs
# print "defined:", self._registry.keys()
self.freeSymbols.extend(remain(obj_freeSymbols,
- self._registry.keys()+self.freeSymbols))
+ list(self._registry.keys())+self.freeSymbols))
# print "resulting self.free:", self.freeSymbols
# return objname in case _register is being called recursively
return objname
@@ -754,8 +754,8 @@
parentname = tempname[0]
try:
self.components[parentname].remove("".join(tempname[1:]))
- except ValueError, e:
- print e
+ except ValueError as e:
+ print(e)
raise ValueError("Error recognizing parent object '%s' in "
"sub-component '%s'"%(parentname,objname))
else:
@@ -780,23 +780,23 @@
self._componentNameMap = {}
self._componentTypeMap = {}
nameResolver.clear(self)
- for v in self.variables.values():
+ for v in list(self.variables.values()):
self._register(v)
- for p in self.pars.values():
+ for p in list(self.pars.values()):
self._register(p)
- for i in self.inputs.values():
+ for i in list(self.inputs.values()):
self._register(i)
- for a in self.auxfns.values():
+ for a in list(self.auxfns.values()):
self._register(a)
# do components, if any, last, so that self._componentNameMap is
# built up properly (otherwise get validation error)
if hasattr(self, 'components'):
# leaf nodes do not have this
- for c in self.components.values():
+ for c in list(self.components.values()):
self._register(c)
try:
self.validate()
- except AssertionError, e:
+ except AssertionError as e:
raise RuntimeError("Model spec structure inconsistent: "+str(e))
@@ -821,7 +821,7 @@
utils_info(self.__dict__, "ModelSpec " + self.name,
recurseDepthLimit=1+verboselevel)
else:
- print self.__repr__()
+ print(self.__repr__())
def __repr__(self):
@@ -832,19 +832,19 @@
if verbose > 0:
if len(self.components) > 0:
base_str += "\n Components: ( "
- base_str += ", ".join([c._infostr(verbose-1) for c in self.components.values()]) + " )"
+ base_str += ", ".join([c._infostr(verbose-1) for c in list(self.components.values())]) + " )"
if len(self.variables) > 0:
base_str += "\n Variables: ( "
- base_str += ", ".join([str(c) for c in self.variables.values()]) + " )"
+ base_str += ", ".join([str(c) for c in list(self.variables.values())]) + " )"
if len(self.pars) > 0:
base_str += "\n Parameters: ( "
- base_str += ", ".join([str(c) for c in self.pars.values()]) + " )"
+ base_str += ", ".join([str(c) for c in list(self.pars.values())]) + " )"
if len(self.inputs) > 0:
base_str += "\n Inputs: ( "
- base_str += ", ".join([str(c) for c in self.inputs.values()]) + " )"
+ base_str += ", ".join([str(c) for c in list(self.inputs.values())]) + " )"
if len(self.auxfns) > 0:
base_str += "\n Functions: ( "
- base_str += ", ".join([str(c) for c in self.auxfns.values()]) + " )"
+ base_str += ", ".join([str(c) for c in list(self.auxfns.values())]) + " )"
return base_str
@@ -885,7 +885,7 @@
fsdict['vars'] = []
fsdict['pars'] = []
fsdict['auxfns'] = []
- for objname, regObj in self._registry.iteritems():
+ for objname, regObj in self._registry.items():
objtype = regObj.obj.typestr+'s'
add_obj = regObj.obj.renderForCode()
if regObj.namemap != {}:
@@ -897,11 +897,11 @@
mappedName = regObj.namemap[name]
if mappedName in add_obj.freeSymbols and not \
isinstance(self._registry[mappedName].obj, (Par, Fun)):
- print "Problem with registry object:", \
- self._registry[mappedName].obj
- print "in auxiliary function:", add_obj.name
- print " that has free symbols:", \
- add_obj.freeSymbols
+ print("Problem with registry object:", \
+ self._registry[mappedName].obj)
+ print("in auxiliary function:", add_obj.name)
+ print(" that has free symbols:", \
+ add_obj.freeSymbols)
raise TypeError("Fun '" + add_obj.name + "' "
"cannot bind symbols to non-"
"pars (info printed above)")
@@ -920,7 +920,7 @@
# Quantity is defined if it has a specified definition
# (even with unbound references)
defined = ModelSpec.isDefined(self, verbose, ignoreInputs)
- for c in self.components.values():
+ for c in list(self.components.values()):
if not c.isDefined(verbose, ignoreInputs):
return False
return defined
@@ -932,7 +932,7 @@
def _register(self, obj, depth=0, parent_obj=None):
if not compareBaseClass(obj, Quantity):
- print "Bad argument %s (type %s) to register"%(str(obj), type(obj))
+ print("Bad argument %s (type %s) to register"%(str(obj), type(obj)))
raise TypeError("Not a valid Quantity type")
return ModelSpec._register(self, obj, 0, parent_obj)
@@ -947,10 +947,10 @@
assert self.isDefined(ignoreInputs=ignoreInputs), \
"Node '" + self.name + "' is not completely defined"
fsdict = {}
- fsdict['vars'] = [deepcopy(v) for v in self.variables.values()]
- fsdict['pars'] = [deepcopy(p) for p in self.pars.values()]
- fsdict['inputs'] = [deepcopy(i) for i in self.inputs.values()]
- fsdict['auxfns'] = [deepcopy(a) for a in self.auxfns.values()]
+ fsdict['vars'] = [deepcopy(v) for v in list(self.variables.values())]
+ fsdict['pars'] = [deepcopy(p) for p in list(self.pars.values())]
+ fsdict['inputs'] = [deepcopy(i) for i in list(self.inputs.values())]
+ fsdict['auxfns'] = [deepcopy(a) for a in list(self.auxfns.values())]
self.funcSpecDict = fsdict
@@ -1126,7 +1126,7 @@
elif len(sourceList) == 0:
RefactoringTool: Refactored ./PyDSTool/ModelConstructor.py
sourceName = ""
else:
- print "Found: ", sourceList
+ print("Found: ", sourceList)
raise ValueError("source list for macro resolution should have no "
"more than one entry")
targList_new, ctStr, opStr = resolveMacroTargets(qtemp.parser.tokenized,
@@ -1210,7 +1210,7 @@
try:
return self.namemap[self.objLocalName]
except KeyError:
- print "Namemap for '%s' is: "%self.__repr__(), self.namemap
+ print("Namemap for '%s' is: "%self.__repr__(), self.namemap)
raise ValueError("Namemap for registry object didn't "
"contain object's name "
"'%s'"%self.objLocalName)
--- ./PyDSTool/ModelConstructor.py (original)
+++ ./PyDSTool/ModelConstructor.py (refactored)
@@ -33,11 +33,11 @@
"""
# PyDSTool imports
-from errors import *
-from common import *
-from utils import info, remain, intersect
-import Model, Generator, ModelSpec, Symbolic, Events, MProject
-from parseUtils import symbolMapClass, NAMESEP, isNumericToken
+from .errors import *
+from .common import *
+from .utils import info, remain, intersect
+from . import Model, Generator, ModelSpec, Symbolic, Events, MProject
+from .parseUtils import symbolMapClass, NAMESEP, isNumericToken
# Other imports
from numpy import Inf, NaN, isfinite, array, \
@@ -53,8 +53,8 @@
# -----------------------------------------------------------------------------
-mathNameMap = dict(zip(Symbolic.allmathnames_symbolic,
- Symbolic.allmathnames))
+mathNameMap = dict(list(zip(Symbolic.allmathnames_symbolic,
+ Symbolic.allmathnames)))
class Descriptor(args):
@@ -65,15 +65,15 @@
def __init__(self, **kw):
self.__dict__ = filteredDict(kw, self._validKeys)
- if remain(kw.keys(), self._validKeys) != []:
- print "Valid keys: ", self._validKeys
+ if remain(list(kw.keys()), self._validKeys) != []:
+ print("Valid keys: ", self._validKeys)
raise ValueError("Invalid keys provided for Model Descriptor")
done_defs = []
- for def_key in remain(self._defaults.keys(), kw.keys()):
+ for def_key in remain(list(self._defaults.keys()), list(kw.keys())):
def_value = self._defaults[def_key]
done_defs.append(def_key)
self.__dict__[def_key] = def_value
- for key in remain(self._validKeys, kw.keys()+done_defs):
+ for key in remain(self._validKeys, list(kw.keys())+done_defs):
self.__dict__[key] = None
def validate(self):
@@ -148,7 +148,7 @@
assert hasattr(self.generatorspecs, 'values') and \
hasattr(self.generatorspecs, 'keys')
validated = alltrue([isinstance(gd, GDescriptor) for \
- gd in self.generatorspecs.values()])
+ gd in list(self.generatorspecs.values())])
# !!!TO DO!!!
# Check for consistency of any internal interfaces defined
inconsistencies = []
@@ -159,23 +159,23 @@
vars_i_all = True
pars_i_all = True
inps_i_all = True
- for ms in self.generatorspecs.values():
+ for ms in list(self.generatorspecs.values()):
all_vars = ms.modelspec.search('Var')
dyn_vars = [v for v in all_vars if ms.modelspec._registry[v].obj.specType == 'RHSfuncSpec']
vars_i = alltrue([varname in self.icvalues for \
varname in dyn_vars])
pars_i = alltrue([(parname in self.parvalues or \
par.spec.specStr !='') \
- for parname, par in ms.modelspec.pars.items()])
+ for parname, par in list(ms.modelspec.pars.items())])
inps_i = alltrue([inpname in self.inputs for \
inpname in ms.modelspec.inputs])
if verbose:
if not vars_i:
- print ms.modelspec.name, "Some ICs missing"
+ print(ms.modelspec.name, "Some ICs missing")
if not pars_i:
- print ms.modelspec.name, "Some param values missing"
+ print(ms.modelspec.name, "Some param values missing")
if not inps_i:
- print ms.modelspec.name, "Some input values missing"
+ print(ms.modelspec.name, "Some input values missing")
vars_i_all = vars_i_all and vars_i
pars_i_all = pars_i_all and pars_i
inps_i_all = inps_i_all and inps_i
@@ -350,7 +350,7 @@
### Instantiate (flatten) target model structured specification
## Flatten ModelSpec self.mspec using indepvarname global and inputs
# and using connectivity bindings (latter not yet implemented)
- globalRefs = [self.indepvarname] + self.inputs.keys()
+ globalRefs = [self.indepvarname] + list(self.inputs.keys())
self.mspec.eventPars = copy.copy(self.eventPars)
if not self.preFlat:
@@ -361,8 +361,8 @@
except KeyboardInterrupt:
raise
except:
- print "Problem flattening Model Spec '%s'"%self.mspec.name
- print "Global refs: ", globalRefs
+ print("Problem flattening Model Spec '%s'"%self.mspec.name)
+ print("Global refs: ", globalRefs)
raise
else:
flatspec = self.mspec.flatSpec
@@ -377,17 +377,17 @@
raise ValueError("Incompatible target language between supplied"
" ModelSpec and target Generator")
else:
- print "ModelSpec's compatible Generators:", \
- ", ".join(self.mspec.compatibleGens)
- print "ModelConstructor target Generator:", self.targetGen
+ print("ModelSpec's compatible Generators:", \
+ ", ".join(self.mspec.compatibleGens))
+ print("ModelConstructor target Generator:", self.targetGen)
raise ValueError("Target Generator mismatch during generator "
"construction")
self.targetLang = gsh.lang
## Make Generator initialization argument dictionary
a = args(abseps=self.abseps)
a.pars = {}
- parnames = flatspec['pars'].keys()
- for p, valstr in flatspec['pars'].iteritems():
+ parnames = list(flatspec['pars'].keys())
+ for p, valstr in flatspec['pars'].items():
if valstr == '':
if FScompatibleNamesInv(p) not in self.parvalues:
raise ValueError("Parameter %s is missing a value"%FScompatibleNamesInv(p))
@@ -404,7 +404,7 @@
" for '%s', value: %s"%(p,valstr))
# override any par vals set in ModelSpec with those explicitly set
# here
- for p, val in self.parvalues.iteritems():
+ for p, val in self.parvalues.items():
try:
pr = FScompatibleNames(p)
except KeyError:
@@ -414,7 +414,7 @@
a.pars[pr] = val
if self.icvalues != {}:
a.ics = {}
- for v, val in self.icvalues.iteritems():
+ for v, val in self.icvalues.items():
try:
vr = FScompatibleNames(v)
except KeyError:
@@ -431,7 +431,7 @@
xdomain = {}
xtype = {}
pdomain = {}
- for k, d in flatspec['domains'].iteritems():
+ for k, d in flatspec['domains'].items():
# e.g. d == (float, Continuous, [-Inf, Inf])
if k in flatspec['vars']:
if isinstance(d[2], _num_types):
@@ -451,11 +451,11 @@
a.xdomain = xdomain
a.pdomain = pdomain
a.xtype = xtype
- exp_vars = [v for (v,t) in flatspec['spectypes'].items() \
+ exp_vars = [v for (v,t) in list(flatspec['spectypes'].items()) \
if t == 'ExpFuncSpec']
- rhs_vars = [v for (v,t) in flatspec['spectypes'].items() \
+ rhs_vars = [v for (v,t) in list(flatspec['spectypes'].items()) \
if t == 'RHSfuncSpec']
- imp_vars = [v for (v,t) in flatspec['spectypes'].items() \
+ imp_vars = [v for (v,t) in list(flatspec['spectypes'].items()) \
if t == 'ImpFuncSpec']
if gsh.specType == 'RHSfuncSpec':
assert imp_vars == [], "Cannot use implicitly defined variables"
@@ -473,8 +473,8 @@
varnames = remain(varnames, self.forcedAuxVars)
auxvarnames = self.forcedAuxVars
else:
- print "Invalid auxiliary variable names:"
- print invalid_auxvars
+ print("Invalid auxiliary variable names:")
+ print(invalid_auxvars)
# raise ValueError("Forced auxiliary variable names were invalid")
elif gsh.specType == 'ImpFuncSpec':
assert rhs_vars == [], "Cannot use RHS-type variables"
@@ -504,9 +504,9 @@
flatspec, self.mspec._registry,
FScompatibleNames, FScompatibleNamesInv)
- clash_reused = intersect(reuseTerms.keys(), self.reuseTerms.keys())
+ clash_reused = intersect(list(reuseTerms.keys()), list(self.reuseTerms.keys()))
if clash_reused != []:
- print "Clashing terms:", clash_reused
+ print("Clashing terms:", clash_reused)
raise ValueError("User-supplied reused terms clash with auto-"
"generated terms")
# second pass, this time to actually make the substitutions
@@ -518,8 +518,8 @@
else:
a.reuseterms = self.preReuseTerms
- a.varspecs = dict(zip(varnames+auxvarnames, [flatspec['vars'][v] \
- for v in varnames+auxvarnames]))
+ a.varspecs = dict(list(zip(varnames+auxvarnames, [flatspec['vars'][v] \
+ for v in varnames+auxvarnames])))
a.auxvars = auxvarnames
a.fnspecs = self.userfns
try:
@@ -560,7 +560,7 @@
a.events = events
# Add any additional special options (e.g. 'nobuild' directive)
- for k,v in self.optDict.iteritems():
+ for k,v in self.optDict.items():
if hasattr(a, k):
raise KeyError("'%s' already exists as a Generator argument"%k)
a.k = v
@@ -581,7 +581,7 @@
return gsh.genClass(args(**filteredDict(a.__dict__,
gsh.genClass._needKeys+gsh.genClass._optionalKeys)))
except:
- print "Problem initializing target Generator '%s'"%self.targetGen
+ print("Problem initializing target Generator '%s'"%self.targetGen)
raise
@@ -732,7 +732,7 @@
return "ModelConstructor %s"%self.name
def preprocessFlatten(self):
- globalRefs = [self.indepvarname] + self.inputs.keys()
+ globalRefs = [self.indepvarname] + list(self.inputs.keys())
for g in self._generators:
gspec = self._generators[g]['modelspec']
try:
@@ -741,8 +741,8 @@
except KeyboardInterrupt:
raise
except:
- print "Problem flattening Model Spec %s"%self.mspec.name
- print "Global refs: ", globalRefs
+ print("Problem flattening Model Spec %s"%self.mspec.name)
+ print("Global refs: ", globalRefs)
raise
self.preFlat[g] = True
@@ -756,11 +756,11 @@
FScompatibleNames = flatspec['FScompatibleNames']
FScompatibleNamesInv = flatspec['FScompatibleNamesInv']
- exp_vars = [v for (v,t) in flatspec['spectypes'].items() \
+ exp_vars = [v for (v,t) in list(flatspec['spectypes'].items()) \
if t == 'ExpFuncSpec']
- rhs_vars = [v for (v,t) in flatspec['spectypes'].items() \
+ rhs_vars = [v for (v,t) in list(flatspec['spectypes'].items()) \
if t == 'RHSfuncSpec']
- imp_vars = [v for (v,t) in flatspec['spectypes'].items() \
+ imp_vars = [v for (v,t) in list(flatspec['spectypes'].items()) \
if t == 'ImpFuncSpec']
if gsh.specType == 'RHSfuncSpec':
assert imp_vars == [], "Cannot use implicitly defined variables"
@@ -790,9 +790,9 @@
flatspec, gspec._registry,
FScompatibleNames, FScompatibleNamesInv)
- clash_reused = intersect(reuseTerms.keys(), self.reuseTerms.keys())
+ clash_reused = intersect(list(reuseTerms.keys()), list(self.reuseTerms.keys()))
if clash_reused != []:
- print "Clashing terms:", clash_reused
+ print("Clashing terms:", clash_reused)
raise ValueError("User-supplied reused terms clash with auto-"
"generated terms")
@@ -848,7 +848,7 @@
if makeEvts:
gspec = self._generators[g]['modelspec']
if not self.preFlat[g]:
- print "Flattening"
+ print("Flattening")
gspec.flattenSpec()
fspec = gspec.flatSpec
# name maps
@@ -865,7 +865,7 @@
# Make event functions for auxfns
evtTypeList = expEvtTypeList
for s in specList:
- if s not in fspec.keys():
+ if s not in list(fspec.keys()):
continue
# auxfns are only explicit types
@@ -876,7 +876,7 @@
evtTypeList = []
checkEvtType = True
- for f in fspec[s].keys():
+ for f in list(fspec[s].keys()):
if checkEvtType:
if fspec['spectypes'][f] == 'ExpFuncSpec':
evtTypeList = expEvtTypeList
@@ -935,7 +935,7 @@
targetlang=targetLang,
flatspec=fspec,
reuseterms=reuseterms)
- except ValueError, errinfo:
+ except ValueError as errinfo:
evtSuccess = False
#print "Warning: Could not make standard event " + evtName + " with definition " + evtStr
#print " Original problem: ", errinfo
@@ -957,7 +957,7 @@
# add event par name mappings
FScNM.update(FSc_update_dict)
FScNMInv.update(FScInv_update_dict)
- if g in self._eventPars.keys():
+ if g in list(self._eventPars.keys()):
self._eventPars[g].extend(evtParList)
else:
self._eventPars[g] = evtParList
@@ -977,7 +977,7 @@
vars[vname] = gspec.flatSpec['vars'][vname]
elif v.specType == 'ExpFuncSpec':
auxvars[vname] = gspec.flatSpec['vars'][vname]
- varnames = vars.keys()
+ varnames = list(vars.keys())
varnames.sort()
# RHS specs may contain aux vars, so need to substitute their
# definitions from flatSpec
@@ -1023,7 +1023,7 @@
vars[vname] = gspec.flatSpec['vars'][vname]
elif v.specType == 'ExpFuncSpec':
auxvars[vname] = gspec.flatSpec['vars'][vname]
- varnames = vars.keys()
+ varnames = list(vars.keys())
varnames.sort()
# RHS specs may contain aux vars, so need to substitute their
# definitions from flatSpec
@@ -1048,7 +1048,7 @@
FScompatibleNamesInv = {}
genObjs = {}
assert len(self._generators) > 0, "No Generator descriptions found"
- for gname, geninfo in self._generators.iteritems():
+ for gname, geninfo in self._generators.items():
if isinstance(geninfo, args):
if isinstance(geninfo.modelspec, args):
# assume geninfo is traditional string definition
@@ -1062,13 +1062,13 @@
# GDescriptor already
gen = self._genFromMSpec(geninfo)
if gname != gen.name:
- print gname, " vs.", gen.name
+ print(gname, " vs.", gen.name)
raise ValueError("Generator name mismatch in gen descriptor")
genObjs[gen.name] = gen
# assume that there won't be any name clashes (there shouldn't be)
FScompatibleNames.update(gen._FScompatibleNames.lookupDict)
FScompatibleNamesInv.update(gen._FScompatibleNamesInv.lookupDict)
- return genObjs, genObjs.keys(), FScompatibleNames, FScompatibleNamesInv
+ return genObjs, list(genObjs.keys()), FScompatibleNames, FScompatibleNamesInv
def _genFromStrings(self, geninfodesc):
genStrings = geninfodesc['modelspec']
@@ -1130,14 +1130,14 @@
# extract par values and ic values relevant to this generator
genPars = {}
- for p, val in self.parvalues.iteritems():
+ for p, val in self.parvalues.items():
# don't bother to check that p is a valid param name
# for this generator -- that will be checked by
# GeneratorConstructor
if p in genSpec._registry:
genPars[p] = val
genICs = {}
- for v, val in self.icvalues.iteritems():
+ for v, val in self.icvalues.items():
# don't bother to check that v is a valid variable name
# for this generator -- that will be checked by
# GeneratorConstructor
@@ -1182,13 +1182,13 @@
# hack to allow test trajectories for one-gen models to avoid needing
# pre-computation in order to test a trivial condition
test_trajs = {}
- for genname, gen in genObjs.iteritems():
+ for genname, gen in genObjs.items():
test_trajs[genname] = None
if len(genObjs)==1:
# singleton generator may need non-hybrid Model class unless
# it contains discrete event state changes that map to itself
useMI = False # initial value
- genname = genObjs.keys()[0]
+ genname = list(genObjs.keys())[0]
if genname in self.eventmaps:
for emap in self.eventmaps[genname]:
if emap[1] != 'terminate':
@@ -1205,7 +1205,7 @@
test_trajs[genname] = 1
else:
useMI = True
- for hostGen, genObj in genObjs.iteritems():
+ for hostGen, genObj in genObjs.items():
if useMI:
m = embed(genObj,
tdata=genObj.indepvariable.depdomain.get())
@@ -1244,12 +1244,12 @@
for evname in allGenTermEvNames:
genMaps.append((evname, 'terminate'))
if not isfinite(genObj.indepvariable.depdomain[1]):
- print "Warning: Generator %s has no termination event"%genObj.name
- print "because it has an non-finite end computation time..."
+ print("Warning: Generator %s has no termination event"%genObj.name)
+ print("because it has an non-finite end computation time...")
modelInfoEntries[hostGen] = makeModelInfoEntry(DSi,
allDSnames,
genMaps)
- modelInfoDict = makeModelInfo(modelInfoEntries.values())
+ modelInfoDict = makeModelInfo(list(modelInfoEntries.values()))
# 3. build model
mod_args = {'name': self.name,
'modelInfo': modelInfoDict,
@@ -1311,7 +1311,7 @@
elif isinstance(fnTarg, dict):
# for compatibility with list style of _funcs for symbolic Fun
# objects, convert the string defs to symbolic form
- for k, v in fnTarg.items():
+ for k, v in list(fnTarg.items()):
self._funcs[hostGen].append(Symbolic.Fun(v[1], v[0], k))
else:
self._funcs[hostGen].append(fnTarg)
@@ -1347,7 +1347,7 @@
You must have declared all generators before calling this function!
"""
allGenNames = []
- for gname, geninfo in self._generators.iteritems():
+ for gname, geninfo in self._generators.items():
# geninfo may be an args(dict) type or a GDescriptor
if isinstance(geninfo, GDescriptor):
allGenNames.append(geninfo.modelspec.name)
@@ -1429,7 +1429,7 @@
for infodict in dsList:
assert len(infodict) == 1, \
"Incorrect length of info dictionary"
- dsName = infodict.keys()[0]
+ dsName = list(infodict.keys())[0]
if dsName not in allDSNames:
allDSNames.append(dsName)
returnDict.update(infodict)
@@ -1437,7 +1437,7 @@
raise ValueError("clashing DS names in info "
"dictionaries")
try:
- assert remain(infodict.values()[0].keys(), ['dsi',
+ assert remain(list(infodict.values())[0].keys(), ['dsi',
'swRules', 'globalConRules', 'domainTests']) == []
except AttributeError:
raise TypeError("Expected dictionary in modelInfo entry")
@@ -1500,7 +1500,7 @@
pars = model.query('pars')
except:
raise ValueError("Must pass instantiated Model")
- for key, value in assignDict.items():
+ for key, value in list(assignDict.items()):
rhs = ModelSpec.QuantSpec('rhs', value)
rhs_str = ''
for tok in rhs.parser.tokenized:
@@ -1547,29 +1547,29 @@
fnString = self.defString
else:
if len(self.assignDict) > 0:
- for lhs, rhs in self.assignDict.iteritems():
+ for lhs, rhs in self.assignDict.items():
if not(type(lhs)==type(rhs)==str):
raise TypeError("Assignment dictionary for event "
"mapping must consist of strings for "
"both keys and values")
fnString += "\n" + indent + ("\n"+indent).join(["%s = %s"%(l,r) \
- for l, r in self.assignDict.items()])
+ for l, r in list(self.assignDict.items())])
if len(self.defString) > 0:
fnString += "\n" + indent + ("\n"+indent).join(self.defString.split("\n"))
if len(self.activeDict) > 0:
- for evname, state in self.activeDict.iteritems():
+ for evname, state in self.activeDict.items():
if not(type(evname)==str and type(state)==bool):
raise TypeError("Invalid types given for setting "
"active events")
fnString += "\n" + indent + \
("\n"+indent).join(["estruct.setActiveFlag('%s',%s)"%(evname,str(state)) \
- for evname, state in self.activeDict.items()])
+ for evname, state in list(self.activeDict.items())])
self.defString = fnString
try:
- exec fnString
+ exec(fnString)
except:
- print 'Invalid function definition for event mapping:'
- print fnString
+ print('Invalid function definition for event mapping:')
+ print(fnString)
raise
setattr(self, 'evmapping', types.MethodType(locals()['evmapping'],
self, self.__class__))
@@ -1579,7 +1579,7 @@
try:
del d['evmapping']
except KeyError:
- print "'evmapping' local function not in self.__dict__"
+ print("'evmapping' local function not in self.__dict__")
return d
def __setstate__(self, state):
@@ -1638,7 +1638,7 @@
for (name, target) in swmap_list:
if isinstance(target, str):
if target != 'terminate':
- print name, target
+ print(name, target)
raise AssertionError("Generators can only be used "
"directly for non-hybrid systems")
else:
@@ -1647,10 +1647,10 @@
assert target[0] != name
except (TypeError, AssertionError):
# type error if not subscriptable
- print name, target
+ print(name, target)
raise AssertionError("Generators can only be used "
"directly for non-hybrid systems")
- for vname, var in dsi.model.variables.iteritems():
+ for vname, var in dsi.model.variables.items():
if alltrue(var.depdomain.isfinite()):
doms[vname] = Model.domain_test(vname+'_domtest',
pars=args(coordname=vname,
@@ -1665,7 +1665,7 @@
raise TypeError("Invalid type for DS interface: "
"must be a GeneratorInterface or ModelInterface")
# continue here only for ModelInterface
- for vname, dom in model.query('vardomains').iteritems():
+ for vname, dom in model.query('vardomains').items():
if alltrue(dom.isfinite()):
#vname_compat = model._FScompatibleNames(vname)
doms[vname] = Model.domain_test(vname+'_domtest',
@@ -1677,17 +1677,17 @@
validateTransitionName(model.name, special_reasons)
try:
# BUG !!! should only collect terminal events
- allEndReasonNames = model.query('events').keys() \
+ allEndReasonNames = list(model.query('events').keys()) \
+ special_reasons
except AttributeError:
# no events associated with the model
allEndReasonNames = special_reasons
if model.name not in allModelNames:
- print model.name, allModelNames
+ print(model.name, allModelNames)
raise ValueError('Sub-model`s name not in list of all '
'available names!')
if not alltrue([name not in allEndReasonNames for name in allModelNames]):
- print model.name, allModelNames
+ print(model.name, allModelNames)
raise ValueError('Sub-model names overlapped with event or '
'variable names')
allTargNames = allModelNames + ['terminate']
@@ -1728,13 +1728,13 @@
' once in map domain')
seenReasons.append(reason)
if reason not in allEndReasonNames:
- print "Model %s:"%model.name
- print allEndReasonNames
+ print("Model %s:"%model.name)
+ print(allEndReasonNames)
raise ValueError("name '"+reason+"' in map "
"domain is missing")
if targetName not in allTargNames:
- print "Model %s:"%model.name
- print allTargNames
+ print("Model %s:"%model.name)
+ print(allTargNames)
raise ValueError("name '"+targetName+"' in "
"map range is missing")
unseen_sr = remain(allEndReasonNames, seenReasons)
@@ -1746,11 +1746,11 @@
swmap_RefactoringTool: Refactored ./PyDSTool/Model.py
pairs.append((r, ('terminate', EvMapping())))
if len(swmap_pairs) != len(allEndReasonNames):
info(dict(swmap_pairs))
- print "(%i in total), versus:"%len(swmap_pairs)
- print allEndReasonNames, "(%i in total)"%len(allEndReasonNames)
- sw_keys = dict(swmap_pairs).keys()
- print remain(sw_keys, allEndReasonNames)
- print remain(allEndReasonNames, sw_keys)
+ print("(%i in total), versus:"%len(swmap_pairs))
+ print(allEndReasonNames, "(%i in total)"%len(allEndReasonNames))
+ sw_keys = list(dict(swmap_pairs).keys())
+ print(remain(sw_keys, allEndReasonNames))
+ print(remain(allEndReasonNames, sw_keys))
raise ValueError('Incorrect number of map pairs given in argument')
return {model.name: {'dsi': dsi, 'domainTests': doms,
'swRules': dict(swmap_pairs), 'globalConRules': globcon_list}}
@@ -1789,7 +1789,7 @@
loopCount += 1
# print "Loop count: ", loopCount
tempMap = {}
- for auxtok, sx in u_subsMap.iteritems():
+ for auxtok, sx in u_subsMap.items():
# print "** ", auxtok
if purgeDone[auxtok]:
# print " Continue 1"
@@ -1809,7 +1809,7 @@
u_subsMap.update(tempMap)
if not purgeDone and len(auxvarnames)>0:
# then must have maxed out
- print "Declared auxilary variables:", auxvarnames
+ print("Declared auxilary variables:", auxvarnames)
raise RuntimeError("You probably have an infinite loop of auxiliary "
"variable inter-dependencies: recursion depth of "
"more than %i encountered during model build"%loopCount)
@@ -1823,7 +1823,7 @@
for u in dummyQ.usedSymbols:
if u in auxvarnames:
new_reusedname = "__"+u
- if new_reusedname in reuseTerms.values():
+ if new_reusedname in list(reuseTerms.values()):
# simple way to avoid name clashes
new_reusedname += '_'+str(num_reused)
num_reused += 1
--- ./PyDSTool/Model.py (original)
+++ ./PyDSTool/Model.py (refactored)
@@ -36,17 +36,17 @@
# ----------------------------------------------------------------------------
## PyDSTool imports
-import Generator, Events, MProject
-from utils import *
-from common import *
-from errors import *
-from Interval import *
-from Trajectory import *
-from Variable import *
-from Points import *
-from ModelSpec import *
-from Symbolic import isMultiRef
-from parseUtils import isHierarchicalName, NAMESEP, mapNames, symbolMapClass
+from . import Generator, Events, MProject
+from .utils import *
+from .common import *
+from .errors import *
+from .Interval import *
+from .Trajectory import *
+from .Variable import *
+from .Points import *
+from .ModelSpec import *
+from .Symbolic import isMultiRef
+from .parseUtils import isHierarchicalName, NAMESEP, mapNames, symbolMapClass
## Other imports
import math, sys
@@ -119,8 +119,8 @@
# verify whether event exists and was flagged in associated model
try:
evpts = traj.getEvents(self.pars.bd_eventname)
- except ValueError, errinfo:
- print errinfo
+ except ValueError as errinfo:
+ print(errinfo)
raise RuntimeError("Could not find flagged events for this trajectory")
try:
evpt = evpts[self.pars.coordname]
@@ -132,8 +132,8 @@
if self.pars.abseps > 0:
# would like to re-evaluate event at its threshold+abseps, but
# leave for now
- print "Warning -- Boundary containment feature %s:"%self.name
- print " Check for uncertain case using events not implemented"
+ print("Warning -- Boundary containment feature %s:"%self.name)
+ print(" Check for uncertain case using events not implemented")
self.results.output = None
self.results.uncertain = False
else:
@@ -145,8 +145,8 @@
if self.pars.abseps > 0:
# would like to re-evaluate event at its threshold+abseps, but
# leave for now
- print "Warning -- Boundary containment feature %s:"%self.name
- print " Check for uncertain case using events not implemented"
+ print("Warning -- Boundary containment feature %s:"%self.name)
+ print(" Check for uncertain case using events not implemented")
self.results.output = evpt[0] # only use first event (in case not Terminal)
self.results.uncertain = False
else:
@@ -168,7 +168,7 @@
diffs = [p - self.pars.thresh for p in \
traj.sample(coords=self.pars.coordname)]
if self.pars.verbose_level > 1:
- print "%s diffs in coord %s ="%(self.name,self.pars.coordname), diffs
+ print("%s diffs in coord %s ="%(self.name,self.pars.coordname), diffs)
res_strict = array([sign(d) \
== self.pars.interior_dirn for d in diffs])
satisfied_strict = alltrue(res_strict)
@@ -281,7 +281,7 @@
def evaluate(self, traj):
# Arg is a traj!
- for sf in self.subfeatures.values():
+ for sf in list(self.subfeatures.values()):
self.propagate_verbosity(sf)
sf.super_pars = self.pars
sf.super_results = self.results
@@ -289,7 +289,7 @@
xlo_test = xlo_bc(traj)
if xlo_bc.results.uncertain:
if self.pars.verbose_level > 0:
- print "Lo bd uncertain"
+ print("Lo bd uncertain")
if self.isdiscrete:
# accept uncertain case for discrete domain
xlo_test = True
@@ -300,14 +300,14 @@
xhi_test = xhi_bc(traj)
if xhi_bc.results.uncertain:
if self.pars.verbose_level > 0:
- print "Hi bd uncertain"
+ print("Hi bd uncertain")
if self.isdiscrete:
# accept uncertain case for discrete domain
xhi_test = True
else:
# check transversality at critical (boundary) value of domain
xhi_test = self.subfeatures['dx_test_hi'](traj)
- for sf in self.subfeatures.values():
+ for sf in list(self.subfeatures.values()):
self.results[sf.name] = sf.results
return xlo_test and xhi_test
@@ -318,9 +318,9 @@
# Trajectory satified domain conditions!
return None
lowest_idx = Inf
- for sfname, sf in self.subfeatures.items():
+ for sfname, sf in list(self.subfeatures.items()):
if self.pars.verbose_level > 0:
- print "\n", sfname, sf.results
+ print("\n", sfname, sf.results)
try:
res = list(self.results[sfname].output)
except AttributeError:
@@ -329,7 +329,7 @@
if sf.results.satisfied:
continue
if self.pars.verbose_level > 0:
- print res
+ print(res)
# Find first index at which value is non-zero.
# Will not raise ValueError because test satisfaction
# was already checked, so must have a zero crossing
@@ -369,7 +369,7 @@
raise RuntimeError("Only use HybridModel or NonHybridModel classes")
if len(a) > 0:
if len(a) == 1 and isinstance(a[0], dict):
- if intersect(a[0].keys(),kw.keys()) != []:
+ if intersect(list(a[0].keys()),list(kw.keys())) != []:
raise ValueError("Cannot have initialization keys "
"common to both dictionary and keyword arguments")
kw.update(a[0])
@@ -404,7 +404,7 @@
# Using registry provides a shortcut for accessing a sub-model regardless
# of whether it's a Generator or a Model class
self.registry = {}
- for name, infodict in self.modelInfo.iteritems():
+ for name, infodict in self.modelInfo.items():
# set super model tag of ds object (which is either a
# ModelInterface or Generator)
try:
@@ -477,7 +477,7 @@
def sub_models(self):
"""Return a list of all sub-model instances (model interfaces or generators)"""
- return self.registry.values()
+ return list(self.registry.values())
def _makeDefaultVarNames(self):
"""Return default observable, internal, and auxiliary variable names
@@ -485,7 +485,7 @@
obsvars = []
auxvars = []
all_known_varnames = []
- for infodict in self.modelInfo.values():
+ for infodict in list(self.modelInfo.values()):
varnames = infodict['dsi'].query('variables')
all_known_varnames.extend(varnames)
auxvarnames = infodict['dsi'].query('auxvariables')
@@ -510,7 +510,7 @@
# that uses _ versions of hierarchical names that are used natively
# here.
self.pars = {}
- for model in self.registry.values():
+ for model in list(self.registry.values()):
try:
self.pars.update(model.query('pars'))
except AttributeError:
@@ -525,7 +525,7 @@
target language code for the specifications. 'modelspec' refers to
the pre-compiled abstract specifications of the model."""
if target is None:
- print "Use showInfo() to find names of defined sub-models"
+ print("Use showInfo() to find names of defined sub-models")
return
else:
showAll = type==''
@@ -548,19 +548,19 @@
raise ValueError("Model named %s is not known"%target)
def showSpec(self):
- for ds in self.registry.values():
+ for ds in list(self.registry.values()):
ds.showSpec()
def showAuxSpec(self):
- for ds in self.registry.values():
+ for ds in list(self.registry.values()):
ds.showAuxSpec()
def showAuxFnSpec(self):
- for ds in self.registry.values():
+ for ds in list(self.registry.values()):
ds.showAuxFnSpec()
def showEventSpec(self):
- for ds in self.registry.values():
+ for ds in list(self.registry.values()):
ds.showEventSpec()
def current_defining_args(self):
@@ -634,9 +634,9 @@
assert isinstance(querykey, str), \
("Query argument must be a single string")
if querykey not in self._querykeys:
- print 'Valid query keys are:', self._querykeys
- print "('events' key only queries model-level events, not those"
- print " inside sub-models)"
+ print('Valid query keys are:', self._querykeys)
+ print("('events' key only queries model-level events, not those")
+ print(" inside sub-models)")
if querykey != '':
raise TypeError('Query key '+querykey+' is not valid')
if querykey in ['pars', 'parameters']:
@@ -645,7 +645,7 @@
result = copy.copy(self.icdict)
elif querykey == 'events':
result = {}
- for dsName, model in self.registry.iteritems():
+ for dsName, model in self.registry.items():
try:
result.update(model.eventstruct.events)
except AttributeError:
@@ -658,12 +658,12 @@
elif querykey in ['vardomains', 'xdomains']:
result = {}
# accumulate domains from each sub-model for regular variables
- for model in self.registry.values():
+ for model in list(self.registry.values()):
vardoms = model.query('vardomains')
if len(result)==0:
result.update(vardoms)
else:
- for vname, vdom in result.iteritems():
+ for vname, vdom in result.items():
if vdom.issingleton:
# singleton
vdom_lo = vdom.get()
@@ -682,17 +682,17 @@
result[vname]._abseps = vdom._abseps
result[vname] = vdom
# remaining vars are promoted aux vars
- for vname in remain(self.allvars, result.keys()):
+ for vname in remain(self.allvars, list(result.keys())):
result[vname] = Interval(vname, float, [-Inf, Inf])
elif querykey in ['pardomains', 'pdomains']:
result = {}
# accumulate domains from each sub-model for regular variables
- for model in self.registry.values():
+ for model in list(self.registry.values()):
pardoms = model.query('pardomains')
if len(result)==0:
result.update(pardoms)
else:
- for pname, pdom in result.iteritems():
+ for pname, pdom in result.items():
if pdom.issingleton:
# singleton
pdom_lo = pdom.get()
@@ -713,7 +713,7 @@
elif querykey in ['auxvars', 'auxvariables']:
result = copy.copy(self.auxvars)
elif querykey == 'abseps':
- result = min([ds.query('abseps') for ds in self.registry.values()])
+ result = min([ds.query('abseps') for ds in list(self.registry.values())])
return result
def getEventMappings(self, dsName):
@@ -758,7 +758,7 @@
# find out: is root of p a valid 'type' in model spec?
# find all occurrences of last p
allFoundNames = []
- for mspecinfo in self._mspecdict.values():
+ for mspecinfo in list(self._mspecdict.values()):
foundNames = searchModelSpec(mspecinfo['modelspec'], p)
# don't add duplicates
allFoundNames.extend(remain(foundNames,allFoundNames))
@@ -810,7 +810,7 @@
# find out: is root of p a valid 'type' in model spec?
# find all occurrences of last p
allFoundNames = []
- for mspecinfo in self._mspecdict.values():
+ for mspecinfo in list(self._mspecdict.values()):
foundNames = searchModelSpec(mspecinfo['modelspec'], p)
# don't add duplicates
allFoundNames.extend(remain(foundNames,allFoundNames))
@@ -847,19 +847,19 @@
# Handle initial conditions here, because compute will pass
# the values on to the appropriate sub-models when they are called.
if 'ics' in kw:
- self.icdict.update(filteredDict(dict(kw['ics']), self.icdict.keys()))
+ self.icdict.update(filteredDict(dict(kw['ics']), list(self.icdict.keys())))
if 'tdata' in kw:
self.tdata = kw['tdata']
if 'abseps' in kw:
self._abseps = kw['abseps']
if 'inputs_t0' in kw:
- for model in self.registry.values():
+ for model in list(self.registry.values()):
# Propagate values to sub-models.
# If any values are strings they must refer to a parameter, so
# here we evaluate them. We keep a record of these for later
# automated updating.
t0val_dict = kw['inputs_t0']
- for inp, val in t0val_dict.items():
+ for inp, val in list(t0val_dict.items()):
if isinstance(val, str):
try:
new_val = self.pars[val]
@@ -884,7 +884,7 @@
self.verboselevel = kw['verboselevel']
else:
raise ValueError("Verbosity level value must be 0, 1, or 2")
- for model in self.registry.values():
+ for model in list(self.registry.values()):
# propagate to sub-models
try:
model.set(verboselevel=self.verboselevel)
@@ -892,24 +892,24 @@
# generator doesn't support verboselevel
pass
if restrictDSlist == []:
- restrictDSlist = self.registry.keys()
+ restrictDSlist = list(self.registry.keys())
# For the remaining keys, must propagate parameter changes to all
# sub-models throughout modelInfo structure.
#
# Changed by WES 10FEB06 to handle problem of 'new' pars being
# added if the parameter names do not exist in any generators
- dsis = self.modelInfo.values()
+ dsis = list(self.modelInfo.values())
numDSs = len(dsis)
# loop over keywords
for key, value in filteredDict(kw, ['ics', 'tdata',
'inputs_t0', 'restrictDSlist', 'globalt0'],
- neg=True).iteritems():
+ neg=True).items():
# keep track of the number of errors on this keyword
if isinstance(value, dict):
# keep track of entry errors for this key
entry_err_attr = {}
entry_err_val = {}
- for entrykey, entryval in value.iteritems():
+ for entrykey, entryval in value.items():
entry_err_attr[entrykey] = 0
entry_err_val[entrykey] = 0
else:
@@ -930,7 +930,7 @@
# only apply these keys to the restricted list
continue
if isinstance(value, dict):
- for entrykey, entryval in value.iteritems():
+ for entrykey, entryval in value.items():
try:
ds.set(**{key:{entrykey:entryval}})
except PyDSTool_AttributeError:
@@ -953,7 +953,7 @@
# Check that none of the entries in the dictionary caused errors
# in each sub-model
if isinstance(value, dict):
- for entrykey, entryval in value.iteritems():
+ for entrykey, entryval in value.items():
if entry_err_attr[entrykey] == numDSs:
raise PyDSTool_AttributeError('Parameter does not' +\
' exist in any sub-model: %s = %f'%(entrykey,
@@ -994,9 +994,9 @@
# (e.g. after an unxpected error or ^C interruption)
##raise ValueError('No such trajectory.')
l = len(trajname)
- for m in self.registry.values():
+ for m in list(self.registry.values()):
# delete all matching pieces (of form trajname + '_' + <digits>)
- for n in m.trajectories.keys():
+ for n in list(m.trajectories.keys()):
if n[:l] == trajname and n[l] == '_' and n[l+1:].isdigit():
m._delTraj(trajname)
else:
@@ -1046,8 +1046,8 @@
xdict[endtraj._FScompatibleNamesInv(xname)] = \
endtraj.variables[xname](tend)
except PyDSTool_BoundsError:
- print "Value out of bounds in variable call:"
- print " variable '%s' was called at time %f"%(xname, tend)
+ print("Value out of bounds in variable call:")
+ print(" variable '%s' was called at time %f"%(xname, tend))
raise
return Point({'coorddict': xdict,
'coordnames': endtraj._FScompatibleNamesInv(endtraj.coordnames),
@@ -1137,7 +1137,7 @@
def info(self, verboselevel=1):
- print self._infostr(verboselevel)
+ print(self._infostr(verboselevel))
def __repr__(self):
@@ -1251,9 +1251,9 @@
idx -- (optional) index into value if algorithmic parameter val is a
list of values.
"""
- if target in self.registry.keys():
+ if target in list(self.registry.keys()):
algpars = self.registry[target].get('algparams')
- if par in algpars.keys():
+ if par in list(algpars.keys()):
if isinstance(algpars[par], list):
if idx is not None:
if isinstance(idx, list):
@@ -1291,13 +1291,13 @@
subModelList = [target]
for dsName in subModelList:
algpars = self.registry[dsName].get('algparams')
- if par in algpars.keys():
+ if par in list(algpars.keys()):
# If target is a list, make sure that the input list is of the
# appropriate length, otherwise warn and skip
if isinstance(algpars[par], list):
if isinstance(val, list):
if len(algpars[par]) != len(val):
- print "Warning: par %s list len (%d) in generator %s doesn't match val list len (%d). Skipping."%(par, len(algpars[par]), dsName, len(val))
+ print("Warning: par %s list len (%d) in generator %s doesn't match val list len (%d). Skipping."%(par, len(algpars[par]), dsName, len(val)))
continue
else:
algpars[par] = val
@@ -1307,7 +1307,7 @@
algpars[par][x] = val
else:
if isinstance(val, list):
- print "Warning: par %s type (%s) in generator %s doesn't match val type (%s). Skipping."%(par, type(algpars[par]), dsName, type(val))
+ print("Warning: par %s type (%s) in generator %s doesn't match val type (%s). Skipping."%(par, type(algpars[par]), dsName, type(val)))
else:
algpars[par] = val
else:
@@ -1348,7 +1348,7 @@
if dsName is None:
result = {}
res_str = "Sub-models defined in model %s:\n" % self.name
- for name, infodict in self.modelInfo.iteritems():
+ for name, infodict in self.modelInfo.items():
result[name] = infodict['dsi'].model._infostr(verbosity)
return res_str + pp.pprint(result)
else:
@@ -1600,7 +1600,7 @@
def resetEventTimes(self):
"""Internal method"""
- for ds in self.registry.values():
+ for ds in list(self.registry.values()):
ds.resetEventTimes()
def _set_for_hybrid_DS(self, state):
@@ -1608,7 +1608,7 @@
trajectory computation.
Useful to indicate that high level events should not be reset when a
Generator is reused between hybrid trajectory segments."""
- for ds in self.registry.values():
+ for ds in list(self.registry.values()):
ds._set_for_hybrid_DS(state)
def searchForNames(self, template):
@@ -1618,7 +1618,7 @@
raise PyDSTool_ExistError("Cannot use this function for models"
" not defined through ModelSpec")
result = {}
- for modelName, mspecinfo in self._mspecdict.iteritems():
+ for modelName, mspecinfo in self._mspecdict.items():
# HACK to force compatibility of mspecinfo being a dict/args vs. a GDescriptor
if isinstance(mspecinfo, dict):
foundNames = searchModelSpec(mspecinfo['modelspec'], template)
@@ -1637,14 +1637,14 @@
" not defined through ModelSpec")
# all sub-models must define the same variables, so need only
# to look at one
- a_ds_name = self._mspecdict.keys()[0]
+ a_ds_name = list(self._mspecdict.keys())[0]
a_ds_mspec = self._mspecdict[a_ds_name]['modelspec']
foundNames = searchModelSpec(a_ds_mspec, template)
try:
fspec = self.registry[a_ds_name].get('funcspec')
except AttributeError:
# for non-hybrid models
- fspec = self.registry[a_ds_name].registry.values()[0].get('funcspec')
+ fspec = list(self.registry[a_ds_name].registry.values())[0].get('funcspec')
# funcspec won't have its internal names converted to
# hierarchical form, so do it here on the attributes we
# need
@@ -1667,7 +1667,7 @@
# elements for compatibility with HybridModel._findTrajInitiator:
# swRules, globalConRules, nextModelName, reused (True b/c always same),
# epochStateMaps, notDone
- infodict = self.modelInfo.values()[0]
+ infodict = list(self.modelInfo.values())[0]
return infodict['dsi'], infodict['swRules'], \
infodict['globalConRules'], infodict['dsi'].model.name, \
True, None, True
@@ -1676,17 +1676,17 @@
"""Clean up memory usage from past runs of a solver that is interfaced through
a dynamic link library. This will prevent the 'continue' integration option from
being accessible and will delete other data about the last integration run."""
- self.registry.values()[0].cleanupMemory()
+ list(self.registry.values())[0].cleanupMemory()
def haveJacobian(self):
"""Returns True iff all objects in modelInfo have
defined Jacobians."""
- return self.registry.values()[0].haveJacobian()
+ return list(self.registry.values())[0].haveJacobian()
def haveJacobian_pars(self):
"""Returns True iff all objects in modelInfo have
defined Jacobians."""
- return self.registry.values()[0].haveJacobian_pars()
+ return list(self.registry.values())[0].haveJacobian_pars()
def Rhs(self, t, xdict, pdict=None, asarray=False):
"""Direct access to a generator's Rhs function.
@@ -1700,7 +1700,7 @@
in state name alphabetical order, else a Point
"""
# get Generator as 'ds'
- ds = self.registry.values()[0]
+ ds = list(self.registry.values())[0]
fscm = ds._FScompatibleNames
fscmInv = ds._FScompatibleNamesInv
vars = ds.get('funcspec').vars # FS compatible
@@ -1717,8 +1717,8 @@
# re-ordered according to alphabetical order of non-FS compatible names
rhsval = array(ds.Rhs(t, x_fs, pdict))[fscm.reorder()]
else:
- rhsval = Point({'coorddict': dict(zip(fscmInv(vars),
- ds.Rhs(t, x_fs, pdict))),
+ rhsval = Point({'coorddict': dict(list(zip(fscmInv(vars),
+ ds.Rhs(t, x_fs, pdict)))),
'coordtype': float,
'norm': self._normord})
ds.initialconditions.update(old_ics)
@@ -1736,7 +1736,7 @@
asarray (Bool, optional, default False) If true, will return an array
in state name alphabetical order, else a Point
"""
- ds = self.registry.values()[0]
+ ds = list(self.registry.values())[0]
if not ds.haveJacobian():
raise PyDSTool_ExistError("Jacobian not defined")
fscm = ds._FScompatibleNames
@@ -1753,8 +1753,8 @@
if asarray:
J = array(ds.Jacobian(t, x_fs, pdict))[fscm.reorder()]
else:
- J = Pointset({'coorddict': dict(zip(fscmInv(vars),
- ds.Jacobian(t, x_fs, pdict))),
+ J = Pointset({'coorddict': dict(list(zip(fscmInv(vars),
+ ds.Jacobian(t, x_fs, pdict)))),
'coordtype': float,
'norm': self._normord})
ds.initialconditions.update(old_ics)
@@ -1772,7 +1772,7 @@
asarray (Bool, optional, default False) If true, will return an array
in state name alphabetical order, else a Point
"""
- ds = self.registry.values()[0]
+ ds = list(self.registry.values())[0]
if not ds.haveJacobian_pars():
raise PyDSTool_ExistError("Jacobian w.r.t. pars not defined")
fscm = ds._FScompatibleNames
@@ -1788,8 +1788,8 @@
if asarray:
Jp = array(ds.JacobianP(t, x_fs, pdict))[fscm.reorder()]
else:
- Jp = Pointset({'coorddict': dict(zip(fscmInv(ds.get('funcspec').pars),
- ds.JacobianP(t, x_fs, pdict))),
+ Jp = Pointset({'coorddict': dict(list(zip(fscmInv(ds.get('funcspec').pars),
+ ds.JacobianP(t, x_fs, pdict)))),
'coordtype': float,
'norm': self._normord})
ds.initialconditions.update(old_ics)
@@ -1807,7 +1807,7 @@
asarray (Bool, optional, default False) If true, will return an array
in state name alphabetical order, else a Point
"""
- ds = self.registry.values()[0]
+ ds = list(self.registry.values())[0]
if not ds.haveMass():
raise PyDSTool_ExistError("Mass matrix not defined")
fscm = ds._FScompatibleNames
@@ -1824,8 +1824,8 @@
if asarray:
M = array(ds.MassMatrix(t, x_fs, pdict))[fscm.reorder()]
else:
- M = Point({'coorddict': dict(zip(fscmInv(vars),
- ds.MassMatrix(t, x_fs, pdict))),
+ M = Point({'coorddict': dict(list(zip(fscmInv(vars),
+ ds.MassMatrix(t, x_fs, pdict)))),
'coordtype': float,
'norm': self._normord})
ds.initialconditions.update(old_ics)
@@ -1857,8 +1857,8 @@
if asarray:
A = array(ds.AuxVars(t, x_fs, pdict))[fscm.reorder()]
else:
- A = Point({'coorddict': dict(zip(fscmInv(ds.get('funcspec').auxvars),
- ds.AuxVars(t, x_fs, pdict))),
+ A = Point({'coorddict': dict(list(zip(fscmInv(ds.get('funcspec').auxvars),
+ ds.AuxVars(t, x_fs, pdict)))),
'coordtype': float,
'norm': self._normord})
ds.initialconditions.update(old_ics)
@@ -1884,12 +1884,12 @@
if self.icdict == {}:
# just get i.c. from the single generator,
# making sure it's non-empty
- self.icdict = self.registry.values()[0].get('initialconditions')
+ self.icdict = list(self.registry.values())[0].get('initialconditions')
if self.icdict == {}:
# gen's i.c.s were empty too
raise PyDSTool_ExistError("No initial conditions specified")
xdict = {}
- for xname, value in self.icdict.iteritems():
+ for xname, value in self.icdict.items():
#if xname not in self.obsvars+self.intvars:
# raise ValueError("Invalid variable name in initial "
# "conditions: " + xname)
@@ -1898,7 +1898,7 @@
self.icdict = xdict.copy()
## compute trajectory segment until an event or t1 is reached
- gen = self.registry.values()[0] # sole entry, a Generator
+ gen = list(self.registry.values())[0] # sole entry, a Generator
# print "N-h model before fiddling: t0_global =", t0_global, "t1_global =", t1_global
t0_global += gen.globalt0
t1_global += gen.globalt0
@@ -1906,7 +1906,7 @@
if t1_global > gen.indepvariable.indepdomain[1]+t0:
if isfinite(gen.indepvariable.indepdomain[1]):
if self.verboselevel > 0:
- print "Warning: end time was truncated to max size of specified independent variable domain"
+ print("Warning: end time was truncated to max size of specified independent variable domain")
t1 = gen.indepvariable.indepdomain[1]+t0
else:
t1 = t1_global
@@ -1931,9 +1931,9 @@
try:
if gen.algparams['init_step'] > t1-t0:
if self.verboselevel > 0:
- print "Warning: time step too large for remaining time"\
+ print("Warning: time step too large for remaining time"\
+ " interval. Temporarily reducing time step to " \
- + "1/10th of its previous value"
+ + "1/10th of its previous value")
setup_pars['algparams'].update({'init_step': (t1-t0)/10})
except (AttributeError, KeyError):
# system does not support this integration parameter
@@ -1942,7 +1942,7 @@
# global t0 offsets are updated in case epoch state map changed them
if self._inputt0_par_links != {}:
t0val_dict = {}
- for inp, val in self._inputt0_par_links.items():
+ for inp, val in list(self._inputt0_par_links.items()):
t0val_dict[inp] = self.pars[val]
gen.set(inputs_t0=t0val_dict)
gen.set(**setup_pars)
@@ -1953,37 +1953,37 @@
#print "Entering generator %s at t0=%f, t1=%f"%(gen.name, t0, t1)
try:
traj = gen.compute(trajname+'_0')
- except PyDSTool_ValueError, e:
- print "\nError in Generator:", gen.name
+ except PyDSTool_ValueError as e:
+ print("\nError in Generator:", gen.name)
gen.diagnostics.showWarnings()
gen.diagnostics.showErrors()
- print "Are the constituent generator absolute epsilon "
- print " tolerances too small? -- this abseps =", gen._abseps
+ print("Are the constituent generator absolute epsilon ")
+ print(" tolerances too small? -- this abseps =", gen._abseps)
raise
except KeyboardInterrupt:
raise
except:
- print "\nError in Generator:", gen.name
+ print("\nError in Generator:", gen.name)
gen.diagnostics.showWarnings()
gen.diagnostics.showErrors()
self.diagnostics.traceback = {}
- for k,v in gen.diagnostics.traceback.iteritems():
+ for k,v in gen.diagnostics.traceback.items():
if isinstance(v, dict):
dentry = {}
- for vk, vv in v.iteritems():
+ for vk, vv in v.items():
dentry[gen._FScompatibleNamesInv(vk)] = vv
else:
dentry = v
self.diagnostics.traceback[k] = dentry
if self.diagnostics.traceback != {}:
- print "Traceback dictionary copied to model"
+ print("Traceback dictionary copied to model")
raise
if traj is None:
raise ValueError("Generator %s failed to create a trajectory"%gen.name)
else:
if self._abseps is not None:
assert traj.indepdomain._abseps == self._abseps
- for v in traj.depdomain.values():
+ for v in list(traj.depdomain.values()):
assert v._abseps == self._abseps
if not isparameterized(traj):
raise ValueError("Generator " + gen.name + " produced a " \
@@ -1998,8 +1998,8 @@
# look at warnings etc. for any terminating events that occurred
if gen.diagnostics.hasErrors() and self.verboselevel > 0:
for e in gen.diagnostics.errors:
- print 'Generator ' + gen.name + \
- ' in trajectory segment had errors'
+ print('Generator ' + gen.name + \
+ ' in trajectory segment had errors')
gen.diagnostics.showErrors()
end_reasons = ['time']
# NB. end reason will always be 'time' for ExplicitFnGen
@@ -2014,18 +2014,18 @@
if w[0] == Generator.W_TERMEVENT or \
w[0] == Generator.W_TERMSTATEBD:
if self.verboselevel > 1:
- print "Time:", ti_1+t0
- print 'Generator ' + gen.name + \
+ print("Time:", ti_1+t0)
+ print('Generator ' + gen.name + \
' had a terminal event. Details (in local ' + \
- 'system time) ...\n ' + str(w[1])
+ 'system time) ...\n ' + str(w[1]))
# w[1] always has t as first entry, and
# either a state variable name
# or a list of terminal event names as second.
if isinstance(w[1][1], list):
if len(w[1][1]) > 1:
if self.verboselevel > 0:
- print 'Warning: More than one terminal event found.'
- print ' Consider altering event pars.'
+ print('Warning: More than one terminal event found.')
+ print(' Consider altering event pars.')
end_reasons = [w[1][1][ri] \
for ri in range(len(w[1][1]))]
else:
@@ -2041,8 +2041,8 @@
# rejected.
global_end_reasons = {}
global_end_ixs = []
- dsi = self.modelInfo.values()[0]['dsi']
- for globalDS in self.modelInfo.values()[0]['globalConRules']:
+ dsi = list(self.modelInfo.values())[0]['dsi']
+ for globalDS in list(self.modelInfo.values())[0]['globalConRules']:
if globalDS(dsi):
global_end_reasons[Inf] = \
globalDS.conditions.collate_results('reasons',
@@ -2055,7 +2055,7 @@
try:
final_ok_idx = globalDS.conditions._find_idx()
except (AttributeError, RuntimeError):
- print "Trajectory creation failed..."
+ print("Trajectory creation failed...")
globalDS.conditions.results.info()
raise PyDSTool_ExistError("Global consistency checks failed for"
" model interface %s for trajectory %s"%(str(globalDS),
@@ -2076,15 +2076,15 @@
# overwrite current end reason
end_reasons = global_end_reasons[smallest_ok_idx]
if self.verboselevel > 1:
- print "End reason in %s was %s"%(self.name,str(end_reasons))
+ print("End reason in %s was %s"%(self.name,str(end_reasons)))
# DEBUG
# print "Nonhybrid traj info:", traj.indepdomain.get(), traj.globalt0, type(traj)
# print "traj vars:", traj.variables.keys(), "\n"
#### Clean up
if ti_1 > t1_global-t0:
- print "Warning: Generator time interval exceeds prescribed limits:"
- print " ... ", ti_1, " > ", t1_global-t0
+ print("Warning: Generator time interval exceeds prescribed limits:")
+ print(" ... ", ti_1, " > ", t1_global-t0)
epochEvents = {}
try:
epochEvents.update(gen.getEvents(asGlobalTime=True))
@@ -2108,7 +2108,7 @@
# ensure that modelInfo is a single Generator object only
assert len(self.modelInfo) == 1, \
"Non-hybrid model must contain a single Generator"
- infodict = self.modelInfo.values()[0]
+ infodict = list(self.modelInfo.values())[0]
if not isinstance(infodict['dsi'], MProject.GeneratorInterface):
raise TypeError("Must provide a single Generator object"
" wrapped in a GeneratorInterface")
@@ -2116,10 +2116,10 @@
def _infostr(self, verbose=1):
if verbose > 0:
outputStr = 'Non-Hybrid Model '+self.name+" containing components:"
- print "Observable variables:", self.obsvars
- print "Internal variables:", self.intvars
- print "Auxiliary variables:", self.auxvars
- name, infodict = self.modelInfo.items()[0]
+ print("Observable variables:", self.obsvars)
+ print("Internal variables:", self.intvars)
+ print("Auxiliary variables:", self.auxvars)
+ name, infodict = list(self.modelInfo.items())[0]
outputStr += "\n--- Generator: "+name
outputStr += "\n "+infodict['dsi'].model._infostr(verbose-1)
else:
@@ -2174,22 +2174,22 @@
xdict[xname] = traj.variables[xname_compat](ti_1)
except RuntimeError:
# traj is a hybrid traj
- print "**********"
- print xname, " dep domain:", traj.variables[xname_compat].depdomain.get()
- print traj.depdomain[xname_compat].get()
- print "indep domain:", traj.variables[xname_compat].indepdomain.get()
- print "Var val at t-eps %f = "%(ti_1-1e-4), \
- traj.variables[xname_compat](ti_1-1e-4)
+ print("**********")
+ print(xname, " dep domain:", traj.variables[xname_compat].depdomain.get())
+ print(traj.depdomain[xname_compat].get())
+ print("indep domain:", traj.variables[xname_compat].indepdomain.get())
+ print("Var val at t-eps %f = "%(ti_1-1e-4), \
+ traj.variables[xname_compat](ti_1-1e-4))
raise
except:
- print "**********"
- print xname, " dep domain:", traj.variables[xname_compat].depdomain.get()
- print traj.depdomain[xname_compat].get()
- print traj.trajSeq[-1].variables[xname_compat].depdomain.get()
+ print("**********")
+ print(xname, " dep domain:", traj.variables[xname_compat].depdomain.get())
+ print(traj.depdomain[xname_compat].get())
+ print(traj.trajSeq[-1].variables[xname_compat].depdomain.get())
raise
except PyDSTool_BoundsError:
- print "Value out of bounds in variable call:"
- print " variable '%s' was called at time %f"%(xname, ti_1)
+ print("Value out of bounds in variable call:")
+ print(" variable '%s' was called at time %f"%(xname, ti_1))
raise
@@ -2220,9 +2220,9 @@
for k in extinputs_ic:
extinputs_ic[k] = dsinps[k](t0)
except PyDSTool_BoundsError:
- print "Cannot proceed - sub-model '" + model_interface.model.name \
+ print("Cannot proceed - sub-model '" + model_interface.model.name \
+ "' had an external input undefined " \
- + "at t =", t0
+ + "at t =", t0)
raise
else:
extinputs_ic = {}
@@ -2258,7 +2258,7 @@
integration option from being accessible and will delete other data
about the last integration run.
"""
- for MI in self.registry.values():
+ for MI in list(self.registry.values()):
MI.model.cleanupMemory()
def _findTrajInitiator(self, end_reasons, partition_num, t0, xdict,
@@ -2271,33 +2271,33 @@
# first time in the while loop, so set up xnames
assert partition_num == 0, ("end_reasons was None on a "
"non-initial epoch")
- xnames = self.icdict.keys()
+ xnames = list(self.icdict.keys())
xnames.sort()
# only for the initial Generator of a trajectory
try:
infodict = findTrajInitiator(self.modelInfo, t0, xdict,
self.pars, self.intvars,
self.verboselevel)
- except PyDSTool_ValueError, errinfo:
- print errinfo
+ except PyDSTool_ValueError as errinfo:
+ print(errinfo)
raise PyDSTool_ExistError('No unique eligible Model found:'
' cannot continue (check active terminal event definitions'
' or error message above)')
mi = infodict['dsi']
swRules = infodict['swRules']
globalConRules = infodict['globalConRules']
- missing = remain(mi.get('variables', ics=xdict, t0=t0).keys(),
+ missing = remain(list(mi.get('variables', ics=xdict, t0=t0).keys()),
xnames+self.auxvars+self.intvars)
if missing != []:
raise AssertionError('Missing initial condition specifications'
' for %s' % str(missing))
- for entry, val in xdict.iteritems():
+ for entry, val in xdict.items():
if not isfinite(val):
- print "Warning: %s initial condition for "%mi.model.name \
- + str(entry) + " = " + str(val)
+ print("Warning: %s initial condition for "%mi.model.name \
+ + str(entry) + " = " + str(val))
if self.verboselevel > 1:
- print "\nStarting partition 0"
- print "Chose initiator '%s'"%mi.model.name
+ print("\nStarting partition 0")
+ print("Chose initiator '%s'"%mi.model.name)
nextModelName = None
else:
# find new Generator using switching rules
@@ -2338,9 +2338,9 @@
epochStateMaps = None # will not be needed
if nextModelName == 'terminate':
if self.verboselevel > 0:
- print 'Trajectory calculation for Model `'+mi.model.name\
+ print('Trajectory calculation for Model `'+mi.model.name\
+'` terminated without a DS specified in switch'\
- +' rules with which to continue.'
+ +' rules with which to continue.')
globalConRules = None
notDone = False # terminates compute method
elif nextModelName == mi.model.name:
@@ -2361,8 +2361,8 @@
swRules = next['swRules']
globalConRules = next['globalConRules']
if self.verboselevel > 1:
- print "\nStarting partition #%i"%partition_num
- print "Chose model '%s'"%mi.model.name
+ print("\nStarting partition #%i"%partition_num)
+ print("Chose model '%s'"%mi.model.name)
return mi, swRules, globalConRules, nextModelName, reused, \
epochStateMaps, notDone
@@ -2378,9 +2378,9 @@
# for gn in modelNames]))
# TEMP
#print "Model: avoid copying eventstructs?"
- genEvStructs = dict(zip(modelNames,
+ genEvStructs = dict(list(zip(modelNames,
[self.modelInfo[gn]['dsi'].eventstruct \
- for gn in modelNames]))
+ for gn in modelNames])))
# time_range is whole time range over sequence
time_range = [None, None]
indepvarname = ''
@@ -2444,7 +2444,7 @@
DS_t_typestr = 'discrete'
# discrete time can be floats or ints
traj_vars = traj._FScompatibleNamesInv(traj.variables)
- assert intersect(self.allvars, traj_vars.keys()), \
+ assert intersect(self.allvars, list(traj_vars.keys())), \
"variable name for traj not present in sub-model's variables"
# Pick one observable variable ('varname') to test with -- they
# must all have the same type. This variable must be present in
@@ -2524,7 +2524,7 @@
"""Returns True iff all objects in modelInfo have
defined Jacobians."""
result = True
- for model in self.registry.values():
+ for model in list(self.registry.values()):
result = result and model.haveJacobian()
return result
@@ -2532,7 +2532,7 @@
"""Returns True iff all objects in modelInfo have
defined Jacobians."""
result = True
- for model in self.registry.values():
+ for model in list(self.registry.values()):
result = result and model.haveJacobian_pars()
return result
@@ -2559,8 +2559,8 @@
else:
# get returns FS compatible names
varnames = dsi.get('funcspec', xdict, t).vars
- return Point({'coorddict': dict(zip(varnames,
- dsi.Rhs(t, xdict, pdict))),
+ return Point({'coorddict': dict(list(zip(varnames,
+ dsi.Rhs(t, xdict, pdict)))),
'coordtype': float,
'norm': self._normord})
@@ -2587,8 +2587,8 @@
return dsi.Jacobian(t, xdict, pdict, asarray=True)
else:
varnames = dsi.get('funcspec', xdict, t).vars
- return Pointset({'coorddict': dict(zip(varnames,
- dsi.Jacobian(t, xdict, pdict))),
+ return Pointset({'coorddict': dict(list(zip(varnames,
+ dsi.Jacobian(t, xdict, pdict)))),
'coordtype': float,
'norm': self._normord})
else:
@@ -2617,8 +2617,8 @@
return dsi.JacobianP(t, xdict, pdict, asarray=True)
else:
parnames = dsi.get('funcspec', xdict, t).pars
- return Pointset({'coorddict': dict(zip(parnames,
- dsi.JacobianP(t, xdict, pdict))),
+ return Pointset({'coorddict': dict(list(zip(parnames,
+ dsi.JacobianP(t, xdict, pdict)))),
'coordtype': float,
'norm': self._normord})
else:
@@ -2646,8 +2646,8 @@
dsi.MassMatrix(t, xdict, pdict, asarray=True)
else:
varnames = dsi.get('funcspec', xdict, t).vars
- return Point({'coorddict': dict(zip(varnames,
- dsi.MassMatrix(t, xdict, pdict))),
+ return Point({'coorddict': dict(list(zip(varnames,
+ dsi.MassMatrix(t, xdict, pdict)))),
'coordtype': float,
'norm': self._normord})
@@ -2675,8 +2675,8 @@
return dsi.AuxVars(t, xdict, pdict, asarray=True)
else:
auxvarnames = dsi.get('funcspec', xdict, t).auxvars
- return Point({'coorddict': dict(zip(auxvarnames,
- dsi.AuxVars(t, xdict, pdict))),
+ return Point({'coorddict': dict(list(zip(auxvarnames,
+ dsi.AuxVars(t, xdict, pdict)))),
'coordtype': float,
'norm': self._normord})
@@ -2710,7 +2710,7 @@
raise PyDSTool_ExistError("No initial conditions specified")
xdict = {}
- for xname, value in self.icdict.iteritems():
+ for xname, value in self.icdict.items():
if xname not in self.allvars:
raise ValueError("Invalid variable name in initial "
"conditions: " + xname)
@@ -2760,7 +2760,7 @@
pars_copy = copy.copy(self.pars)
self._applyStateMap(epochStateMaps, MI_prev, MI, traj, xdict, t0)
## if changed last MI's event delay, then change it back.
- for event, delay in event_delay_record.items():
+ for event, delay in list(event_delay_record.items()):
event.eventdelay = delay
## temporarily set terminal events from previous in this MI to have
@@ -2790,7 +2790,7 @@
# global t0 offsets are updated in case epoch state map changed them
if self._inputt0_par_links != {} and pars_copy != self.pars:
t0val_dict = {}
- for inp, val in self._inputt0_par_links.items():
+ for inp, val in list(self._inputt0_par_links.items()):
t0val_dict[inp] = self.pars[val]
model.set(inputs_t0=t0val_dict)
@@ -2799,8 +2799,8 @@
if t1_global > indepvar.indepdomain[1]+t0:
if isfinite(indepvar.indepdomain[1]):
if self.verboselevel > 0:
- print "Warning: end time was truncated to max size " + \
- "of specified independent variable domain"
+ print("Warning: end time was truncated to max size " + \
+ "of specified independent variable domain")
t1 = indepvar.indepdomain[1]+t0
else:
t1 = t1_global
@@ -2826,9 +2826,9 @@
try:
if MI.get('algparams', xdict, t0)['init_step'] > t1-t0:
if self.verboselevel > 0:
- print "Warning: time step too large for remaining time"\
+ print("Warning: time step too large for remaining time"\
+ " interval. Temporarily reducing time step to " \
- + "1/10th of its previous value"
+ + "1/10th of its previous value")
setup_pars['algparams'].update({'init_step': (t1-t0)/10})
except (AttributeError, KeyError, ValueError):
# system does not support this integration parameter
@@ -2855,28 +2855,28 @@
# print "DEBUG: Entering model %s at t0=%f, t1=%f"%(model.name, t0, t1)
try:
traj = MI.get_test_traj(force=True)
- except PyDSTool_ValueError, e:
- print "\nError in Model:", model.name
+ except PyDSTool_ValueError as e:
+ print("\nError in Model:", model.name)
model.diagnostics.showWarnings()
model.diagnostics.showErrors()
- print "Are the constituent generator absolute epsilon "
- print " tolerances too small? -- this abseps =", model._abseps
+ print("Are the constituent generator absolute epsilon ")
+ print(" tolerances too small? -- this abseps =", model._abseps)
raise
except KeyboardInterrupt:
raise
except:
- print "\nError in Model:", model.name
+ print("\nError in Model:", model.name)
self.diagnostics.traceback = {}
- for k,v in model.diagnostics.traceback.iteritems():
+ for k,v in model.diagnostics.traceback.items():
if isinstance(v, dict):
dentry = {}
- for vk, vv in v.iteritems():
+ for vk, vv in v.items():
dentry[traj._FScompatibleNamesInv(vk)] = vv
else:
dentry = v
self.diagnostics.traceback[k] = dentry
if self.diagnostics.traceback != {}:
- print "Traceback dictionary copied to model"
+ print("Traceback dictionary copied to model")
raise
# ensure this is reset to False
model._set_for_hybrid_DS(False)
@@ -2899,11 +2899,11 @@
# this is a local time
ti_1 = time_interval[1]
if self.verboselevel > 1:
- print "\nt0=", t0, "traj.globalt0=", traj.globalt0
- print "traj.indepdomain = ", traj.indepdomain.get()
- for vn, v in traj.variables.items():
- print vn + ":", v.trajirange, v.indepdomain.get()
- print "Last point of traj %s was: "%traj.name, traj(ti_1)
+ print("\nt0=", t0, "traj.globalt0=", traj.globalt0)
+ print("traj.indepdomain = ", traj.indepdomain.get())
+ for vn, v in list(traj.variables.items()):
+ print(vn + ":", v.trajirange, v.indepdomain.get())
+ print("Last point of traj %s was: "%traj.name, traj(ti_1))
# update original copy of the model with new event times during
# this trajectory, for high level event detection to be able to check
# eventinterval for terminal events between hybrid steps
@@ -2917,8 +2917,8 @@
# look at warnings etc. for any terminating events that occurred
if model.diagnostics.hasErrors() and self.verboselevel > 0:
for e in model.diagnostics.errors:
- print 'Model ' + model.name + \
- ' in trajectory segment had errors'
+ print('Model ' + model.name + \
+ ' in trajectory segment had errors')
model.diagnostics.showErrors()
# default end reason is time (may be overwritten)
end_reasons = ['time']
@@ -2933,18 +2933,18 @@
if w[0] == Generator.W_TERMEVENT or \
w[0] == Generator.W_TERMSTATEBD:
if self.verboselevel > 1:
- print "Time:", ti_1+t0
- print 'Model ' + model.name + \
+ print("Time:", ti_1+t0)
+ print('Model ' + model.name + \
' had a terminal event. Details (in local ' + \
- 'system time) ...\n ' + str(w[1])
+ 'system time) ...\n ' + str(w[1]))
# w[1] always has t as first entry, and
# either a state variable name
# or a list of terminal event names as second.
if isinstance(w[1][1], list):
if len(w[1][1]) > 1:
if self.verboselevel > 0:
- print 'Warning: More than one terminal event found.'
- print ' Consider altering event pars.'
+ print('Warning: More than one terminal event found.')
+ print(' Consider altering event pars.')
end_reasons = [w[1][1][ri] \
for ri in range(len(w[1][1]))]
else:
@@ -2973,7 +2973,7 @@
try:
final_ok_idx = globalDS.conditions._find_idx()
except (AttributeError, RuntimeError):
- print "Trajectory creation failed..."
+ print("Trajectory creation failed...")
globalDS.conditions.results.info()
raise PyDSTool_ExistError("Global consistency checks failed for"
" model interface %s for trajectory %s"%(str(globalDS),
@@ -2997,7 +2997,7 @@
if new_reason != []:
end_reasons = new_reason
if self.verboselevel > 1:
- print "End reason in %s was %s"%(self.name,str(end_reasons))
+ print("End reason in %s was %s"%(self.name,str(end_reasons)))
# DEBUG
# print "\nTraj segment %i info:"%partition_num, traj.indepdomain.get(), traj.globalt0, type(traj)
@@ -3010,8 +3010,8 @@
notDone = False
if ti_1 > t1_global-t0:
# We computed too far for the time interval
- print "Warning: Segment time interval exceeds prescribed limits:"
- print " ... ", ti_1, " > ", t1_global-t0
+ print("Warning: Segment time interval exceeds prescribed limits:")
+ print(" ... ", ti_1, " > ", t1_global-t0)
notDone = False
# last Model's time == t1 should hold after successful traj computation
# otherwise t1 needs to be updated according to last terminating
@@ -3020,22 +3020,22 @@
if end_reasons[0] not in swRules:
# there's prescribed time left to compute but no
# eligible DS to transfer control to
- print 'Trajectory calculation for Model `'+model.name+'` ' \
+ print('Trajectory calculation for Model `'+model.name+'` ' \
+'terminated without a DS specified in the ' \
- +'switching rules from which to continue.'
- print 'Perhaps a variable went out of bounds:'
+ +'switching rules from which to continue.')
+ print('Perhaps a variable went out of bounds:')
model.diagnostics.showWarnings()
- print 'Last reasons for stopping were: ', end_reasons
- print "Trajectory calculated: "
+ print('Last reasons for stopping were: ', end_reasons)
+ print("Trajectory calculated: ")
dt_sample = (ti_1-time_interval[0])/10.
- print traj.sample(dt=dt_sample)
+ print(traj.sample(dt=dt_sample))
notDone = False
raise PyDSTool_ValueError("Premature termination of "
"trajectory calculation")
elif swRules[end_reasons[0]][0] == 'terminate':
if self.verboselevel > 0:
- print 'Trajectory calculation for Model `'+model.name+'` ' \
- +'terminated.'
+ print('Trajectory calculation for Model `'+model.name+'` ' \
+ +'terminated.')
notDone = False
t1 = ti_1+t0
else:
@@ -3132,24 +3132,24 @@
def _validateParameters(self):
pars_found = {}
- for infodict in self.modelInfo.values():
+ for infodict in list(self.modelInfo.values()):
try:
- pars_recognized = intersect(pars_found.keys(),
+ pars_recognized = intersect(list(pars_found.keys()),
infodict['dsi'].pars)
except AttributeError:
# gen doesn't have any pars
continue # for loop
- pars_unknown = remain(infodict['dsi'].pars, pars_found.keys())
+ pars_unknown = remain(infodict['dsi'].pars, list(pars_found.keys()))
for parname in pars_recognized:
if infodict['dsi'].pars[parname] != pars_found[parname]:
- print "Inconsistent parameter values between model objects inside model"
- print "probably means that they were changed during trajectory computation"
- print "at discrete events: you should reset the pars when calling compute()"
+ print("Inconsistent parameter values between model objects inside model")
+ print("probably means that they were changed during trajectory computation")
+ print("at discrete events: you should reset the pars when calling compute()")
raise ValueError("Inconsistency between parameter values"
" of same name ('%s') in different constiutent Generator"%parname +\
" objects: reset during call to compute")
- new_vals = dict(zip(pars_unknown, [infodict['dsi'].pars[p] \
- for p in pars_unknown]))
+ new_vals = dict(list(zip(pars_unknown, [infodict['dsi'].pars[p] \
+ for p in pars_unknown])))
pars_found.update(new_vals)
@@ -3159,7 +3159,7 @@
outputStr += "Observable variables: " + ",".join(self.obsvars)
outputStr += "Internal variables: " + ",".join(self.intvars)
outputStr += "Auxiliary variables: " + ",".join(self.auxvars)
- for name, infodict in self.modelInfo.iteritems():
+ for name, infodict in self.modelInfo.items():
outputStr += "\n--- Sub-model: "+name
outputStr += "\n "+infodict['dsi'].model._infostr(verbose-1)
else:
@@ -3188,9 +3188,8 @@
auxdict = {}
else:
try:
- auxdict = dict(zip(fspec.auxvars,
- apply(dsi.get('AuxVars', icdict, t),
- (t, icdict_local, pardict)) ))
+ auxdict = dict(list(zip(fspec.auxvars,
+ dsi.get('AuxVars', icdict, t)(*(t, icdict_local, pardict)) )))
except (ValueError, TypeError):
# no auxiliary variables for this model
# e.g. ExplicitFnGen has its auxvars defined through the
@@ -3209,13 +3208,13 @@
"""
eligibleMI = []
if len(modelInfo) == 1:
- return modelInfo.values()[0]
+ return list(modelInfo.values())[0]
outcome = {}
- for infodict in modelInfo.values():
+ for infodict in list(modelInfo.values()):
MI = infodict['dsi']
MI_vars = MI.query('vars')
xdict = filteredDict(vardict, MI_vars)
- dxdt_zeros = dict(zip(xdict.keys(),[0.]*len(xdict)))
+ dxdt_zeros = dict(list(zip(list(xdict.keys()),[0.]*len(xdict))))
domtests = infodict['domainTests']
globalConRules = infodict['globalConRules']
model = MI.model
@@ -3228,18 +3227,18 @@
dsinps = MI.get('inputs', xdict, t)
if dsinps != {}:
try:
- input_ics = [dsinps[in_name](t) for in_name in dsinps.keys()]
+ input_ics = [dsinps[in_name](t) for in_name in list(dsinps.keys())]
except KeyboardInterrupt:
raise
except:
raise RuntimeError("Error in evaluating inputs for generator at"
" initial condition")
- pardict.update(dict(zip(dsinps.keys(), input_ics)))
+ pardict.update(dict(list(zip(list(dsinps.keys()), input_ics))))
icdict = copy.copy(xdict)
# don't overwrite any aux vars that are treated as regular variables
# at this level, but fetch other aux vars and external inputs
icdict.update(filteredDict(getAuxVars(MI, t, icdict, pardict),
- icdict.keys(), neg=True))
+ list(icdict.keys()), neg=True))
# override icdict with any finite-valued generator
# initial condition (deliberately preset in generator definition)
# for non-internal variables, and any auxiliary variables that aren't
@@ -3270,7 +3269,7 @@
# no Rhs for the underlying generator
dxdt = dxdt_zeros
else:
- for vname, val in dxdt.items():
+ for vname, val in list(dxdt.items()):
# hack to fix NaNs showing up for VODE Rhs function
# but very large finite values come back from Dopri/Radau
# and Nan's mess up call to numeric_to_traj below
@@ -3282,7 +3281,7 @@
# print "Temp in findTrajInitiator for %s: x, dxdt ="%MI.model.name
# print icdict
# print dxdt
- for xname, x in icdict.iteritems():
+ for xname, x in icdict.items():
# don't count time 't' or any internal variables
if xname == 't' or xname in intvars or xname not in domtests:
# 't' is a special value inserted into icdict, for use
@@ -3294,14 +3293,14 @@
# print " discrete? ", domtests[xname].isdiscrete
newtest = domtests[xname](xtraj)
if verboselevel >=2:
- print "\nstate dom test for '%s' @ value %f:"%(xname, icdict[xname])
- print "depdomain is ", MI.get('variables', xdict, t)[xname].depdomain.get()
- print "-> test result is ", newtest
+ print("\nstate dom test for '%s' @ value %f:"%(xname, icdict[xname]))
+ print("depdomain is ", MI.get('variables', xdict, t)[xname].depdomain.get())
+ print("-> test result is ", newtest)
x_test = x_test and newtest
g_test = True # initial value
xdict = filteredDict(icdict, intvars, neg=True)
- MI.test_traj = numeric_to_traj(array([xdict.values()]).T, 'ic_trajpt',
- xdict.keys(), t)
+ MI.test_tRefactoringTool: Refactored ./PyDSTool/MProject.py
raj = numeric_to_traj(array([list(xdict.values())]).T, 'ic_trajpt',
+ list(xdict.keys()), t)
# ensure that events are cleared in case global con rules in a MI
# check for events (for when used after trajectories computed)
# don't use MI.get('diagnostics', xdict, t) as that will return a copy
@@ -3326,14 +3325,14 @@
globtest = False
else:
if verboselevel >= 2:
- print "\nglobal con test for '%s' @ value %f:"%(str(gc), icdict[xname])
- print "-> test result is ", globtest
+ print("\nglobal con test for '%s' @ value %f:"%(str(gc), icdict[xname]))
+ print("-> test result is ", globtest)
g_test = g_test and globtest
if verboselevel >= 1:
- print "\nModel '%s' tests..."%model.name
- print " ...for initial time: " + str(t_test)
- print " ...for initial state: " + str(x_test)
- print " ...for global conditions: " + str(g_test)
+ print("\nModel '%s' tests..."%model.name)
+ print(" ...for initial time: " + str(t_test))
+ print(" ...for initial state: " + str(x_test))
+ print(" ...for global conditions: " + str(g_test))
outcome[model.name]['time dom. test'] = t_test
outcome[model.name]['state dom. test'] = x_test
outcome[model.name]['global con. test'] = g_test
--- ./PyDSTool/MProject.py (original)
+++ ./PyDSTool/MProject.py (refactored)
@@ -10,10 +10,10 @@
import numpy as npy
# PyDSTool imports
-import Model, Generator, Events, ModelSpec, ModelConstructor, Symbolic, \
+from . import Model, Generator, Events, ModelSpec, ModelConstructor, Symbolic, \
Trajectory
-import utils, common, parseUtils
-from errors import *
+from . import utils, common, parseUtils
+from .errors import *
# --------------------
@@ -300,7 +300,7 @@
self.trans_gen.changelog = copy.copy(self.changelog)
return self.trans_gen
else:
- print "Remaining free symbols: ", freeSymbols
+ print("Remaining free symbols: ", freeSymbols)
raise PyDSTool_ValueError("New Generator spec cannot be committed")
@@ -382,7 +382,7 @@
self.trans_model.changelog = copy.copy(self.changelog)
return self.trans_model
else:
- print "Internal interface inconsistencies: ", inconsistencies
+ print("Internal interface inconsistencies: ", inconsistencies)
raise PyDSTool_ValueError("New Model spec cannot be committed")
@@ -458,7 +458,7 @@
mdesc = copy.deepcopy(self._mReg[name])
except KeyError:
raise KeyError("No such model description")
- for gd in mdesc.generatorspecs.values():
+ for gd in list(mdesc.generatorspecs.values()):
gd.modelspec.flattenSpec(ignoreInputs=True, force=True)
filt_keys = ('userevents', 'userfns', 'unravelInfo',
'inputs', 'checklevel', 'activateAllBounds',
@@ -484,7 +484,7 @@
mc = ModelConstructor.ModelConstructor(mdesc.name,
**common.filteredDict(dict(mdesc), filt_keys))
assert len(mdesc.generatorspecs) > 0, "No Generator descriptions found"
- for gdname, gd in mdesc.generatorspecs.iteritems():
+ for gdname, gd in mdesc.generatorspecs.items():
if gd.userEvents is not None:
mc.addEvents(gdname, gd.userEvents)
if gd.userFunctions is not None:
@@ -522,7 +522,7 @@
__str__ = __repr__
def info(self, verboselevel=1):
- print self._infostr(verboselevel)
+ print(self._infostr(verboselevel))
# -----------------------------------------------------------------------------
@@ -599,16 +599,16 @@
display_error = self.pars.verbose_level > 0 or self.pars.debug
if display_error:
exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
- print "******************************************"
- print "Problem evaluating feature:", self.name
- print " ", exceptionType, exceptionValue
+ print("******************************************")
+ print("Problem evaluating feature:", self.name)
+ print(" ", exceptionType, exceptionValue)
for line in traceback.format_exc().splitlines()[-12:-1]:
- print " " + line
- print " originally on line:", traceback.tb_lineno(exceptionTraceback)
+ print(" " + line)
+ print(" originally on line:", traceback.tb_lineno(exceptionTraceback))
if self.pars.debug: #and self.pars.verbose_level > 1:
raise
else:
- print "(Proceeding as 'unsatisfied')\n"
+ print("(Proceeding as 'unsatisfied')\n")
satisfied = False
if hasattr(self, 'metric'):
self.metric.results = self.pars.penalty * \
@@ -708,10 +708,10 @@
assert isinstance(sf, feature), \
"Only define quantitative or qualitative features"
self.subfeatures = subfeatures
- self._namemap = dict(zip([sf.name for sf in subfeatures],
- subfeatures))
+ self._namemap = dict(list(zip([sf.name for sf in subfeatures],
+ subfeatures)))
elif isinstance(subfeatures, dict):
- for sfname, sf in subfeatures.items():
+ for sfname, sf in list(subfeatures.items()):
assert isinstance(sf, feature), \
"Only define quantitative or qualitative features"
self.subfeatures = subfeatures
@@ -733,13 +733,13 @@
else:
feats.append(self)
# continue gathering from sub-features
- for sf in self._namemap.values():
+ for sf in list(self._namemap.values()):
sf._residual_info(feats, sizes)
def __str__(self):
s = "Feature %s "%self.name
- if len(self._namemap.keys()) > 0:
- s += "- " + str(self._namemap.keys())
+ if len(list(self._namemap.keys())) > 0:
+ s += "- " + str(list(self._namemap.keys()))
return s
__repr__ = __str__
@@ -790,7 +790,7 @@
sf.super_results.update(self.results)
sf.reset_metric()
if self.pars.verbose_level > 1:
- print "feature_node.evaluate: sf=", sf
+ print("feature_node.evaluate: sf=", sf)
error_raised = False
try:
new_result = sf(target)
@@ -807,7 +807,7 @@
# for potential use by a residual function
satisfied = satisfied and new_result
if error_raised:
- print " ... error raised"
+ print(" ... error raised")
if hasattr(self, 'metric'):
# kludgy penalty function in lieu of something smarter
if sf.metric.results is None:
@@ -823,7 +823,7 @@
self.ref_traj = ref_traj
self.postprocess_ref_traj()
if isinstance(self.subfeatures, dict):
- sfs = self.subfeatures.values()
+ sfs = list(self.subfeatures.values())
else:
sfs = self.subfeatures
for sf in sfs:
@@ -892,7 +892,7 @@
# False (unwanted feature)
self.namemap = {}
try:
- for f, c in feature_composition_dict.iteritems():
+ for f, c in feature_composition_dict.items():
assert isinstance(c, bool), \
"Feature composition dictionary requires boolean values"
assert isinstance(f, (ql_feature_leaf, qt_feature_leaf,
@@ -917,13 +917,13 @@
return True
def keys(self):
- return self.namemap.keys()
+ return list(self.namemap.keys())
def values(self):
- return self.namemap.values()
+ return list(self.namemap.values())
def items(self):
- return self.namemap.items()
+ return list(self.namemap.items())
def __getitem__(self, name):
return self.namemap[name]
@@ -935,14 +935,14 @@
"""Set reference trajectory for the features (if used, otherwise will
be ignored or overridden in feature _local_init methods).
"""
- for f,c in self.fcd.iteritems():
+ for f,c in self.fcd.items():
f.set_ref_traj(ref_traj)
def evaluate(self, target):
"""Apply conditions to trajectory segments
and returns True if all are satisfied."""
satisfied = True
- for f,c in self.fcd.iteritems():
+ for f,c in self.fcd.items():
# have to call new separately to ensure f calcs its residual
new = f(target) == c
satisfied = satisfied and new
@@ -953,15 +953,15 @@
def __str__(self):
s = "Condition "
- if len(self.namemap.keys()) > 0:
- s += "- " + str(self.namemap.keys())
+ if len(list(self.namemap.keys())) > 0:
+ s += "- " + str(list(self.namemap.keys()))
return s
__repr__ = __str__
def _find_idx(self):
min_ix = npy.Inf
- for f in self.fcd.keys():
+ for f in list(self.fcd.keys()):
f_ix = f._find_idx()
if f_ix is not None and f_ix < min_ix:
min_ix = f_ix
@@ -976,16 +976,16 @@
#feats and sizes updated in place
feats = []
sizes = []
- for f in self.fcd.keys():
+ for f in list(self.fcd.keys()):
f._residual_info(feats, sizes)
- return {'features': dict(zip(feats,sizes)),
+ return {'features': dict(list(zip(feats,sizes))),
'total_size': sum(sizes)}
def collate_results(self, result_name, merge_lists=False,
feature_names=None):
res = []
if feature_names is None:
- feature_list = self.fcd.keys()
+ feature_list = list(self.fcd.keys())
else:
feature_list = [self.namemap[f] for f in feature_names]
for f in feature_list:
@@ -1020,12 +1020,12 @@
metric_features = {}
res_feature_list = []
tot_size = 0
- for test_mi, ref_mi_class in self.interfaces.iteritems():
+ for test_mi, ref_mi_class in self.interfaces.items():
# list of suitable features for each test_mi
metric_features[test_mi] = test_mi.conditions._residual_info()
tot_size += metric_features[test_mi]['total_size']
res_feature_list.extend([(test_mi, f) for f in \
- metric_features[test_mi]['features'].keys()])
+ list(metric_features[test_mi]['features'].keys())])
self.metric_features = metric_features
self.res_feature_list = res_feature_list
self.res_len = tot_size
@@ -1045,9 +1045,9 @@
self.weight_index_mapping = {}
self.feat_weights = {}
ix = 0
- for test_mi, feat_dict in self.metric_features.iteritems():
+ for test_mi, feat_dict in self.metric_features.items():
self.weight_index_mapping[test_mi] = {}
- for f, size in feat_dict['features'].iteritems():
+ for f, size in feat_dict['features'].items():
self.weight_index_mapping[test_mi][f] = (ix, ix+size)
# weights are constant for a given feature
self.feat_weights[(test_mi, f)] = self.weights[ix]
@@ -1057,10 +1057,10 @@
"""Set weights for a single feature given as an (interface, feature)
pair, setting all others to zero."""
wdict = {}
- for test_mi, feat_dict in self.metric_features.iteritems():
+ for test_mi, feat_dict in self.metric_features.items():
if test_mi != feat[0]:
continue
- w = {}.fromkeys(feat_dict['features'].keys(), 0)
+ w = {}.fromkeys(list(feat_dict['features'].keys()), 0)
if feat[1] in w:
w[feat[1]] = weight
wdict[test_mi] = w
@@ -1074,20 +1074,20 @@
Features and model interfaces must correspond to those declared for the
context.
"""
- for test_mi, fs in weight_dict.iteritems():
+ for test_mi, fs in weight_dict.items():
try:
- flist = self.metric_features[test_mi]['features'].keys()
+ flist = list(self.metric_features[test_mi]['features'].keys())
except KeyError:
raise AssertionError("Invalid test model interface")
if isinstance(fs, common._num_types):
feat_dict = {}.fromkeys(flist, fs)
elif isinstance(fs, dict):
assert npy.alltrue([isinstance(w, common._num_types) for \
- w in fs.values()]), "Invalid scalar weight"
- assert npy.alltrue([f in flist for f in fs.keys()]), \
+ w in list(fs.values())]), "Invalid scalar weight"
+ assert npy.alltrue([f in flist for f in list(fs.keys())]), \
"Invalid features given for this test model interface"
feat_dict = fs
- for f, w in feat_dict.iteritems():
+ for f, w in feat_dict.items():
self.feat_weights[(test_mi, f)] = w
# update weight value
start_ix, end_ix = self.weight_index_mapping[test_mi][f]
@@ -1097,8 +1097,8 @@
"""Show detail of feature -> residual mapping for a given residual
vector."""
i = 0
- for test_mi, feat_dict in self.metric_features.iteritems():
- print "Test model interface:", test_mi
+ for test_mi, feat_dict in self.metric_features.items():
+ print("Test model interface:", test_mi)
for f in feat_dict['features']:
if self.feat_weights[(test_mi, f)] == 0:
continue
@@ -1108,12 +1108,12 @@
# ' unweighted:' is 13 chars long
extra_space_w = " "*max([0, 13-len(f_str)])
extra_space_unw = " "*max([0, len(f_str)-13])
- print f_str + extra_space_w , resvec[i:i+len_w]
+ print(f_str + extra_space_w , resvec[i:i+len_w])
try:
- print " unweighted:" + extra_space_unw, \
- resvec[i:i+len_w]/self.weights[ix0:ix1]
+ print(" unweighted:" + extra_space_unw, \
+ resvec[i:i+len_w]/self.weights[ix0:ix1])
except ZeroDivisionError:
- print " (unweighted values unavailable)"
+ print(" (unweighted values unavailable)")
i += len_w
def _map_to_features(self, x):
@@ -1124,7 +1124,7 @@
"""
out = {}
i = 0
- for test_mi, feat_dict in self.metric_features.iteritems():
+ for test_mi, feat_dict in self.metric_features.items():
for f in feat_dict['features']:
if self.feat_weights[(test_mi, f)] == 0:
continue
@@ -1157,9 +1157,9 @@
if self.debug_mode:
raise
else:
- print "******************************************"
- print "Problem evaluating interface", test_mi, "on ", ref_mi
- print " ", sys.exc_info()[0], sys.exc_info()[1]
+ print("******************************************")
+ print("Problem evaluating interface", test_mi, "on ", ref_mi)
+ print(" ", sys.exc_info()[0], sys.exc_info()[1])
new_result = False
# must create new_res first, to ensure all interfaces are
# evaluated (to create their results for possible post-processing)
@@ -1218,7 +1218,7 @@
except KeyboardInterrupt:
RefactoringTool: Refactored ./PyDSTool/Interval.py
raise
except:
- print "Failed to find trajectory values for given variable name: %s"%self.pars.varname
+ print("Failed to find trajectory values for given variable name: %s"%self.pars.varname)
raise
self.results.output = pts
return all(self.results.output==1)
@@ -1536,9 +1536,9 @@
except KeyboardInterrupt:
raise
except:
- print "Model interface compute_traj method for model " + \
- "'%s' failed" % self.model.name
- print sys.exc_info()[0], sys.exc_info()[1]
+ print("Model interface compute_traj method for model " + \
+ "'%s' failed" % self.model.name)
+ print(sys.exc_info()[0], sys.exc_info()[1])
return False
else:
return True
@@ -1687,17 +1687,17 @@
("Query argument must be a single string")
_keylist = ['orig_name', 'in_description']
if querykey not in _keylist:
- print 'Valid query keys are:', _keylist
+ print('Valid query keys are:', _keylist)
raise TypeError('Query key '+querykey+' is not valid')
if querykey == 'orig_name':
res = []
- for name, regentry in self.descs.iteritems():
+ for name, regentry in self.descs.items():
if regentry.orig_name == value:
res.append(name)
return res
if querykey == 'in_description':
res = []
- for name, regentry in self.descs.iteritems():
+ for name, regentry in self.descs.items():
if value in regentry.description:
res.append(name)
return res
--- ./PyDSTool/Interval.py (original)
+++ ./PyDSTool/Interval.py (refactored)
@@ -17,9 +17,9 @@
# supporting finitely-sampled real ranges.
## PyDSTool imports
-from utils import *
-from common import *
-from errors import *
+from .utils import *
+from .common import *
+from .errors import *
## Other imports
from numpy import Inf, NaN, isfinite, isinf, isnan, array, sign, linspace, arange
@@ -141,7 +141,7 @@
info(self.__dict__, "Interval " + self.name,
recurseDepthLimit=1+verboselevel)
else:
- print self.__repr__()
+ print(self.__repr__())
# Return all the interval's relevant data in a tuple
@@ -503,7 +503,7 @@
intervalsize = self._hival - self._loval
assert isfinite(intervalsize), "Interval must be finite"
if dt > intervalsize:
- print "Interval size = %f, dt = %f"%(intervalsize, dt)
+ print("Interval size = %f, dt = %f"%(intervalsize, dt))
raise ValueError('dt must be smaller than size of interval')
if dt <= 0:
raise ValueError('Must pass dt >= 0')
@@ -526,8 +526,8 @@
raise ValueError("dt must be an integer for integer "
"intervals")
if strict:
- print "Warning: 'strict' option is invalid for integer " + \
- "interval types"
+ print("Warning: 'strict' option is invalid for integer " + \
+ "interval types")
if avoidendpoints:
loval = self._loval+1
hival = self._hival-1
@@ -536,7 +536,7 @@
else:
loval = self._loval
hival = self._hival
- samplelist = range(loval, hival+1, dt)
+ samplelist = list(range(loval, hival+1, dt))
# extra +1 on hival because of python range() policy!
else:
raise TypeError("Unsupported value type")
@@ -560,8 +560,8 @@
#assert not isnan(loval) and not isnan(hival), \
# "Cannot specify NaN as interval endpoint"
if not loval < hival:
- print "set() was passed loval = ", loval, \
- RefactoringTool: No changes to ./PyDSTool/Generator/messagecodes.py
RefactoringTool: Refactored ./PyDSTool/Generator/baseclasses.py
" and hival = ", hival
+ print("set() was passed loval = ", loval, \
+ " and hival = ", hival)
raise PyDSTool_ValueError('Interval endpoints must be '
'given in order of increasing size')
self._intervalstr = '['+str(loval)+',' \
@@ -600,7 +600,7 @@
self._hival = arg
self.defined = True
else:
- print "Error in argument: ", arg, "of type", type(arg)
+ print("Error in argument: ", arg, "of type", type(arg))
raise PyDSTool_TypeError('Interval spec must be a numeric or '
'a length-2 sequence type')
@@ -676,7 +676,7 @@
def info(self, verboselevel=1):
- print self._infostr(verboselevel)
+ print(self._infostr(verboselevel))
def __copy__(self):
--- ./PyDSTool/Generator/baseclasses.py (original)
+++ ./PyDSTool/Generator/baseclasses.py (refactored)
@@ -1,7 +1,7 @@
# Generator base classes: Generator, ctsGen, discGen
-from __future__ import division
-
-from allimports import *
+
+
+from .allimports import *
from PyDSTool.utils import *
from PyDSTool.common import *
from PyDSTool.Symbolic import ensureStrArgDict, Quantity, QuantSpec, mathNameMap
@@ -89,7 +89,7 @@
def __repr__(self):
s = "Generator internal database class: "
- s += str(self.database.keys())
+ s += str(list(self.database.keys()))
return s
__str__ = __repr__
@@ -121,30 +121,30 @@
raise KeyError("Function %s not present"%k)
def keys(self):
- return [k for k in self.__dict__.keys() \
+ return [k for k in list(self.__dict__.keys()) \
if k not in ['genref', 'map_ixs']]
def __contains__(self, k):
- return k in self.keys()
+ return k in list(self.keys())
def values(self):
- return [self.__dict__[k] for k in self.__dict__.keys() \
+ return [self.__dict__[k] for k in list(self.__dict__.keys()) \
if k not in ['genref', 'map_ixs']]
def items(self):
- return zip(self.keys(), self.values())
+ return list(zip(list(self.keys()), list(self.values())))
def __repr__(self):
- return "Aux functions: " + ", ".join(self.keys())
+ return "Aux functions: " + ", ".join(list(self.keys()))
class ixmap(dict):
def __init__(self, genref):
self.parixmap = {}
self.pars = genref.pars
- i = genref.inputs.keys()
+ i = list(genref.inputs.keys())
i.sort()
- p = genref.pars.keys()
+ p = list(genref.pars.keys())
p.sort()
allnames = p + i
for pair in enumerate(allnames):
@@ -237,7 +237,7 @@
self._abseps = 1e-13
# `Checklevel` code determining response to uncertain float comparisons
if 'checklevel' in kw:
- if kw['checklevel'] not in range(4):
+ if kw['checklevel'] not in list(range(4)):
raise ValueError('Invalid interval endpoint checking option')
self.checklevel = kw['checklevel']
self.foundKeys += 1
@@ -317,7 +317,7 @@
The events are not guaranteed to be ordered by the value of the
independent variable.
"""
- compat_evnames = self._FScompatibleNamesInv(self.trajevents.keys())
+ compat_evnames = self._FScompatibleNamesInv(list(self.trajevents.keys()))
if evnames is None:
evnames = compat_evnames
if asGlobalTime:
@@ -340,7 +340,7 @@
assert all([ev in compat_evnames for ev in evnames]), \
"Invalid event name(s) provided: %s"%str(evnames)
result = {}
- for (evname, evptset) in self.trajevents.iteritems():
+ for (evname, evptset) in self.trajevents.items():
compat_evname = self._FScompatibleNamesInv(evname)
if compat_evname not in evnames:
continue
@@ -370,7 +370,7 @@
t_offset = self.globalt0
else:
t_offset = 0
- compat_evnames = self._FScompatibleNamesInv(self.trajevents.keys())
+ compat_evnames = self._FScompatibleNamesInv(list(self.trajevents.keys()))
if evnames is None:
evnames = compat_evnames
if isinstance(evnames, str):
@@ -386,7 +386,7 @@
# assume a sequence of strings
assert all([ev in compat_evnames for ev in evnames]), \
"Invalid event name(s) provided: %s"%str(evnames)
- for (evname, evptset) in self.trajevents.iteritems():
+ for (evname, evptset) in self.trajevents.items():
compat_evname = self._FScompatibleNamesInv(evname)
if compat_evname not in compat_evnames:
continue
@@ -407,9 +407,9 @@
assert isinstance(querykey, str), \
("Query argument must be a single string")
if querykey not in self._querykeys:
- print 'Valid query keys are:', self._querykeys
- print "('events' key only queries model-level events, not those"
- print " inside sub-models)"
+ print('Valid query keys are:', self._querykeys)
+ print("('events' key only queries model-level events, not those")
+ print(" inside sub-models)")
raise ValueError('Query key '+querykey+' is not valid')
if querykey in ['pars', 'parameters']:
result = self._FScompatibleNamesInv(self.pars)
@@ -426,12 +426,12 @@
result = self._FScompatibleNamesInv(self.funcspec.auxvars)
elif querykey == 'vardomains':
result = {}
- for varname, var in self.variables.iteritems():
+ for varname, var in self.variables.items():
result[self._FScompatibleNamesInv(varname)] = \
var.depdomain
elif querykey == 'pardomains':
result = {}
- for parname, pardom in self.parameterDomains.iteritems():
+ for parname, pardom in self.parameterDomains.items():
result[self._FScompatibleNamesInv(parname)] = \
pardom
elif querykey == 'abseps':
@@ -456,7 +456,7 @@
def info(self, verbose=1):
- print self._infostr(verbose)
+ print(self._infostr(verbose))
def _kw_process_dispatch(self, keys, kw):
@@ -478,12 +478,12 @@
def _kw_process_varspecs(self, kw, fs_args):
if 'varspecs' in kw:
- for varname, varspec in kw['varspecs'].items():
+ for varname, varspec in list(kw['varspecs'].items()):
if not isinstance(varname, (str, QuantSpec, Quantity)):
- print "Expected string, QuantSpec, or Quantity to name variable, got type %s" %(type(varname))
+ print("Expected string, QuantSpec, or Quantity to name variable, got type %s" %(type(varname)))
raise PyDSTool_TypeError("Invalid type for Variable name: %s"%str(varname))
if not isinstance(varspec, (str, QuantSpec, Quantity)):
- print "Expected string, QuantSpec, or Quantity definition for %s, got type %s" %(varname, type(varspec))
+ print("Expected string, QuantSpec, or Quantity definition for %s, got type %s" %(varname, type(varspec)))
raise PyDSTool_TypeError("Invalid type for Variable %s's specification."%varname)
self.foundKeys += 1
fs_args['varspecs'] = \
@@ -494,7 +494,7 @@
all_vars = []
# record number of variables defined by macros for FuncSpec checks
fs_args['_for_macro_info'] = args(totforvars=0, numfors=0, varsbyforspec={})
- for specname, specstr in fs_args['varspecs'].items():
+ for specname, specstr in list(fs_args['varspecs'].items()):
if not '[' in specname:
all_vars.append(specname)
fs_args['_for_macro_info'].varsbyforspec[specname] = [specname]
@@ -526,8 +526,8 @@
if 'tdomain' in kw:
self.tdomain = kw['tdomain']
if self.tdomain[0] >= self.tdomain[1]:
- print "Time domain specified: [%s, %s]"%(self.tdomain[0],
- self.tdomain[1])
+ print("Time domain specified: [%s, %s]"%(self.tdomain[0],
+ self.tdomain[1]))
raise PyDSTool_ValueError("tdomain values must be in order of "
"increasing size")
self.foundKeys += 1
@@ -607,7 +607,7 @@
elif isinstance(inputs, dict):
self.inputs.update(self._FScompatibleNames(inputs))
# ensure values are Variables or Pointsets
- for k, v in self.inputs.iteritems():
+ for k, v in self.inputs.items():
if not isinstance(v, Variable):
try:
self.inputs[k]=Variable(v)
@@ -621,22 +621,22 @@
# defined, e.g. inputs may be formally present in the keys but in
# fact unused
self._extInputsChanged = (self.inputs != {})
- fs_args['inputs'] = self.inputs.keys()
+ fs_args['inputs'] = list(self.inputs.keys())
else:
self._extInputsChanged = False
def _kw_process_ics(self, kw, fs_args):
if 'ics' in kw:
self._xdatadict = {}
- for k, v in dict(kw['ics']).iteritems():
+ for k, v in dict(kw['ics']).items():
self._xdatadict[self._FScompatibleNames(str(k))] = ensurefloat(v)
self.initialconditions = self._xdatadict.copy()
- unspecd = remain(self._xdatadict.keys(), self.__all_vars)
+ unspecd = remain(list(self._xdatadict.keys()), self.__all_vars)
if unspecd != []:
# ics were declared for variables not in varspecs
raise ValueError("Missing varspec entries for declared ICs: " + str(unspecd))
for name in remain(self.__all_vars,
- self._xdatadict.keys()):
+ list(self._xdatadict.keys())):
self.initialconditions[name] = NaN
self.foundKeys += 1
else:
@@ -679,7 +679,7 @@
self.xtype = {}
if 'xtype' in kw:
xts = kw['xtype']
- for name_temp, xt in dict(xts).iteritems():
+ for name_temp, xt in dict(xts).items():
if compareNumTypes(xt, _all_int):
xt_actual = int
elif compareNumTypes(xt, _all_float):
@@ -696,7 +696,7 @@
self.xtype[base+str(name_i)] = xt_actual
else:
self.xtype[name] = xt_actual
- for name in remain(fs_args['varspecs'].keys(), self.xtype.keys()):
+ for name in remain(list(fs_args['varspecs'].keys()), list(self.xtype.keys())):
self.xtype[name] = float
self.foundKeys += 1
else:
@@ -714,7 +714,7 @@
def _kw_process_xdomain(self, kw, fs_args):
if 'xdomain' in kw:
self.xdomain = {}
- for k, v in dict(kw['xdomain']).iteritems():
+ for k, v in dict(kw['xdomain']).items():
name = self._FScompatibleNames(str(k))
if isinstance(v, _seq_types):
assert len(v) == 2, \
@@ -729,7 +729,7 @@
else:
raise PyDSTool_TypeError('Invalid type for xdomain spec'
' '+name)
- for name in remain(fs_args['varspecs'].keys(), self.xdomain.keys()):
+ for name in remain(list(fs_args['varspecs'].keys()), list(self.xdomain.keys())):
if name[-1] == ']':
# for macro -- FuncSpec.py will double check for correct syntax
base = name[:name.index('[')]
@@ -781,9 +781,9 @@
except (AttributeError, TypeError):
raise TypeError("Invalid parameter symbolic definition")
else:
- for k, v in dict(kw['pars']).iteritems():
+ for k, v in dict(kw['pars']).items():
self.pars[self._FScompatibleNames(str(k))] = ensurefloat(v)
- fs_args['pars'] = self.pars.keys()
+ fs_args['pars'] = list(self.pars.keys())
self._register(self.pars)
self.foundKeys += 1
self.numpars = len(self.pars)
@@ -792,14 +792,14 @@
if 'pdomain' in kw:
if self.pars:
self.pdomain = {}
- for k, v in dict(kw['pdomain']).iteritems():
+ for k, v in dict(kw['pdomain']).items():
assert len(v) == 2, \
"Invalid size of domain specification for "+k
self.pdomain[self._FScompatibleNames(str(k))] = v
for name in self.pdomain:
if self.pdomain[name][0] >= self.pdomain[name][1]:
raise PyDSTool_ValueError('pdomain values must be in order of increasing size')
- for name in remain(self.pars.keys(), self.pdomain.keys()):
+ for name in remain(list(self.pars.keys()), list(self.pdomain.keys())):
self.pdomain[name] = [-Inf, Inf]
self.foundKeys += 1
else:
@@ -822,9 +822,9 @@
if self.checklevel < 3:
if cval is not notcontained:
if cval is uncertain and self.checklevel == 2:
- print 'Warning: Parameter value at bound'
+ print('Warning: Parameter value at bound')
else:
- print self.pars[pname], "not in", self.parameterDomains[pname].get()
+ print(self.pars[pname], "not in", self.parameterDomains[pname].get())
raise PyDSTool_ValueError('Parameter %s: value out of bounds'%pname)
else:
if cval is uncertain:
@@ -841,7 +841,7 @@
fs_args['targetlang'] = theGenSpecHelper(self).lang
if 'compiler' in kw:
if fs_args['targetlang'] == 'python':
- print "Warning: redundant option 'compiler' for python target"
+ print("Warning: redundant option 'compiler' for python target")
self._compiler = kw['compiler']
self.foundKeys += 1
elif fs_args['targetlang'] != 'python':
@@ -880,7 +880,7 @@
if self.pars:
# automatically pass par values on to embedded system
# when Rhs called
- parlist = self.pars.keys()
+ parlist = list(self.pars.keys())
parstr = "".join(["'%s': %s, "%(parname,parname) \
for parname in parlist])
if 'codeinsert_start' in fs_args:
@@ -914,11 +914,11 @@
outputStr += self.funcspec._infostr(verbose)
if verbose == 2:
outputStr += '\nVariables` validity intervals:'
- for v in self.variables.values():
+ for v in list(self.variables.values()):
outputStr += '\n ' + str(v.depdomain)
if self.eventstruct is not None:
outputStr += '\nEvents defined:'
- outputStr += '\n ' + str(self.eventstruct.events.keys())
+ outputStr += '\n ' + str(list(self.eventstruct.events.keys()))
if self._modeltag is not None:
outputStr += '\nAssociated Model: ' + self._modeltag.name
if verbose > 0:
@@ -928,28 +928,28 @@
def showEventSpec(self):
if self.eventstruct is not None:
- for evname, ev in self.eventstruct.events.iteritems():
- print evname + ":\n" + ev._funcstr
- print "\n"
+ for evname, ev in self.eventstruct.events.items():
+ print(evname + ":\n" + ev._funcstr)
+ print("\n")
def showSpec(self):
- print self.funcspec.spec[0]
+ print(self.funcspec.spec[0])
def showAuxSpec(self):
- print self.funcspec.auxspec[0]
+ print(self.funcspec.auxspec[0])
def showAuxFnSpec(self, auxfnname=None):
if auxfnname is None:
retdict = {}
- for aname, aspec in self.funcspec.auxfns.iteritems():
+ for aname, aspec in self.funcspec.auxfns.items():
retdict[aname] = aspec[0]
info(retdict)
else:
try:
- print self.funcspec.auxfns[auxfnname][0]
+ print(self.funcspec.auxfns[auxfnname][0])
except KeyError:
raise NameError("Aux function %s not found"%auxfnname)
@@ -975,7 +975,7 @@
assert isinstance(self.pars[name], _num_types)
assert type(self.pars[name]) == self._registry[name]
if self.inputs:
- for subjectname, obj in self.inputs.iteritems():
+ for subjectname, obj in self.inputs.items():
# test for containment of input's interval in independent
# variable interval
# (use checklevel = 1 for this o/w could get errors)
@@ -989,7 +989,7 @@
# check consistency with FuncSpec type of self.funcspec
# (unnecessary for dictionary version of FuncSpec)
if isinstance(self.funcspec, FuncSpec):
- varnames = self.variables.keys()
+ varnames = list(self.variables.keys())
fsvars = self.funcspec.vars
if len(varnames) > 1:
varnames.sort()
@@ -998,7 +998,7 @@
'variable names')
else:
assert varnames == fsvars
- parnames = self.pars.keys()
+ parnames = list(self.pars.keys())
fspars = self.funcspec.pars
if len(parnames) > 1:
parnames.sort()
@@ -1008,7 +1008,7 @@
else:
assert parnames == fspars
if self.inputs:
- inputnames = self.inputs.keys()
+ inputnames = list(self.inputs.keys())
fsinputs = self.funcspec.inputs
if len(inputnames) > 1:
inputnames.sort()
@@ -1020,7 +1020,7 @@
else:
assert len(self.funcspec) == self.dimension
except:
- print 'Invalid system specification'
+ print('Invalid system specification')
raise
@@ -1034,10 +1034,10 @@
if name not in self._needKeys + self._optionalKeys:
raise PyDSTool_KeyError('Key name ' + name + ' is invalid')
else:
- print 'Keywords supplied:\n\t' + str(kw.keys())
- print '# keywords found: ' + str(self.foundKeys)
- print 'Needed:\n\t' + str(self._needKeys)
- print 'Optional:\n\t' + str(self._optionalKeys)
+ print('Keywords supplied:\n\t' + str(list(kw.keys())))
+ print('# keywords found: ' + str(self.foundKeys))
+ print('Needed:\n\t' + str(self._needKeys))
+ print('Optional:\n\t' + str(self._optionalKeys))
raise PyDSTool_KeyError('Invalid keyword arguments for this class')
del self.foundKeys
@@ -1057,7 +1057,7 @@
if isinstance(items, dict):
# for parameter and variable dictionaries
- for name, v in items.iteritems():
+ for name, v in items.items():
if isinstance(self.funcspec, FuncSpec):
assert name in self.funcspec.vars \
or name in self.funcspec.auxvars \
@@ -1108,7 +1108,7 @@
def _addEvents(self, evs):
if isinstance(evs, list):
- map(self.eventstruct.add, copy(evs))
+ RefactoringTool: Refactored ./PyDSTool/Generator/allimports.py
list(map(self.eventstruct.add, copy(evs)))
elif isinstance(evs, Event):
# singleton
self.eventstruct.add(evs)
@@ -1132,7 +1132,7 @@
allnames = self.funcspec.vars + nonEvtPars
if activatedbounds in (None,{}):
activatedbounds = {}.fromkeys(allnames, (False,False))
- for xname, xdom in alldoms.iteritems():
+ for xname, xdom in alldoms.items():
if xname not in allnames:
# don't make bound constraints for non-state variables
continue
@@ -1195,7 +1195,7 @@
self.algparams['checkBounds'] = kw['checklevel']
if 'abseps' in kw:
self._abseps = kw['abseps']
- if remain(kw.keys(), ['globalt0', 'checklevel', 'abseps']) != []:
+ if remain(list(kw.keys()), ['globalt0', 'checklevel', 'abseps']) != []:
raise PyDSTool_KeyError('Invalid keywords passed')
@@ -1203,7 +1203,7 @@
"""Set initialconditions attribute of all generator's events, in
case event uses auxiliary functions that access this information."""
try:
- evs = self.eventstruct.events.values()
+ evs = list(self.eventstruct.events.values())
except AttributeError:
# no events present
pass
@@ -1329,7 +1329,7 @@
# Methods for pickling protocol
def __getstate__(self):
d = copy(self.__dict__)
- for fname, finfo in self._funcreg.iteritems():
+ for fname, finfo in self._funcreg.items():
try:
del d[fname]
except KeyError:
@@ -1347,7 +1347,7 @@
# delete object-specific class methods etc. before deleting
# to avoid crowding namespace
try:
- for fname, finfo in self._funcreg.iteritems():
+ for fname, finfo in self._funcreg.items():
try:
delattr(eval(finfo[0]), fname)
except AttributeError:
@@ -1362,10 +1362,10 @@
self.eventstruct.__del__()
if self.indepvariable is not None:
del self.indepvariable
- for v in self.variables.values():
+ for v in list(self.variables.values()):
v.__del__()
if hasattr(self, 'inputs'):
- for v in self.inputs.values():
+ for v in list(self.inputs.values()):
v.__del__()
except AttributeError:
# self does not have _funcreg
@@ -1467,18 +1467,18 @@
f.diagnostics.clearWarnings()
ilist.append(f(t, checklevel))
except AssertionError:
- print 'External input call has t out of range: t = ', t
- print 'Maybe checklevel is 3 and initial time is not', \
- 'completely inside valid time interval'
+ print('External input call has t out of range: t = ', t)
+ print('Maybe checklevel is 3 and initial time is not', \
+ 'completely inside valid time interval')
raise
except ValueError:
- print 'External input call has value out of range: t = ', t
- print 'Check beginning and end time of integration'
+ print('External input call has value out of range: t = ', t)
+ print('Check beginning and end time of integration')
for f in inputVarList:
if f.diagnostics.hasWarnings():
- print 'External input %s out of range:' % f.name
- print ' t = ', repr(f.diagnostics.warnings[-1][0]), ', ', \
- f.name, ' = ', repr(f.diagnostics.warnings[-1][1])
+ print('External input %s out of range:' % f.name)
+ print(' t = ', repr(f.diagnostics.warnings[-1][0]), ', ', \
+ f.name, ' = ', repr(f.diagnostics.warnings[-1][1]))
raise
return ilist
--- ./PyDSTool/Generator/allimports.py (original)
+++ ./PyDSTool/Generator/allimports.py (refactored)
@@ -10,6 +10,6 @@
from PyDSTool.TrajectoryRefactoringTool: Refactored ./PyDSTool/Generator/__init__.py
RefactoringTool: Refactored ./PyDSTool/Generator/Vode_ODEsystem.py
import *
from PyDSTool.FuncSpec import *
from PyDSTool.Events import *
-from messagecodes import *
+from .messagecodes import *
from math import *
import math, random, scipy
--- ./PyDSTool/Generator/__init__.py (original)
+++ ./PyDSTool/Generator/__init__.py (refactored)
@@ -3,20 +3,20 @@
Robert Clewley, September 2005
"""
-from baseclasses import *
-from ODEsystem import *
-from Euler_ODEsystem import *
-from Vode_ODEsystem import *
-from Dopri_ODEsystem import *
-from Radau_ODEsystem import *
-from ADMC_ODEsystem import *
-from ExplicitFnGen import *
-from ImplicitFnGen import *
-from EmbeddedSysGen import *
-from LookupTable import *
-from InterpolateTable import *
-from ExtrapolateTable import *
-from MapSystem import *
+from .baseclasses import *
+from .ODEsystem import *
+from .Euler_ODEsystem import *
+from .Vode_ODEsystem import *
+from .Dopri_ODEsystem import *
+from .Radau_ODEsystem import *
+from .ADMC_ODEsystem import *
+from .ExplicitFnGen import *
+from .ImplicitFnGen import *
+from .EmbeddedSysGen import *
+from .LookupTable import *
+from .InterpolateTable import *
+from .ExtrapolateTable import *
+from .MapSystem import *
def findGenSubClasses(superclass):
@@ -25,7 +25,7 @@
"findGenSubClasses requires a string as the name of the class to search for subclasses."
subclasslist = []
sc = eval(superclass)
- for x in theGenSpecHelper.gshDB.keys():
+ for x in list(theGenSpecHelper.gshDB.keys()):
if compareClassAndBases(theGenSpecHelper.gshDB[x].genClass,sc):
subclasslist.append(x)
return subclasslist
--- ./PyDSTool/Generator/Vode_ODEsystem.py (original)
+++ ./PyDSTool/Generator/Vode_ODEsystem.py (refactored)
@@ -1,11 +1,11 @@
"""VODE integrator for ODE systems, imported from a mild modification of
the scipy-wrapped VODE Fortran solver.
"""
-from __future__ import division
-
-from allimports import *
+
+
+from .allimports import *
from PyDSTool.Generator import ODEsystem as ODEsystem
-from baseclasses import Generator, theGenSpecHelper, _pollInputs
+from .baseclasses import Generator, theGenSpecHelper, _pollInputs
from PyDSTool.utils import *
from PyDSTool.common import *
from PyDSTool.scipy_ode import ode
@@ -61,7 +61,7 @@
# note: VODE only supports array atol, not rtol.
algparams_def = {'poly_interp': False,
'rtol': 1e-9,
- 'atol': [1e-12 for dimix in xrange(self.dimension)],
+ 'atol': [1e-12 for dimix in range(self.dimension)],
'stiff': False,
'max_step': 0.0,
'min_step': 0.0,
@@ -71,7 +71,7 @@
'use_special': False,
'specialtimes': []
}
- for k, v in algparams_def.iteritems():
+ for k, v in algparams_def.items():
if k not in self.algparams:
self.algparams[k] = v
@@ -126,11 +126,11 @@
'dimension')
else:
atol = self.algparams['atol']
- self.algparams['atol'] = [atol for dimix in xrange(self.dimension)]
+ self.algparams['atol'] = [atol for dimix in range(self.dimension)]
indepdom0, indepdom1 = self.indepvariable.depdomain.get()
if continue_integ:
if indepdom0 > self._solver.t:
- print "Previous end time is %f"%self._solver.t
+ print("Previous end time is %f"%self._solver.t)
raise ValueError("Start time not correctly updated for "
"continuing orbit")
x0 = self._solver.y
@@ -197,7 +197,7 @@
## solver.set_initial_value(x0, indepdom1)
# wrap up each dictionary initial value as a singleton list
alltData = [t0]
- allxDataDict = dict(zip(xnames, map(listid, x0)))
+ allxDataDict = dict(list(zip(xnames, list(map(listid, x0)))))
plist = sortedDictValues(self.pars)
extralist = copy(plist)
if self.inputs:
@@ -220,12 +220,12 @@
if do_poly:
rhsfn = getattr(self, self.funcspec.spec[1])
dx0 = rhsfn(t0, x0, extralist)
- alldxDataDict = dict(zip(xnames, map(listid, dx0)))
+ alldxDataDict = dict(list(zip(xnames, list(map(listid, dx0)))))
auxvarsfn = getattr(self,self.funcspec.auxspec[1])
strict = self.algparams['strictdt']
# Make t mesh if it wasn't given as 'specialtimes'
if not all(isfinite(self.indepvariable.depdomain.get())):
- print "Time domain was: ", self.indepvariable.depdomain.get()
+ print("Time domain was: ", self.indepvariable.depdomain.get())
raise ValueError("Ensure time domain is finite")
if dt == indepdom1 - indepdom0:
# single-step integration required
@@ -284,24 +284,24 @@
try:
allaDataDict[aname] = [avals[aix]]
except IndexError:
- print "\nVODE generator: There was a problem evaluating " \
- + "an auxiliary variable"
- print "Debug info: avals (length", len(avals), ") was ", avals
- print "Index out of range was ", aix
- print self.funcspec.auxspec[1]
- print hasattr(self, self.funcspec.auxspec[1])
- print "Args were:", [t0, x0, extralist]
+ print("\nVODE generator: There was a problem evaluating " \
+ + "an auxiliary variable")
+ print("Debug info: avals (length", len(avals), ") was ", avals)
+ print("Index out of range was ", aix)
+ print(self.funcspec.auxspec[1])
+ print(hasattr(self, self.funcspec.auxspec[1]))
+ print("Args were:", [t0, x0, extralist])
raise
# Initialize signs of event detection objects at IC
self.setEventICs(self.initialconditions, self.globalt0)
if self.inputs:
parsinps = copy(self.pars)
- parsinps.update(dict(zip(inames,ilist)))
+ parsinps.update(dict(list(zip(inames,ilist))))
else:
parsinps = self.pars
if eventslist != []:
dataDict = copy(self.initialconditions)
- dataDict.update(dict(zip(anames, avals)))
+ dataDict.update(dict(list(zip(anames, avals))))
dataDict['t'] = t0
evsflagged = self.eventstruct.pollHighLevelEvents(None,
dataDict,
@@ -352,8 +352,8 @@
Evtimes[evname] = []
Evpoints[evname] = []
# temp storage for repeatedly used object attributes (for lookup efficiency)
- depdomains = dict(zip(range(self.dimension),
- [self.variables[xn].depdomain for xn in xnames]))
+ depdomains = dict(list(zip(list(range(self.dimension)),
+ [self.variables[xn].depdomain for xn in xnames])))
# Main integration loop
num_points = 0
breakwhile = False
@@ -367,14 +367,14 @@
try:
errcode = solver.integrate(new_t)
except:
- print "Error calling right hand side function:"
+ print("Error calling right hand side function:")
self.showSpec()
- print "Numerical traceback information (current state, " \
- + "parameters, etc.)"
- print "in generator dictionary 'traceback'"
- self.traceback = {'vars': dict(zip(xnames,solver.y)),
- 'pars': dict(zip(pnames,plist)),
- 'inputs': dict(zip(inames,ilist)),
+ print("Numerical traceback information (current state, " \
+ + "parameters, etc.)")
+ print("in generator dictionary 'traceback'")
+ self.traceback = {'vars': dict(list(zip(xnames,solver.y))),
+ 'pars': dict(list(zip(pnames,plist))),
+ 'inputs': dict(list(zip(inames,ilist))),
self.indepvariable.name: new_t}
raise
avals = auxvarsfn(new_t, solver.y, extralist)
@@ -382,14 +382,14 @@
# assert all([isfinite(a) for a in avals]), \
# "Some auxiliary variable values not finite"
if eventslist != []:
- dataDict = dict(zip(xnames,solver.y))
- dataDict.update(dict(zip(anames,avals)))
+ dataDict = dict(list(zip(xnames,solver.y)))
+ dataDict.update(dict(list(zip(anames,avals))))
dataDict['t'] = new_t
if self.inputs:
parsinps = copy(self.pars)
- parsinps.update(dict(zip(inames,
+ parsinps.update(dict(list(zip(inames,
_pollInputs(inputVarList, new_t+self.globalt0,
- self.checklevel))))
+ self.checklevel)))))
else:
parsinps = self.pars
evsflagged = self.eventstruct.pollHighLevelEvents(None,
@@ -398,9 +398,8 @@
eventslist)
## print new_t, evsflagged
## evsflagged = [ev for ev in evsflagged if solver.t-indepdom0 > ev[1].eventinterval]
- termevsflagged = filter(lambda e: e in evsflagged, termevents)
- nontermevsflagged = filter(lambda e: e not in termevsflagged,
- evsflagged)
+ termevsflagged = [e for e in termevents if e in evsflagged]
+ nontermevsflagged = [e for e in evsflagged if e not in termevsflagged]
# register any non-terminating events in the warnings
# list, unless they are 'precise' in which case flag
# them to be resolved after integration completes
@@ -557,7 +556,7 @@
# choose slightly smaller dt to fit trange exactly
dt = trangewidth/numpoints
- tmesh = [told + i*dt for i in xrange(1, numpoints+1)]
+ tmesh = [told + i*dt for i in range(1, numpoints+1)]
# linspace version is *much* slower for numpoints ~ 10 and 100
#tmesh = list(told+linspace(dt, numpoints*dt, numpoints))
@@ -585,7 +584,7 @@
# much less accurately determined)
if not breakwhile:
# only here if a terminal event hasn't just flagged
- for xi in xrange(self.dimension):
+ for xi in range(self.dimension):
if not self.contains(depdomains[xi],
solver.y[xi],
self.checklevel):
@@ -615,17 +614,17 @@
self.checklevel) \
for f in inputVarList]
except ValueError:
- print 'External input call caused value out of range error:',\
- 't = ', solver.t
+ print('External input call caused value out of range error:',\
+ 't = ', solver.t)
for f in inputVarList:
if f.diagnostics.hasWarnings():
- print 'External input variable %s out of range:'%f.name
- print ' t = ', repr(f.diagnostics.warnings[-1][0]), ', ', \
- f.name, ' = ', repr(f.diagnostics.warnings[-1][1])
+ print('External input variable %s out of range:'%f.name)
+ print(' t = ', repr(f.diagnostics.warnings[-1][0]), ', ', \
+ f.name, ' = ', repr(f.diagnostics.warnings[-1][1]))
raise
except AssertionError:
- print 'External input call caused t out of range error: t = ', \
- solver.t
+ print('External input call caused t out of range error: t = ', \
+ solver.t)
raise
solver.set_f_params(extralist)
breakwhile = not solver.successful()
@@ -643,8 +642,8 @@
try:
if self.diagnostics.warnings[-1][0] not in [W_TERMEVENT,
W_TERMSTATEBD]:
- print "t =", solver.t
- print "state =", dict(zip(xnames,solver.y))
+ print("t =", solver.t)
+ print("state =", dict(list(zip(xnames,solver.y))))
raise RuntimeError("Event finding code for terminal event "
"failed in Generator " + self.name + \
": try decreasing eventdelay or "
@@ -652,8 +651,8 @@
"atol and rtol parameters")
except IndexError:
info(self.diagnostics.outputStats, "Output statistics")
- print "t =", solver.t
- print "x =", solver.y
+ print("t =", solver.t)
+ print("x =", solver.y)
raise RuntimeError("Event finding failed in Generator " + \
self.name + ": try decreasing eventdelay "
"or eventinterval below eventtol, or the "
@@ -692,18 +691,18 @@
interp = interp1d(alltData, xvals)
variables[x] = Variable(interp, 't', x, x)
else:
- print "Error in Generator:", self.name
- print "t = ", alltData
- print "x = ", allxDataDict
+ print("Error in Generator:", self.name)
+ print("t = ", alltData)
+ print("x = ", allxDataDict)
raise PyDSTool_ValueError("Fewer than 2 data points computed")
for a in anames:
if len(alltData) > 1:
variables[a] = Variable(interp1d(alltData, allaDataDict[a]),
't', a, a)
else:
- print "Error in Generator:", self.name
- print "t = ", alltData
- print "x = ", allxDataDict
+ print("Error in Generator:", self.name)
+ print("t = ", alltData)
+ print("x = ", allxDataDict)
raise PyDSTool_ValueError("Fewer than 2 data points computed")
# Resolve non-terminal 'precise' events that were flagged, using the
# variables created. Then, add them to a new version of the variables.
@@ -739,17 +738,17 @@
else:
lost_evt = True
if lost_evt:
- print "Error: A non-terminal, 'precise' event was lost -- did you reset",
- print "events prior to integration?"
+ print("Error: A non-terminal, 'precise' event was lost -- did you reset", end=' ')
+ print("events prior to integration?")
raise PyDSTool_ExistError("Internal error: A non-terminal, "
"'precise' event '%s' was lost after integration!"%e[0])
# add non-terminal event points to variables
if ntpe_tdict != {}:
# find indices of times at which event times will be inserted
tix = 0
- evts = ntpe_tdict.keys()
+ evts = list(ntpe_tdict.keys())
evts.sort()
- for evix in xrange(len(evts)):
+ for evix in range(len(evts)):
evt = evts[evix]
evnames = ntpe_tdict[evt]
self.diagnostics.warnings.append((W_NONTERMEVENT, (evt, evnames)))
@@ -801,7 +800,7 @@
}
if solver.successful():RefactoringTool: Refactored ./PyDSTool/Generator/Radau_ODEsystem.py
#self.validateSpec()
- for evname, evtlist in Evtimes.iteritems():
+ for evname, evtlist in Evtimes.items():
try:
self.eventstruct.Evtimes[evname].extend([et+self.globalt0 \
for et in evtlist])
@@ -822,7 +821,7 @@
'indepvararray': Evtimes[evname],
'indepvartype': float})
self.defined = True
- return Trajectory(trajname, variables.values(),
+ return Trajectory(trajname, list(variables.values()),
abseps=self._abseps, globalt0=self.globalt0,
checklevel=self.checklevel,
FScompatibleNames=self._FScompatibleNames,
@@ -836,7 +835,7 @@
self.diagnostics._errorcodes[errcode])))
except TypeError:
# e.g. when errcode has been used to return info list
- print "Error information: ", errcode
+ print("Error information: ", errcode)
self.diagnostics.errors.append((E_COMPUTFAIL, (solver.t,
self.diagnostics._errorcodes[0])))
self.defined = False
@@ -857,7 +856,7 @@
p = sortedDictValues(self._FScompatibleNames(pdict))
i = _pollInputs(sortedDictValues(self.inputs),
t, self.checklevel)
- return apply(getattr(self, self.funcspec.spec[1]), [t, x, p+i])
+ return getattr(self, self.funcspec.spec[1])(*[t, x, p+i])
def Jacobian(self, t, xdict, pdict=None, asarray=True):
@@ -875,8 +874,7 @@
p = sortedDictValues(self._FScompatibleNames(pdict))
i = _pollInputs(sortedDictValues(self.inputs),
t, self.checklevel)
- return apply(getattr(self, self.funcspec.auxfns["Jacobian"][1]), \
- [t, x, p+i])
+ return getattr(self, self.funcspec.auxfns["Jacobian"][1])(*[t, x, p+i])
else:
raise PyDSTool_ExistError("Jacobian not defined")
@@ -896,8 +894,7 @@
p = sortedDictValues(self._FScompatibleNames(pdict))
i = _pollInputs(sortedDictValues(self.inputs),
t, self.checklevel)
- return apply(getattr(self, self.funcspec.auxfns["Jacobian_pars"][1]), \
- [t, x, p+i])
+ return getattr(self, self.funcspec.auxfns["Jacobian_pars"][1])(*[t, x, p+i])
else:
raise PyDSTool_ExistError("Jacobian w.r.t. parameters not defined")
@@ -916,7 +913,7 @@
p = sortedDictValues(self._FScompatibleNames(pdict))
i = _pollInputs(sortedDictValues(self.inputs),
t, self.checklevel)
- return apply(getattr(self, self.funcspec.auxspec[1]), [t, x, p+i])
+ return getattr(self, self.funcspec.auxspec[1])(*[t, x, p+i])
def __del__(self):
--- ./PyDSTool/Generator/Radau_ODEsystem.py (original)
+++ ./PyDSTool/Generator/Radau_ODEsystem.py (refactored)
@@ -1,9 +1,9 @@
# Radau ODE system
-from __future__ import division
-
-from allimports import *
+
+
+from .allimports import *
from PyDSTool.Generator import ODEsystem as ODEsystem
-from baseclasses import Generator, theGenSpecHelper, genDB, _pollInputs
+from .baseclasses import Generator, theGenSpecHelper, genDB, _pollInputs
from PyDSTool.utils import *
from PyDSTool.common import *
from PyDSTool.ModelSpec import QuantSpec
@@ -48,8 +48,8 @@
try:
self._integMod = __import__(modname, globals())
except:
- print "Error in importing compiled vector field and integrator."
- print "Did you compile the RHS C code?"
+ print("Error in importing compiled vector field and integrator.")
+ print("Did you compile the RHS C code?")
raise
# check module's directory
assert 'Integrate' in dir(self._integMod), \
@@ -477,14 +477,14 @@
'hasJacP': 0,
'checkBounds': self.checklevel
}
- for k, v in algparams_def.iteritems():
+ for k, v in algparams_def.items():
if k not in self.algparams:
self.algparams[k] = v
# verify that no additional keys are present in algparams, after
# defaults are added above
if len(self.algparams) != len(algparams_def):
raise ValueError("Invalid keys present in algparams argument: " \
- + str(remain(self.algparams.keys(),algparams_def.keys())))
+ + str(remain(list(self.algparams.keys()),list(algparams_def.keys()))))
# Check for non-constant mass matrix
if self.haveMass():
mspec = self.funcspec.auxfns['massMatrix']
@@ -502,9 +502,9 @@
elif thisplatform in ['Linux', 'IRIX', 'Solaris', 'SunOS', 'MacOS', 'Darwin', 'FreeBSD']:
self._dllext = '.so'
else:
- print "Shared library extension not tested on this platform."
- print "If this process fails please report the errors to the"
- print "developers."
+ print("Shared library extension not tested on this platform.")
+ print("If this process fails please report the errors to the")
+ print("developers.")
self._dllext = '.so'
self._compilation_tempdir = os.path.join(os.getcwd(),
"radau5_temp")
@@ -514,8 +514,8 @@
"A file already exists with the same name"
os.mkdir(self._compilation_tempdir)
except:
- print "Could not create compilation temp directory " + \
- self._compilation_tempdir
+ print("Could not create compilation temp directory " + \
+ self._compilation_tempdir)
raise
self._compilation_sourcedir = os.path.join(_pydstool_path,"integrator")
self._vf_file = self.name+"_vf.c"
@@ -529,8 +529,8 @@
self.makeLibSource()
self.compileLib()
else:
- print "Build the library using the makeLib method, or in "
- print "stages using the makeLibSource and compileLib methods."
+ print("Build the library using the makeLib method, or in ")
+ print("stages using the makeLibSource and compileLib methods.")
self._inputVarList = []
self._inputTimeList = []
@@ -562,9 +562,9 @@
## "_radau5"+self._vf_filename_ext+self._dllext)):
## os.remove(os.path.join(os.getcwd(),
## "_radau5"+self._vf_filename_ext+self._dllext))
- print "Cannot rebuild library without restarting session. Sorry."
- print "Try asking the Python developers to make a working module"
- print "unimport function!"
+ print("Cannot rebuild library without restarting session. Sorry.")
+ print("Try asking the Python developers to make a working module")
+ print("unimport function!")
## self.makeLibSource()
@@ -628,7 +628,7 @@
('string.h', STDLIB), ('vfield.h', USERLIB), ('events.h', USERLIB),
('signum.h', USERLIB), ('maxmin.h', USERLIB)])
include_str = ''
- for libstr, libtype in libinclude.iteritems():
+ for libstr, libtype in libinclude.items():
if libtype == STDLIB:
quoteleft = '<'
quoteright = '>'
@@ -641,8 +641,8 @@
for libstr in include:
if libstr in libinclude:
# don't repeat libraries
- print "Warning: library '" + libstr + "' already appears in list"\
- + " of imported libraries"
+ print("Warning: library '" + libstr + "' already appears in list"\
+ + " of imported libraries")
else:
include_str += "#include " + '"' + libstr + '"\n'
allfilestr = "/* Vector field function and events for Radau integrator.\n" \
@@ -682,17 +682,17 @@
inames = self.funcspec.inputs
pnames.sort()
inames.sort()
- for i in xrange(self.numpars):
+ for i in range(self.numpars):
p = pnames[i]
# add to defines
pardefines += self.funcspec._defstr+" "+p+"\tp_["+str(i)+"]\n"
- for i in xrange(self.dimension):
+ for i in range(self.dimension):
v = vnames[i]
# add to defines
vardefines += self.funcspec._defstr+" "+v+"\tY_["+str(i)+"]\n"
for i, v in enumerate(self.funcspec.auxvars):
auxvardefines += self.funcspec._defstr+" "+v+"\t("+self.funcspec._auxdefs_parsed[v]+")\n"
- for i in xrange(len(self.funcspec.inputs)):
+ for i in range(len(self.funcspec.inputs)):
inp = inames[i]
# add to defines
inpdefines += self.funcspec._defstr+" "+inp+"\txv_["+str(i)+"]\n"
@@ -718,7 +718,7 @@
# and add hidden p argument
if self.funcspec.auxfns:
fbody_parsed = addArgToCalls(fbody,
- self.funcspec.auxfns.keys(),
+ list(self.funcspec.auxfns.keys()),
"p_, wk_, xv_")
if 'initcond' in self.funcspec.auxfns:
# convert 'initcond(x)' to 'initcond("x")' for
@@ -733,7 +733,7 @@
# add signature for auxiliary functions
if self.funcspec.auxfns:
allfilestr += "\n"
- for finfo in self.funcspec.auxfns.values():
+ for finfo in list(self.funcspec.auxfns.values()):
allfilestr += finfo[1] + ";\n"
assignEvBody = ""
for evix in range(numevs):
@@ -757,11 +757,11 @@
+ ";\n\n\n"
allfilestr += self.funcspec.spec[0] + "\n\n"
if self.funcspec.auxfns:
- for fname, finfo in self.funcspec.auxfns.iteritems():
+ for fname, finfo in self.funcspec.auxfns.items():
fbody = finfo[0]
# subs _p into auxfn-to-auxfn calls (but not to the signature)
fbody_parsed = addArgToCalls(fbody,
- self.funcspec.auxfns.keys(),
+ list(self.funcspec.auxfns.keys()),
"p_, wk_, xv_", notFirst=fname)
if 'initcond' in self.funcspec.auxfns:
# convert 'initcond(x)' to 'initcond("x")' for
@@ -795,9 +795,9 @@
file = open(vffile, 'w')
file.write(allfilestr)
file.close()
- except IOError, e:
- print "Error opening file "+self._vf_file+" for writing"
- raise IOError, e
+ except IOError as e:
+ print("Error opening file "+self._vf_file+" for writing")
+ raise IOError(e)
def compileLib(self, libsources=[], libdirs=[]):
@@ -813,21 +813,21 @@
# then DLL file already exists and we can't overwrite it at this
# time
proceed = False
- print "\n"
- print "-----------------------------------------------------------"
- print "Present limitation of Python: Cannot rebuild library"
- print "without exiting Python and deleting the shared library"
- print " " + str(os.path.join(os.getcwd(),
- "_radau5"+self._vf_filename_ext+self._dllext))
- print "by hand! If you made any changes to the system you should"
- print "not proceed with running the integrator until you quit"
- print "and rebuild."
- print "-----------------------------------------------------------"
- print "\n"
+ print("\n")
+ print("-----------------------------------------------------------")
+ print("Present limitation of Python: Cannot rebuild library")
+ print("without exiting Python and deleting the shared library")
+ print(" " + str(os.path.join(os.getcwd(),
+ "_radau5"+self._vf_filename_ext+self._dllext)))
+ print("by hand! If you made any changes to the system you should")
+ print("not proceed with running the integrator until you quit")
+ print("and rebuild.")
+ print("-----------------------------------------------------------")
+ print("\n")
else:
proceed = True
if not proceed:
- print "Did not compile shared library."
+ print("Did not compile shared library.")
return
if self._solver is not None:
self.forceLibRefresh()
@@ -844,7 +844,7 @@
ifacefile_orig.close()
ifacefile_copy.close()
except IOError:
- print "radau5.i copying error in radau compilation directory"
+ print("radau5.i copying error in radau compilation directory")
raise
swigfile = os.path.join(self._compilation_tempdir,
"radau5"+self._vf_filename_ext+".i")
@@ -915,8 +915,8 @@
'library_dirs': radlibdirs+['./']})])
except:
rout.stop()
- print "\nError occurred in generating Radau system..."
- print sys.exc_info()[0], sys.exc_info()[1]
+ print("\nError occurred in generating Radau system...")
+ print(sys.exc_info()[0], sys.exc_info()[1])
raise RuntimeError
rout.stop() # restore stdout
# Attempt to unload module through a shutdown() function being
@@ -959,8 +959,8 @@
os.path.join(os.getcwd(),
"radau5"+self._vf_filename_ext+".py"))
except:
- print "\nError occurred in generating Radau system"
- print "(while moving library extension modules to CWD)"
+ print("\nError occurred in generating Radau system")
+ print("(while moving library extension modules to CWD)")
#print sys.exc_info()[0], sys.exc_info()[1]
raise #RuntimeError
@@ -1032,8 +1032,8 @@
bounds[0].append(bds[0])
bounds[1].append(bds[1])
except TypeError:
- print v, type(bds), bds
- print self.xdomain
+ print(v, type(bds), bds)
+ print(self.xdomain)
raise
for p in self.funcspec.pars:
bds = self.pdomain[p]
@@ -1041,7 +1041,7 @@
bounds[0].append(bds[0])
bounds[1].append(bds[1])
except TypeError:
- print type(bds), bds
+ print(type(bds), bds)
raise
if continue_integ:
x0 = self._solver.lastPoint
@@ -1182,12 +1182,12 @@
numevs = len(Evtimes[evix])
if self.algparams['eventTerm'][evix]:
if numevs > 1:
- print "Event info:", Evpoints, Evtimes
+ print("Event info:", Evpoints, Evtimes)
assert numevs <= 1, ("Internal error: more than one "
"terminal event of same type found")
# For safety, we should assert that this event
# also appears in termevents, but we don't
- if Evtimes[evix][0] in termevtimes.keys():
+ if Evtimes[evix][0] in list(termevtimes.keys()):
# append event name to this warning
warning_ix = termevtimes[Evtimes[evix][0]]
self.diagnostics.warnings[warning_ix][1][1].append(evname)
@@ -1200,7 +1200,7 @@
[evname])))
else:
for ev in range(numevs):
- if Evtimes[evix][ev] in nontermevtimes.keys():
+ if Evtimes[evix][ev] in list(nontermevtimes.keys()):
# append event name to this warning
warning_ix = nontermevtimes[Evtimes[evix][ev]]
self.diagnostics.warnings[warning_ix][1][1].append(evname)
@@ -1212,9 +1212,9 @@
(Evtimes[evix][ev],
[evname])))
except IndexError:
- print "Events returned from integrator are the wrong size."
- print " Did you change the system and not refresh the C " \
- + "library using the forcelibrefresh() method?"
+ print("Events returned from integrator are the wrong size.")
+ print(" Did you change the system and not refresh the C " \
+ + "library using the forcelibrefresh() method?")
raise
termcount = 0
for (w,i) in self.diagnostics.warnings:
@@ -1234,10 +1234,10 @@
last_t = Inf
if self.algparams['checkBounds'] > 0:
# temp storage for repeatedly used object attributes (for lookup efficiency)
- depdomains = dict(zip(range(self.dimension),
- [self.variables[xn].depdomain for xn in xnames]))
+ depdomains = dict(list(zip(list(range(self.dimension)),
+ [self.variables[xn].depdomain for xn in xnames])))
offender_ix = None
- for xi in xrange(self.dimension):
+ for xi in range(self.dimension):
if not any(depdomains[xi].isfinite()):
# no point in checking when the bounds are +/- infinity
continue
@@ -1254,7 +1254,7 @@
elif last_ix >= 0 and last_ix < highest_ix:
# truncate data
last_t = alltData[last_ix]
- print "Warning; domain bound reached (because algparams['checkBounds'] > 0)"
+ print("Warning; domain bound reached (because algparams['checkBounds'] > 0)")
self.diagnostics.warnings.append((W_TERMSTATEBD,
(last_t, xnames[offender_ix],
X[offender_ix, last_ix],
@@ -1306,11 +1306,11 @@
X = X[:, :last_ix]
alltData = alltData[:last_ix]
try:
- allxDataDict = dict(zip(xnames,X))
+ allxDataDict = dict(list(zip(xnames,X)))
except IndexError:
- print "Integration returned variable values of unexpected dimensions."
- print " Did you change the system and not refresh the C library" \
- + " using the forcelibrefresh() method?"
+ print("Integration returned variable values of unexpected dimensions.")
+ print(" Did you change the system and not refresh the C library" \
+ + " using the forcelibrefresh() method?")
raise
# storage of all auxiliary variable data
anames = self.funcspec.auxvars
@@ -1319,14 +1319,14 @@
if last_ix < highest_ix:
A = A[:, :last_ix]
try:
- allaDataDict = dict(zip(anames,A))
+ allaDataDict = dict(list(zip(anames,A)))
except TypeError:
- print "Internal error! Type of A: ", type(A)
+ print("Internal error! Type of A: ", type(A))
raise
except IndexError:
- print "Integration returned auxiliary values of unexpected dimensions."
- print " Did you change the system and not refresh the C library" \
- + " using the forcelibrefresh() method?"
+ print("IntegratiRefactoringTool: Refactored ./PyDSTool/Generator/ODEsystem.py
on returned auxiliary values of unexpected dimensions.")
+ print(" Did you change the system and not refresh the C library" \
+ + " using the forcelibrefresh() method?")
raise
if int(Err) == 1 or (int(Err) == 2 and termcount == 1):
# output OK
@@ -1361,7 +1361,7 @@
# final checks
#self.validateSpec()
self.defined = True
- return Trajectory(trajname, variables.values(),
+ return Trajectory(trajname, list(variables.values()),
abseps=self._abseps, globalt0=self.globalt0,
checklevel=self.checklevel,
FScompatibleNames=self._FScompatibleNames,
@@ -1374,7 +1374,7 @@
diagnost_info = self.diagnostics._errorcodes[int(Err)]
except TypeError:
# errcode messed up from Radau
- print "Error code: ", Err
+ print("Error code: ", Err)
diagnost_info = self.diagnostics._errorcodes[0]
if self._solver.verbose:
info(self.diagnostics.outputStats, "Output statistics")
@@ -1383,8 +1383,8 @@
if (len(alltData) == self.algparams['max_pts'] or \
self.diagnostics.outputStats['num_steps'] >= self.algparams['max_pts']) \
and alltData[-1] < tend:
- print "max_pts algorithmic parameter too small: current " + \
- "value is %i"%self.algparams['max_pts']
+ print("max_pts algorithmic parameter too small: current " + \
+ "value is %i"%self.algparams['max_pts'])
# avstep = (self.algparams['init_step']+self.diagnostics.outputStats['last_step'])/2.
if self.diagnostics.outputStats['last_time']-tbegin > 0:
ms = str(int(round(self.algparams['max_pts'] / \
@@ -1392,8 +1392,8 @@
tbegin)*(tend-tbegin))))
else:
ms = 'Inf'
- print "(recommended value for this trajectory segment is " + \
- "estimated to be %s (saved in diagnostics.errors attribute))"%str(ms)
+ print("(recommended value for this trajectory segment is " + \
+ "estimated to be %s (saved in diagnostics.errors attribute))"%str(ms))
diagnost_info += " -- recommended value is " + ms
self.diagnostics.errors.append((E_COMPUTFAIL,
(self._solver.lastTime, diagnost_info)))
--- ./PyDSTool/Generator/ODEsystem.py (original)
+++ ./PyDSTool/Generator/ODEsystem.py (refactored)
@@ -1,7 +1,7 @@
# ODEsystem base class
-from allimports import *
-from baseclasses import ctsGen, theGenSpecHelper, auxfn_container
+from .allimports import *
+from .baseclasses import ctsGen, theGenSpecHelper, auxfn_container
from PyDSTool.utils import *
from PyDSTool.common import *
from PyDSTool.Variable import Variable, iscontinuous
@@ -51,7 +51,7 @@
self.funcspec = RHSfuncSpec(self._kw_process_dispatch(dispatch_list,
kw))
self.indepvartype = float
- for v in self.inputs.values():
+ for v in list(self.inputs.values()):
if not iscontinuous(v):
raise ValueError("External inputs for ODE system must be "
"continuously defined")
@@ -109,9 +109,9 @@
# user-defined auxiliary functions
# (built-ins are provided explicitly)
try:
- exec fninfo[0]
+ exec(fninfo[0])
except:
- print 'Error in supplied auxiliary function code'
+ print('Error in supplied auxiliary function code')
self._funcreg[fninfo[1]] = ('self', fninfo[0])
setattr(self, fninfo[1], types.MethodType(locals()[fninfo[1]],
self,
@@ -120,9 +120,9 @@
try:
uafi_code = self.funcspec._user_auxfn_interface[auxfnname]
try:
- exec uafi_code
+ exec(uafi_code)
except:
- print 'Error in auxiliary function wrapper'
+ print('Error in auxiliary function wrapper')
raise
setattr(self.auxfns, auxfnname,
types.MethodType(locals()[auxfnname], self.auxfns,
@@ -144,9 +144,9 @@
if self.funcspec.targetlang == 'python':
fninfo = self.funcspec.spec
try:
- exec fninfo[0]
+ exec(fninfo[0])
except:
- print 'Error in supplied functional specification code'
+ print('Error in supplied functional specification code')
raise
self._funcreg[fninfo[1]] = ('self', fninfo[0])
setattr(self, fninfo[1], types.MethodType(locals()[fninfo[1]],
@@ -159,9 +159,9 @@
if self.funcspec.auxspec != '':
fninfo = self.funcspec.auxspec
try:
- exec fninfo[0]
+ exec(fninfo[0])
except:
- print 'Error in supplied auxiliary variable code'
+ print('Error in supplied auxiliary variable code')
raise
self._funcreg[fninfo[1]] = ('self', fninfo[0])
setattr(self, fninfo[1], types.MethodType(locals()[fninfo[1]],
@@ -190,7 +190,7 @@
def checkInitialConditions(self, checkauxvars=False):
- for xname, val in self.initialconditions.iteritems():
+ for xname, val in self.initialconditions.items():
if xname not in self.funcspec.vars and not checkauxvars:
# auxvars do not need initial conditions unless
# explicitly requested (e.g. for user call to RHS
@@ -202,21 +202,21 @@
raise ValueError("Initial condition for "+xname+" has been "
"incorrectly initialized")
except TypeError:
- print "Found: ", val
- print "of type: ", type(val)
+ print("Found: ", val)
+ print("of type: ", type(val))
raise TypeError("Invalid type for %s`s initial"%xname \
+ "condition value")
if not self.contains(self.variables[xname].depdomain,
val, self.checklevel):
- print "Bounds: ", self.variables[xname].depdomain.get()
- print "Variable value: ", val
+ print("Bounds: ", self.variables[xname].depdomain.get())
+ print("Variable value: ", val)
raise ValueError("Initial condition for "+xname+" has been "
"set outside of prescribed bounds")
def set(self, **kw):
"""Set ODE system parameters"""
- if remain(kw.keys(), self._validKeys) != []:
+ if remain(list(kw.keys()), self._validKeys) != []:
raise KeyError("Invalid keys in argument")
if 'globalt0' in kw:
# pass up to generic treatment for this
@@ -233,7 +233,7 @@
# optional keys for this call are ['pars', 'tdomain', 'ics',
# 'algparams', 'tdata', 'xdomain', 'pdomain', 'inputs']
if 'ics' in kw:
- for k_temp, v in kw['ics'].iteritems():
+ for k_temp, v in kw['ics'].items():
k = self._FScompatibleNames(k_temp)
if k in self.funcspec.vars+self.funcspec.auxvars:
self._xdatadict[k] = ensurefloat(v)
@@ -254,31 +254,31 @@
self.diagnostics.warnings.append((W_UNCERTVAL,
(self.tdata[0],self.tdomain)))
else:
- print 'tdata cannot be specified below smallest '\
+ print('tdata cannot be specified below smallest '\
'value in tdomain\n (possibly due to uncertain bounding).'\
' It has been automatically adjusted from\n ', \
self.tdata[0], 'to', self.tdomain[0], '(difference of', \
- self.tdomain[0]-self.tdata[0], ')'
+ self.tdomain[0]-self.tdata[0], ')')
if self._modeltag:
- print 'Try reducing step size in model.'
+ print('Try reducing step size in model.')
self.tdata[0] = self.tdomain[0]
if self.tdomain[1] < self.tdata[1]:
if self.indepvariable.indepdomain.contains(self.tdata[1]) == uncertain:
self.diagnostics.warnings.append((W_UNCERTVAL,
(self.tdata[1],self.tdomain)))
else:
- print 'tdata cannot be specified above largest '\
+ print('tdata cannot be specified above largest '\
'value in tdomain\n (possibly due to uncertain bounding).'\
' It has been automatically adjusted from\n ', \
self.tdomain[1], 'to', \
self.tdomain[1], '(difference of', \
- self.tdata[1]-self.tdomain[1], ')'
+ self.tdata[1]-self.tdomain[1], ')')
if self._modeltag:
- print 'Try reducing step size in model.'
+ print('Try reducing step size in model.')
self.tdata[1] = self.tdomain[1]
self.indepvariable.depdomain.set(self.tdata)
if 'xdomain' in kw:
- for k_temp, v in kw['xdomain'].iteritems():
+ for k_temp, v in kw['xdomain'].items():
k = self._FScompatibleNames(k_temp)
if k in self.funcspec.vars+self.funcspec.auxvars:
if isinstance(v, _seq_types):
@@ -304,13 +304,13 @@
' names -> valid interval 2-tuples or '
'singletons')
try:
- evs = self.eventstruct.events.values()
+ evs = list(self.eventstruct.events.values())
except AttributeError:
evs = []
for ev in evs:
ev.xdomain[k] = self.xdomain[k]
if 'pdomain' in kw:
- for k_temp, v in kw['pdomain'].iteritems():
+ for k_temp, v in kw['pdomain'].items():
k = self._FScompatibleNames(k_temp)
if k in self.funcspec.pars:
if isinstance(v, _seq_types):
@@ -336,13 +336,13 @@
' names -> valid interval 2-tuples or '
'singletons')
try:
- evs = self.eventstruct.events.values()
+ evs = list(self.eventstruct.events.values())
except AttributeError:
evs = []
for ev in evs:
ev.pdomain[k] = self.pdomain[k]
if 'pars' in kw:
- for k_temp, v in kw['pars'].iteritems():
+ for k_temp, v in kw['pars'].items():
k = self._FScompatibleNames(k_temp)
if k in self.pars:
cval = self.parameterDomains[k].contains(v)
@@ -350,7 +350,7 @@
if cval is not notcontained:
self.pars[k] = ensurefloat(v)
if cval is uncertain and self.checklevel == 2:
- print 'Warning: Parameter %s: value at bound'%str(k)
+ print('Warning: Parameter %s: value at bound'%str(k))
else:
raise PyDSRefactoringTool: Refactored ./PyDSTool/Generator/MapSystem.py
Tool_ValueError('Parameter %s: value out of bounds'%str(k))
else:
@@ -363,7 +363,7 @@
else:
raise PyDSTool_ValueError('Illegal parameter name '+str(k))
if 'algparams' in kw:
- for k, v in kw['algparams'].iteritems():
+ for k, v in kw['algparams'].items():
self.algparams[k] = v
if k in ('eventActive', 'eventTol', 'eventDelay', 'eventDir', 'eventInt', 'eventTerm',
'maxbisect'):
@@ -391,12 +391,12 @@
elif isinstance(inputs, dict):
_inputs = self._FScompatibleNames(inputs)
# ensure values are Variables
- for v in _inputs.values():
+ for v in list(_inputs.values()):
if not isinstance(v, Variable):
raise TypeError("Invalid specification of inputs")
else:
raise TypeError("Invalid specification of inputs")
- for v in _inputs.values():
+ for v in list(_inputs.values()):
if not iscontinuous(v):
raise ValueError("External inputs for ODE system must be "
"continously defined")
@@ -411,7 +411,7 @@
assert self.inputs, ('Cannot provide inputs after '
'initialization without them')
inputs_t0 = self._FScompatibleNames(kw['inputs_t0'])
- for iname, t0 in inputs_t0.items():
+ for iname, t0 in list(inputs_t0.items()):
self.inputs[iname]._internal_t_offset = t0
self._extInputsChanged = True
@@ -443,10 +443,10 @@
def validateICs(self):
assert hasattr(self, 'initialconditions')
- if remain(self.initialconditions.keys(),
- self.variables.keys()) != []:
- print "IC names defined:", self.initialconditions.keys()
- print "Varnames defined:", self.variables.keys()
+ if remain(list(self.initialconditions.keys()),
+ list(self.variables.keys())) != []:
+ print("IC names defined:", list(self.initialconditions.keys()))
+ print("Varnames defined:", list(self.variables.keys()))
raise ValueError("Mismatch between initial condition and variable "
"names")
for v in self.funcspec.vars:
@@ -501,7 +501,7 @@
# Methods for pickling protocol
def __getstate__(self):
d = copy(self.__dict__)
- for fname, finfo in self._funcreg.iteritems():
+ for fname, finfo in self._funcreg.items():
try:
del d[fname]
except KeyError:
--- ./PyDSTool/Generator/MapSystem.py (original)
+++ ./PyDSTool/Generator/MapSystem.py (refactored)
@@ -3,10 +3,10 @@
# values for x at a specifc "time". Purely abstract time (i.e., iteration
# steps) is represented using integers. (We could make LookupTable a
# 0-param sequence of maps with explicit time range?)
-from __future__ import division
-
-from allimports import *
-from baseclasses import Generator, discGen, theGenSpecHelper, \
+
+
+from .allimports import *
+from .baseclasses import Generator, discGen, theGenSpecHelper, \
auxfn_container, _pollInputs
from PyDSTool.utils import *
from PyDSTool.common import *
@@ -89,9 +89,9 @@
else:
fnstr = fninfo[0]
try:
- exec fnstr
+ exec(fnstr)
except:
- print 'Error in supplied auxiliary function code'
+ print('Error in supplied auxiliary function code')
self._funcreg[fninfo[1]] = ('self', fnstr)
setattr(self, fninfo[1], types.MethodType(locals()[fninfo[1]],
self,
@@ -100,9 +100,9 @@
try:
uafi_code = self.funcspec._user_auxfn_interface[auxfnname]
try:
- exec uafi_code
+ exec(uafi_code)
except:
- print 'Error in auxiliary function wrapper'
+ print('Error in auxiliary function wrapper')
raise
setattr(self.auxfns, auxfnname,
types.MethodType(locals()[auxfnname], self.auxfns,
@@ -127,9 +127,9 @@
else:
fnstr = fninfo[0]
try:
- exec fnstr
+ exec(fnstr)
except:
- print 'Error in supplied functional specification code'
+ print('Error in supplied functional specification code')
raise
self._funcreg[fninfo[1]] = ('self', fnstr)
setattr(self, fninfo[1], types.MethodType(locals()[fninfo[1]],
@@ -146,9 +146,9 @@
else:
fnstr = fninfo[0]
try:
- exec fnstr
+ exec(fnstr)
except:
- print 'Error in supplied auxiliary variable code'
+ print('Error in supplied auxiliary variable code')
raise
self._funcreg[fninfo[1]] = ('self', fnstr)
setattr(self, fninfo[1], types.MethodType(locals()[fninfo[1]],
@@ -161,7 +161,7 @@
# Method for pickling protocol (setstate same as default)
def __getstate__(self):
d = copy(self.__dict__)
- for fname, finfo in self._funcreg.iteritems():
+ for fname, finfo in self._funcreg.items():
try:
del d[fname]
except KeyError:
@@ -194,7 +194,7 @@
def checkInitialConditions(self, checkauxvars=False):
- for xname, val in self.initialconditions.iteritems():
+ for xname, val in self.initialconditions.items():
if xname not in self.funcspec.vars and not checkauxvars:
# auxvars do not need initial conditions unless
# explicitly requested (e.g. for user call to RHS
@@ -206,21 +206,21 @@
raise ValueError("Initial condition for "+xname+" has been "
"incorrectly initialized")
except TypeError:
- print "Found: ", val
- print "of type: ", type(val)
+ print("Found: ", val)
+ print("of type: ", type(val))
raise TypeError("Invalid type for %s`s initial"%xname \
+ "condition value")
if not self.contains(self.variables[xname].depdomain,
val, self.checklevel):
- print "Bounds: ", self.variables[xname].depdomain.get()
- print "Variable value: ", val
+ print("Bounds: ", self.variables[xname].depdomain.get())
+ print("Variable value: ", val)
raise ValueError("Initial condition for "+xname+" has been "
"set outside of prescribed bounds")
def set(self, **kw):
"""Set map system parameters"""
- if remain(kw.keys(), self._validKeys) != []:
+ if remain(list(kw.keys()), self._validKeys) != []:
raise KeyError("Invalid keys in argument")
if 'globalt0' in kw:
# pass up to generic treatment for this
@@ -234,7 +234,7 @@
# optional keys for this call are ['pars', 'tdomain', 'ics',
# 'algparams', 'tdata', 'xdomain', 'inputs', 'pdomain']
if 'ics' in kw:
- for k_temp, v in kw['ics'].iteritems():
+ for k_temp, v in kw['ics'].items():
k = self._FScompatibleNames(k_temp)
if k in self.funcspec.vars+self.funcspec.auxvars:
self._xdatadict[k] = ensurefloat(v)
@@ -255,27 +255,27 @@
self.diagnostics.warnings.append((W_UNCERTVAL,
(self.tdata[0],self.tdomain)))
else:
- print 'tdata cannot be specified below smallest '\
+ print('tdata cannot be specified below smallest '\
'value in tdomain\n (possibly due to uncertain bounding).'\
' It has been automatically adjusted from\n ', \
self.tdata[0], 'to', self.tdomain[0], '(difference of', \
- self.tdomain[0]-self.tdata[0], ')'
+ self.tdomain[0]-self.tdata[0], ')')
self.tdata[0] = self.tdomain[0]
if self.tdomain[1] < self.tdata[1]:
if self.indepvariable.indepdomain.contains(self.tdata[1]) == uncertain:
self.diagnostics.warnings.append((W_UNCERTVAL,
(self.tdata[1],self.tdomain)))
else:
- print 'tdata cannot be specified above largest '\
+ print('tdata cannot be specified above largest '\
'value in tdomain\n (possibly due to uncertain bounding).'\
' It has been automatically adjusted from\n ', \
self.tdomain[1], 'to', \
self.tdomain[1], '(difference of', \
- self.tdata[1]-self.tdomain[1], ')'
+ self.tdata[1]-self.tdomain[1], ')')
self.tdata[1] = self.tdomain[1]
self.indepvariable.depdomain.set(self.tdata)
if 'xdomain' in kw:
- for k_temp, v in kw['xdomain'].iteritems():
+ for k_temp, v in kw['xdomain'].items():
k = self._FScompatibleNames(k_temp)
if k in self.funcspec.vars+self.funcspec.auxvars:
if isinstance(v, _seq_types):
@@ -302,13 +302,13 @@
' names -> valid interval 2-tuples or '
'singletons')
try:
- evs = self.eventstruct.events.values()
+ evs = list(self.eventstruct.events.values())
except AttributeError:
evs = []
for ev in evs:
ev.xdomain[k] = v
if 'pdomain' in kw:
- for k_temp, v in kw['pdomain'].iteritems():
+ for k_temp, v in kw['pdomain'].items():
k = self._FScompatibleNames(k_temp)
if k in self.funcspec.pars:
if isinstance(v, _seq_types):
@@ -334,7 +334,7 @@
' names -> valid interval 2-tuples or '
'singletons')
try:
- evs = self.eventstruct.events.values()
+ evs = list(self.eventstruct.events.values())
except AttributeError:
evs = []
for ev in evs:
@@ -342,7 +342,7 @@
if 'pars' in kw:
assert self.numpars > 0, ('No pars were declared for this '
'model')
- for k_temp, v in kw['pars'].iteritems():
+ for k_temp, v in kw['pars'].items():
k = self._FScompatibleNames(k_temp)
if k in self.pars:
cval = self.parameterDomains[k].contains(v)
@@ -350,7 +350,7 @@
if cval is not notcontained:
self.pars[k] = ensurefloat(v)
if cval is uncertain and self.checklevel == 2:
- print 'Warning: Parameter value at bound'
+ print('Warning: Parameter value at bound')
else:
raise PyDSTool_ValueError('Parameter value out of bounds')
else:
@@ -365,7 +365,7 @@
# pass on parameter changes to embedded system, if present
if self._solver:
try:
- shared_pars = intersect(kw['pars'].keys(), self._solver.pars)
+ shared_pars = intersect(list(kw['pars'].keys()), self._solver.pars)
except AttributeError:
# no pars for this kind of solver
pass
@@ -396,7 +396,7 @@
elif isinstance(inputs, dict):
_inputs = self._FScompatibleNames(inputs)
# ensure values are Variables
- for v in _inputs.values():
+ for v in list(_inputs.values()):
if not isinstance(v, Variable):
raise TypeError("Invalid specification of inputs")
else:
@@ -412,7 +412,7 @@
assert self.inputs, ('Cannot provide inputs after '
'initialization without them')
inputs_t0 = self._FScompatibleNames(kw['inputs_t0'])
- for iname, t0 in inputs_t0.items():
+ for iname, t0 in list(inputs_t0.items()):
self.inputs[iname]._internal_t_offset = t0
self._extInputsChanged = True
@@ -430,9 +430,9 @@
xnames = self._var_ixmap # ensures correct order
# wrap up each dictionary initial value as a singleton list
alltData = [self.indepvariable.depdomain[0]]
- allxDataDict = dict(zip(xnames, map(listid,
+ allxDataDict = dict(list(zip(xnames, list(map(listid,
sortedDictValues(self.initialconditions,
- self.funcspec.vars))))
+ self.funcspec.vars))))))
rhsfn = getattr(self,self.funcspec.spec[1])
# Check i.c.'s are well defined (finite)
self.checkInitialConditions()
@@ -450,19 +450,19 @@
f.diagnostics.clearWarnings()
ilist.append(f(alltData[0], self.checklevel))
except AssertionError:
- print 'External input call has t out of range: t = ', \
- self.indepvariable.depdomain[0]
- print 'Maybe checklevel is 3 and initial time is not', \
- 'completely inside valid time interval'
+ print('External input call has t out of range: t = ', \
+ self.indepvariable.depdomain[0])
+ print('Maybe checklevel is 3 and initial time is not', \
+ 'completely inside valid time interval')
raise
except ValueError:
- print 'External input call has value out of range: t = ', \
- self.indepvariable.depdomain[0]
+ print('External input call has value out of range: t = ', \
+ self.indepvariable.depdomain[0])
for f in inputVarList:
if f.diagnostics.hasWarnings():
- print 'External input %s out of range:' % f.name
- print ' t = ', repr(f.diagnostics.warnings[-1][0]), ', ', \
- f.name, ' = ', repr(f.diagnostics.warnings[-1][1])
+ print('External input %s out of range:' % f.name)
+ print(' t = ', repr(f.diagnostics.warnings[-1][0]), ', ', \
+ f.name, ' = ', repr(f.diagnostics.warnings[-1][1]))
raise
else:
listend = self.numpars
@@ -502,8 +502,7 @@
# storage of all auxiliary variable data
allaDataDict = {}
anames = self.funcspec.auxvars
- avals = apply(getattr(self,self.funcspec.auxspec[1]),
- [self.indepvariable.depdomain[0],
+ avals = getattr(self,self.funcspec.auxspec[1])(*[self.indepvariable.depdomain[0],
sortedDictValues(self.initialconditions,
self.funcspec.vars),
extralist])
@@ -529,10 +528,10 @@
try:
y = rhsfn(t, x, extralist)
except:
- print "Error in calling right hand side function:"
+ print("Error in calling right hand side function:")
self.showSpec()
raise
- for xi in xrange(self.dimension):
+ for xi in range(self.dimension):
xDataDict[xnames[xi]] = y[xi]
if not self.contains(self.variables[xnames[xi]].depdomain,
y[xi], self.checklevel):
@@ -544,7 +543,7 @@
if breakwhile:
notdone = False
continue
- avals = apply(getattr(self,self.funcspec.auxspec[1]), [t,
+ avals = getattr(self,self.funcspec.auxspec[1])(*[t,
sortedDictValues(xDataDict),
extralist])
if eventslist != []:
@@ -554,9 +553,8 @@
dataDict,
self.pars,
eventslist)
- termevsflagged = filter(lambda e: e in evsflagged, termevents)
- nontermevsflagged = filter(lambda e: e not in termevsflagged,
- evsflagged)
+ termevsflagged = [e for e in termevents if e in evsflagged]
+ nontermevsflagged = [e for e in evsflagged if e not in termevsflagged]
# register any non-terminating events in the warnings list
if len(nontermevsflagged) > 0:
evnames = [ev[0] for ev in nontermevsflagged]
@@ -589,20 +587,19 @@
aname = anames[aix]
allaDataDict[aname].append(avals[aix])
try:
- extralist[self.numpars:listend] = [apply(f,
- [t, self.checklevel]) \
+ extralist[self.numpars:listend] = [f(*[t, self.checklevel]) \
for f in inputVarList]
except ValueError:
- print 'External input call caused value out of range error:', \
- 't = ', t
+ print('External input call caused value out of range error:', \
+ 't = ', t)
for f in inputVarList:
if f.hasWarnings():
- print 'External input variable %s out of range:' % f.name
- print ' t = ', repr(f.diagnostics.warnings[-1][0]), ', ', \
- f.name, ' = ', repr(f.diagnostics.warnings[-1][1])
+ print('External input variable %s out of range:' % f.name)
+ print(' t = ', repr(f.diagnostics.warnings[-1][0]), ', ', \
+ f.name, ' = ', repr(f.diagnostics.warnings[-1][1]))
raise
except AssertionError:
- print 'External input call caused t out of range error: t = ', t
+ print('External input call caused t out of range error: t = ', t)
raise
if i >= len(tmesh) - 1:
notdone = False
@@ -671,7 +668,7 @@
if success:
#self.validateSpec()
self.defined = True
- return Trajectory(trajname, variables.values(),
+ return Trajectory(trajname, list(variables.values()),
abseps=self._abseps, globalt0=self.globalt0,
checklevel=self.checklevel,
FScompatibleNames=self._FScompatibleNames,
@@ -680,7 +677,7 @@
modelNames=self.name,
modelEventStructs=self.eventstruct)
else:
- print 'Trajectory computation failed'
+ print('Trajectory computation failed')
self.diagnostics.errors.append((E_COMPUTFAIL,
(t, self._errorcodes[errcode])))
RefactoringTool: Refactored ./PyDSTool/Generator/LookupTable.py
RefactoringTool: Refactored ./PyDSTool/Generator/InterpolateTable.py
self.defined = False
@@ -701,7 +698,7 @@
p = sortedDictValues(self._FScompatibleNames(pdict))
i = _pollInputs(sortedDictValues(self.inputs),
t, self.checklevel)
- return apply(getattr(self,self.funcspec.spec[1]), [t, x, p+i])
+ return getattr(self,self.funcspec.spec[1])(*[t, x, p+i])
def Jacobian(self, t, xdict, pdict=None, asarray=True):
@@ -718,8 +715,7 @@
p = sortedDictValues(self._FScompatibleNames(pdict))
i = _pollInputs(sortedDictValues(self.inputs),
t, self.checklevel)
- return apply(getattr(self,self.funcspec.auxfns["Jacobian"][1]), \
- [t, x, p+i])
+ return getattr(self,self.funcspec.auxfns["Jacobian"][1])(*[t, x, p+i])
else:
raise PyDSTool_ExistError("Jacobian not defined")
@@ -738,8 +734,7 @@
p = sortedDictValues(self._FScompatibleNames(pdict))
i = _pollInputs(sortedDictValues(self.inputs),
t, self.checklevel)
- return apply(getattr(self,self.funcspec.auxfns["Jacobian_pars"][1]), \
- [t, x, p+i])
+ return getattr(self,self.funcspec.auxfns["Jacobian_pars"][1])(*[t, x, p+i])
else:
raise PyDSTool_ExistError("Jacobian w.r.t. parameters not defined")
@@ -757,7 +752,7 @@
p = sortedDictValues(self._FScompatibleNames(pdict))
i = _pollInputs(sortedDictValues(self.inputs),
t, self.checklevel)
- return apply(getattr(self,self.funcspec.auxspec[1]), [t, x, p+i])
+ return getattr(self,self.funcspec.auxspec[1])(*[t, x, p+i])
def __del__(self):
--- ./PyDSTool/Generator/LookupTable.py (original)
+++ ./PyDSTool/Generator/LookupTable.py (refactored)
@@ -1,8 +1,8 @@
# Lookup table
-from __future__ import division
-from allimports import *
-from baseclasses import discGen, theGenSpecHelper
+
+from .allimports import *
+from .baseclasses import discGen, theGenSpecHelper
from PyDSTool.utils import *
from PyDSTool.common import *
@@ -22,7 +22,7 @@
try:
self.tdata = kw['tdata']
self._xdatadict = {}
- for k, v in dict(kw['ics']).iteritems():
+ for k, v in dict(kw['ics']).items():
self._xdatadict[str(k)] = v
self.foundKeys = 2
# check for other, invalid keys (but currently just ignored)
@@ -71,7 +71,7 @@
#self.validateSpec()
self.diagnostics.clearWarnings()
self.diagnostics.clearErrors()
- return Trajectory(trajname, [copy(v) for v in self.variables.values()],
+ return Trajectory(trajname, [copy(v) for v in list(self.variables.values())],
abseps=self._abseps, globalt0=self.globalt0,
checklevel=self.checklevel,
FScompatibleNames=self._FScompatibleNames,
@@ -83,11 +83,11 @@
discGen.validateSpec(self)
try:
assert isoutputdiscrete(self.indepvariable)
- for v in self.variables.values():
+ for v in list(self.variables.values()):
assert isinstance(v, Variable)
assert not self.inputs
except AssertionError:
- print 'Invalid system specification'
+ print('Invalid system specification')
raise
--- ./PyDSTool/Generator/InterpolateTable.py (original)
+++ ./PyDSTool/Generator/InterpolateTable.py (refactored)
@@ -1,8 +1,8 @@
# Interpolated lookup table
-from __future__ import division
-from allimports import *
-from baseclasses import ctsGen, theGenSpecHelper
+
+from .allimports import *
+from .baseclasses import ctsGen, theGenSpecHelper
from PyDSTool.utils import *
from PyDSTool.common import *
@@ -20,7 +20,7 @@
try:
self.tdata = kw['tdata']
self._xdatadict = {}
- for k, v in dict(kw['ics']).iteritems():
+ for k, v in dict(kw['ics']).items()RefactoringTool: Refactored ./PyDSTool/Generator/ImplicitFnGen.py
:
self._xdatadict[str(k)] = v
self.foundKeys = 2
# check for other, invalid keys (but currently just ignored)
@@ -90,7 +90,7 @@
def compute(self, trajname):
- return Trajectory(trajname, [copy(v) for v in self.variables.values()],
+ return Trajectory(trajname, [copy(v) for v in list(self.variables.values())],
abseps=self._abseps, globalt0=self.globalt0,
checklevel=self.checklevel,
FScompatibleNames=self._FScompatibleNames,
@@ -119,11 +119,11 @@
ctsGen.validateSpec(self)
try:
assert isoutputcts(self.indepvariable)
- for v in self.variables.values():
+ for v in list(self.variables.values()):
assert isinstance(v, Variable)
assert not self.inputs
except AssertionError:
- print 'Invalid system specification'
+ print('Invalid system specification')
raise
--- ./PyDSTool/Generator/ImplicitFnGen.py (original)
+++ ./PyDSTool/Generator/ImplicitFnGen.py (refactored)
@@ -1,8 +1,8 @@
# Implicit function generator
-from __future__ import division
-
-from allimports import *
-from baseclasses import ctsGen, theGenSpecHelper
+
+
+from .allimports import *
+from .baseclasses import ctsGen, theGenSpecHelper
from PyDSTool.utils import *
from PyDSTool.common import *
from PyDSTool.Interval import uncertain
@@ -76,7 +76,7 @@
for x in self.funcspec.vars + self.funcspec.auxvars:
try:
xinterval=Interval(x, self.xtype[x], self.xdomain[x], self._abseps)
- except KeyError, e:
+ except KeyError as e:
raise PyDSTool_KeyError('Mismatch between declared variables'
' and xspecs: ' + str(e))
# placeholder variable so that this class can be
@@ -125,9 +125,9 @@
tempfs.spec = tempspec
# test supplied code
try:
- exec tempspec[0] in globals()
+ exec(tempspec[0], globals())
except:
- print 'Error in supplied functional specification code'
+ print('Error in supplied functional specification code')
raise
# set up implicit function: utils.makeImplicitFunction gets
# called finally in Variable.addMethods() method.
@@ -272,7 +272,7 @@
self._register(self.variables)
#self.validateSpec()
self.defined = True
- return Trajectory(trajname, tempvars.values(),
+ return Trajectory(trajname, list(tempvars.values()),
abseps=self._abseps, globalt0=self.globalt0,
checklevel=self.checklevel,
FScompatibleNames=self._FScompatibleNames,
@@ -293,7 +293,7 @@
def set(self, **kw):
"""Set ImplicitFnGen parameters"""
- if remain(kw.keys(), self._validKeys) != []:
+ if remain(list(kw.keys()), self._validKeys) != []:
raise KeyError("Invalid keys in argument")
if 'globalt0' in kw:
# pass up to generic treatment for this
@@ -306,7 +306,7 @@
ctsGen.set(self, abseps=kw['abseps'])
# optional keys for this call are ['pars', 'tdomain', 'xdomain', 'pdomain']
if 'xdomain' in kw:
- for k_temp, v in kw['xdomain'].iteritems():
+ for k_temp, v in kw['xdomain'].items():
k = self._FScompatibleNames(k_temp)
if k in self.funcspec.vars+self.funcspec.auxvars:
if isinstance(v, _seq_types):
@@ -340,27 +340,27 @@
self.diagnostics.warnings.append((W_UNCERTVAL,
(self.tdata[0],self.tdomain)))
else:
- print 'tdata cannot be specified below smallest '\
+ print('tdata cannot be specified below smallest '\
'value in tdomain\n (possibly due to uncertain bounding).'\
RefactoringTool: Refactored ./PyDSTool/Generator/ExtrapolateTable.py
' It has been automatically adjusted from\n ', self.tdata[0], \
'to', self.tdomain[0], '(difference of', \
- self.tdomain[0]-self.tdata[0], ')'
+ self.tdomain[0]-self.tdata[0], ')')
self.tdata[0] = self.tdomain[0]
if self.tdomain[1] < self.tdata[1]:
if self.indepvariable.indepdomain.contains(self.tdata[1]) == uncertain:
self.diagnostics.warnings.append((W_UNCERTVAL,
(self.tdata[1],self.tdomain)))
else:
- print 'tdata cannot be specified above largest '\
+ print('tdata cannot be specified above largest '\
'value in tdomain\n (possibly due to uncertain bounding).'\
' It has been automatically adjusted from\n ', \
self.tdomain[1], 'to', \
self.tdomain[1], '(difference of', \
- self.tdata[1]-self.tdomain[1], ')'
+ self.tdata[1]-self.tdomain[1], ')')
self.tdata[1] = self.tdomain[1]
self.indepvariable.depdomain.set(self.tdata)
if 'pdomain' in kw:
- for k_temp, v in kw['pdomain'].iteritems():
+ for k_temp, v in kw['pdomain'].items():
k = self._FScompatibleNames(k_temp)
if k in self.funcspec.pars:
if isinstance(v, _seq_types):
@@ -386,7 +386,7 @@
' names -> valid interval 2-tuples or '
'singletons')
if 'ics' in kw:
- for k_temp, v in kw['ics'].iteritems():
+ for k_temp, v in kw['ics'].items():
k = self._FScompatibleNames(k_temp)
if k in self.funcspec.vars+self.funcspec.auxvars:
self._xdatadict[k] = ensurefloat(v)
@@ -397,7 +397,7 @@
if not self.pars:
raise ValueError('No pars were declared for this object'
' at initialization.')
- for k_temp, v in kw['pars'].iteritems():
+ for k_temp, v in kw['pars'].items():
k = self._FScompatibleNames(k_temp)
if k in self.pars:
cval = self.parameterDomains[k].contains(v)
@@ -405,7 +405,7 @@
if cval is not notcontained:
self.pars[k] = ensurefloat(v)
if cval is uncertain and self.checklevel == 2:
- print 'Warning: Parameter value at bound'
+ print('Warning: Parameter value at bound')
else:
raise PyDSTool_ValueError('Parameter value out of bounds')
else:
@@ -418,7 +418,7 @@
else:
raise PyDSTool_AttributeError('Illegal parameter name')
if 'algparams' in kw:
- for k, v in kw['algparams'].iteritems():
+ for k, v in kw['algparams'].items():
self.algparams[k] = v
if 'solvemethod' in self.algparams:
if self.algparams['solvemethod'] not in _implicitSolveMethods:
@@ -428,11 +428,11 @@
def validateSpec(self):
ctsGen.validateSpec(self)
try:
- for v in self.variables.values():
+ for v in list(self.variables.values()):
assert isinstance(v, Variable)
assert not self.inputs
except AssertionError:
- print 'Invalid system specification'
+ print('Invalid system specification')
raise
--- ./PyDSTool/Generator/ExtrapolateTable.py (original)
+++ ./PyDSTool/Generator/ExtrapolateTable.py (refactored)
@@ -1,8 +1,8 @@
# Interpolated lookup table with extrapolated end points
-from __future__ import division
-
-from allimports import *
-from baseclasses import ctsGen, theGenSpecHelper
+
+
+from .allimports import *
+from .baseclaRefactoringTool: Refactored ./PyDSTool/Generator/ExplicitFnGen.py
sses import ctsGen, theGenSpecHelper
from PyDSTool.utils import *
from PyDSTool.common import *
@@ -21,7 +21,7 @@
try:
self.tdata = kw['tdata']
self._xdatadict = {}
- for k, v in dict(kw['ics']).iteritems():
+ for k, v in dict(kw['ics']).items():
self._xdatadict[str(k)] = v
self.foundKeys = 2
# check for other, invalid keys (but currently just ignored)
@@ -174,7 +174,7 @@
def compute(self, trajname):
- return Trajectory(trajname, [copy(v) for v in self.variables.values()],
+ return Trajectory(trajname, [copy(v) for v in list(self.variables.values())],
abseps=self._abseps, globalt0=self.globalt0,
checklevel=self.checklevel,
FScompatibleNames=self._FScompatibleNames,
@@ -202,11 +202,11 @@
ctsGen.validateSpec(self)
try:
assert isoutputcts(self.indepvariable)
- for v in self.variables.values():
+ for v in list(self.variables.values()):
assert isinstance(v, Variable)
assert not self.inputs
except AssertionError:
- print 'Invalid system specification'
+ print('Invalid system specification')
raise
--- ./PyDSTool/Generator/ExplicitFnGen.py (original)
+++ ./PyDSTool/Generator/ExplicitFnGen.py (refactored)
@@ -1,8 +1,8 @@
# Explicit function generator
-from __future__ import division
-
-from allimports import *
-from baseclasses import ctsGen, theGenSpecHelper, \
+
+
+from .allimports import *
+from .baseclasses import ctsGen, theGenSpecHelper, \
auxfn_container, _pollInputs
from PyDSTool.utils import *
from PyDSTool.common import *
@@ -65,7 +65,7 @@
for x in self.funcspec.vars + self.funcspec.auxvars:
try:
xinterval=Interval(x, self.xtype[x], self.xdomain[x], self._abseps)
- except KeyError, e:
+ except KeyError as e:
raise PyDSTool_KeyError('Mismatch between declared variables '
'and xspecs: ' + str(e))
# placeholder variable so that this class can be
@@ -87,9 +87,9 @@
# user-defined auxiliary functions
# (built-ins are provided explicitly)
try:
- exec fninfo[0]
+ exec(fninfo[0])
except:
- print 'Error in supplied auxiliary function code'
+ print('Error in supplied auxiliary function code')
self._funcreg[fninfo[1]] = ('self', fninfo[0])
setattr(self, fninfo[1], types.MethodType(locals()[fninfo[1]],
self,
@@ -98,9 +98,9 @@
try:
uafi_code = self.funcspec._user_auxfn_interface[auxfnname]
try:
- exec uafi_code
+ exec(uafi_code)
except:
- print 'Error in auxiliary function wrapper'
+ print('Error in auxiliary function wrapper')
raise
setattr(self.auxfns, auxfnname,
types.MethodType(locals()[auxfnname], self.auxfns,
@@ -122,9 +122,9 @@
if self.funcspec.targetlang == 'python':
fninfo = self.funcspec.spec
try:
- exec fninfo[0]
+ exec(fninfo[0])
except:
- print 'Error in supplied functional specification code'
+ print('Error in supplied functional specification code')
raise
self._funcreg[fninfo[1]] = ('self', fninfo[0])
setattr(self, fninfo[1], types.MethodType(locals()[fninfo[1]],
@@ -137,9 +137,9 @@
if self.funcspec.auxspec != '':
fninfo = self.funcspec.auxspec
try:
- exec fninfo[0]
+ exec(fninfo[0])
except:
- print 'Error in supplied auxiliary variable code'
+ print('Error in supplied auxiliary variable code')
raise
self._funcreg[fninfo[1]] = ('self', fninfo[0])
setattr(self, fninfo[1], types.MethodType(locals()[fninfo[1]],
@@ -271,12 +271,12 @@
continue
if ev.activeFlag:
if numevs > 1:
- print "Event info:", Evtimes[evname]
+ print("Event info:", Evtimes[evname])
assert numevs <= 1, ("Internal error: more than one "
"terminal event of same type found")
# For safety, we should assert that this event
# also appears in termevents, but we don't
- if Evtimes[evname][0] in termevtimes.keys():
+ if Evtimes[evname][0] in list(termevtimes.keys()):
# append event name to this warning
warning_ix = termevtimes[Evtimes[evname][0]]
self.diagnostics.warnings[warning_ix][1][1].append(evname)
@@ -289,7 +289,7 @@
[evname])))
else:
for ev in range(numevs):
- if Evtimes[evname][ev] in nontermevtimes.keys():
+ if Evtimes[evname][ev] in list(nontermevtimes.keys()):
# append event name to this warning
warning_ix = nontermevtimes[Evtimes[evname][ev]]
self.diagnostics.warnings[warning_ix][1][1].append(evname)
@@ -316,7 +316,7 @@
self.diagnostics.warnings = warn_temp
self.indepvariable.depdomain.set([self.indepvariable.depdomain[0],
earliest_termtime])
- for v in tempvars.values():
+ for v in list(tempvars.values()):
v.indepdomain.set(self.indepvariable.depdomain.get())
## print 'Time interval adjusted according to %s: %s' % \
## (self._warnmessages[w], str(i[0])+", "+ str(i[1]))
@@ -338,7 +338,7 @@
self._register(self.variables)
self.validateSpec()
self.defined = True
- return Trajectory(trajname, tempvars.values(),
+ return Trajectory(trajname, list(tempvars.values()),
abseps=self._abseps, globalt0=self.globalt0,
checklevel=self.checklevel,
FScompatibleNames=self._FScompatibleNames,
@@ -361,7 +361,7 @@
else:
p = sortedDictValues(self._FScompatibleNames(pdict))
i = _pollInputs(sortedDictValues(self.inputs), t, self.checklevel)
- return apply(getattr(self, self.funcspec.auxspec[1]), [t, x, p+i])
+ return getattr(self, self.funcspec.auxspec[1])(*[t, x, p+i])
def haveJacobian_pars(self):
"""Report whether generator has an explicit user-specified Jacobian
@@ -376,7 +376,7 @@
def set(self, **kw):
"""Set ExplicitFnGen parameters"""
- if remain(kw.keys(), self._validKeys) != []:
+ if remain(list(kw.keys()), self._validKeys) != []:
raise KeyError("Invalid keys in argument")
if 'globalt0' in kw:
# pass up to generic treatment for this
@@ -390,7 +390,7 @@
# optional keys for this call are
# ['pars', 'tdomain', 'xdomain', 'pdomain']
if 'xdomain' in kw:
- for k_temp, v in kw['xdomain'].iteritems():
+ for k_temp, v in kw['xdomain'].items():
k = self._FScompatibleNames(k_temp)
if k in self.funcspec.vars+self.funcspec.auxvars:
if isinstance(v, _seq_types):
@@ -414,10 +414,10 @@
raise TypeError('xdomain must be a dictionary of variable'
' names -> valid interval 2-tuples or '
'singletons')
- for ev in self.eventstruct.events.values():
+ for ev in list(self.eventstruct.events.values()):
ev.xdomain[k] = v
if 'pdomain' in kw:
- for k_temp, v in kw['pdomain'].iteritems():
+ for k_temp, v in kw['pdomain'].items():
k = self._FScompatibleNames(k_temp)
if k in self.funcspec.pars:
if isinstance(v, _seq_types):
@@ -442,7 +442,7 @@
raise TypeError('pdomain must be a dictionary of parameter'
' names -> valid interval 2-tuples or '
'singletons')
- for ev in self.eventstruct.events.values():
+ for ev in list(self.eventstruct.events.values()):
ev.pdomain[k] = v
if 'tdata' in kw:
self.tdata = kw['tdata']
@@ -454,27 +454,27 @@
self.diagnostics.warnings.append((W_UNCERTVAL,
(self.tdata[0],self.tdomain)))
else:
- print 'tdata cannot be specified below smallest '\
+ print('tdata cannot be specified below smallest '\
'value in tdomain\n (possibly due to uncertain bounding).'\
' It has been automatically adjusted from\n ', self.tdata[0], \
'to', self.tdomain[0], '(difference of', \
- self.tdomain[0]-self.tdata[0], ')'
+ self.tdomain[0]-self.tdata[0], ')')
self.tdata[0] = self.tdomain[0]
if self.tdomain[1] < self.tdata[1]:
if self.indepvariable.indepdomain.contains(self.tdata[1]) == uncertain:
self.diagnostics.warnings.append((W_UNCERTVAL,
(self.tdata[1],self.tdomain)))
else:
- print 'tdata cannot be specified above largest '\
+ print('tdata cannot be specified above largest '\
'value in tdomain\n (possibly due to uncertain bounding).'\
' It has been automatically adjusted from\n ', \
self.tdomain[1], 'to', \
self.tdomain[1], '(difference of', \
- self.tdata[1]-self.tdomain[1], ')'
+ self.tdata[1]-self.tdomain[1], ')')
self.tdata[1] = self.tdomain[1]
self.indepvariable.depdomain.set(self.tdata)
if 'ics' in kw:
- for k_temp, v in kw['ics'].iteritems():
+ for k_temp, v in kw['ics'].items():
k = self._FScompatibleNames(k_temp)
if k in self.funcspec.vars+self.funcspec.auxvars:
self._xdatadict[k] = ensurefloat(v)
@@ -485,7 +485,7 @@
if not self.pars:
raise ValueError('No pars were declared for this object'
' at initialization.')
- for k_temp, v in kw['pars'].iteritems():
+ for k_temp, v in kw['pars'].items():
k = self._FScompatibleNames(k_temp)
if k in self.pars:
cval = self.parameterDomains[k].contains(v)
@@ -493,7 +493,7 @@
if cval is not notcontained:
self.pars[k] = ensurefloat(v)
if cval is uncertain and self.checklevel == 2:
- print 'Warning: Parameter value at bound'
+ print('Warning: Parameter value at bound')
else:
raise PyDSTool_ValueError('Parameter value out of '
'bounds')
@@ -513,11 +513,11 @@
def validateSpec(self):
ctsGen.validateSpec(self)
try:
- for v in self.variables.values():
+ for v in list(self.variablRefactoringTool: Refactored ./PyDSTool/Generator/Euler_ODEsystem.py
es.values()):
assert isinstance(v, Variable)
assert not self.inputs
except AssertionError:
- print 'Invalid system specification'
+ print('Invalid system specification')
raise
--- ./PyDSTool/Generator/Euler_ODEsystem.py (original)
+++ ./PyDSTool/Generator/Euler_ODEsystem.py (refactored)
@@ -1,10 +1,10 @@
"""Euler integrator for ODE systems, with no step refinement for events.
"""
-from __future__ import division
-
-from allimports import *
+
+
+from .allimports import *
from PyDSTool.Generator import ODEsystem as ODEsystem
-from baseclasses import Generator, theGenSpecHelper, _pollInputs
+from .baseclasses import Generator, theGenSpecHelper, _pollInputs
from PyDSTool.utils import *
from PyDSTool.common import *
@@ -87,7 +87,7 @@
'init_step': 0.01,
'max_pts': 100000
}
- for k, v in algparams_def.iteritems():
+ for k, v in algparams_def.items():
if k not in self.algparams:
self.algparams[k] = v
@@ -125,7 +125,7 @@
indepdom0, indepdom1 = self.indepvariable.depdomain.get()
if continue_integ:
if indepdom0 > self._solver.t:
- print "Previous end time is %f"%self._solver.t
+ print("Previous end time is %f"%self._solver.t)
raise ValueError("Start time not correctly updated for "
"continuing orbit")
x0 = self._solver.y
@@ -142,7 +142,7 @@
solver.dt = dt
# wrap up each dictionary initial value as a singleton list
alltData = [t0]
- allxDataDict = dict(zip(xnames, map(listid, x0)))
+ allxDataDict = dict(list(zip(xnames, list(map(listid, x0)))))
plist = sortedDictValues(self.pars)
extralist = copy(plist)
if self.inputs:
@@ -165,11 +165,11 @@
if do_poly:
rhsfn = getattr(self, self.funcspec.spec[1])
dx0 = rhsfn(t0, x0, extralist)
- alldxDataDict = dict(zip(xnames, map(listid, dx0)))
+ alldxDataDict = dict(list(zip(xnames, list(map(listid, dx0)))))
auxvarsfn = getattr(self,self.funcspec.auxspec[1])
# Make t mesh if it wasn't given as 'specialtimes'
if not all(isfinite(self.indepvariable.depdomain.get())):
- print "Time domain was: ", self.indepvariable.depdomain.get()
+ print("Time domain was: ", self.indepvariable.depdomain.get())
raise ValueError("Ensure time domain is finite")
if dt == indepdom1 - indepdom0:
# single-step integration required
@@ -197,24 +197,24 @@
try:
allaDataDict[aname] = [avals[aix]]
except IndexError:
- print "\nEuler generator: There was a problem evaluating " \
- + "an auxiliary variable"
- print "Debug info: avals (length", len(avals), ") was ", avals
- print "Index out of range was ", aix
- print self.funcspec.auxspec[1]
- print hasattr(self, self.funcspec.auxspec[1])
- print "Args were:", [t0, x0, extralist]
+ print("\nEuler generator: There was a problem evaluating " \
+ + "an auxiliary variable")
+ print("Debug info: avals (length", len(avals), ") was ", avals)
+ print("Index out of range was ", aix)
+ print(self.funcspec.auxspec[1])
+ print(hasattr(self, self.funcspec.auxspec[1]))
+ print("Args were:", [t0, x0, extralist])
raise
# Initialize signs of event detection objects at IC
self.setEventICs(self.initialconditions, self.globalt0)
if self.inputs:
parsinps = copy(self.pars)
- parsinps.update(dict(zip(inames,ilist)))
+ parsinps.update(dict(list(zip(inames,ilist))))
else:
parsinps = self.pars
if eventslist != []:
dataDict = copy(self.initialconditions)
- dataDict.update(dict(zip(anames, avals)))
+ dataDict.update(dict(list(zip(anames, avals))))
dataDict['t'] = t0
evsflagged = self.eventstruct.pollHighLevelEvents(None,
dataDict,
@@ -260,8 +260,8 @@
Evtimes[evname] = []
Evpoints[evname] = []
# temp storage for repeatedly used object attributes (for lookup efficiency)
- depdomains = dict(zip(range(self.dimension),
- [self.variables[xn].depdomain for xn in xnames]))
+ depdomains = dict(list(zip(list(range(self.dimension)),
+ [self.variables[xn].depdomain for xn in xnames])))
# Main integration loop
num_points = 0
breakwhile = False
@@ -276,14 +276,14 @@
try:
errcode = solver.integrate(dt)
except:
- print "Error calling right hand side function:"
+ print("Error calling right hand side function:")
self.showSpec()
- print "Numerical traceback information (current state, " \
- + "parameters, etc.)"
- print "in generator dictionary 'traceback'"
- self.traceback = {'vars': dict(zip(xnames,solver.y)),
- 'pars': dict(zip(pnames,plist)),
- 'inputs': dict(zip(inames,ilist)),
+ print("Numerical traceback information (current state, " \
+ + "parameters, etc.)")
+ print("in generator dictionary 'traceback'")
+ self.traceback = {'vars': dict(list(zip(xnames,solver.y))),
+ 'pars': dict(list(zip(pnames,plist))),
+ 'inputs': dict(list(zip(inames,ilist))),
self.indepvariable.name: new_t}
raise
avals = auxvarsfn(new_t, solver.y, extralist)
@@ -291,14 +291,14 @@
# assert all([isfinite(a) for a in avals]), \
# "Some auxiliary variable values not finite"
if eventslist != []:
- dataDict = dict(zip(xnames,solver.y))
- dataDict.update(dict(zip(anames,avals)))
+ dataDict = dict(list(zip(xnames,solver.y)))
+ dataDict.update(dict(list(zip(anames,avals))))
dataDict['t'] = new_t
if self.inputs:
parsinps = copy(self.pars)
- parsinps.update(dict(zip(inames,
+ parsinps.update(dict(list(zip(inames,
_pollInputs(inputVarList, new_t+self.globalt0,
- self.checklevel))))
+ self.checklevel)))))
else:
parsinps = self.pars
evsflagged = self.eventstruct.pollHighLevelEvents(None,
@@ -307,9 +307,8 @@
eventslist)
## print new_t, evsflagged
## evsflagged = [ev for ev in evsflagged if solver.t-indepdom0 > ev[1].eventinterval]
- termevsflagged = filter(lambda e: e in evsflagged, termevents)
- nontermevsflagged = filter(lambda e: e not in termevsflagged,
- evsflagged)
+ termevsflagged = [e for e in termevents if e in evsflagged]
+ nontermevsflagged = [e for e in evsflagged if e not in termevsflagged]
# register any non-terminating events in the warnings
# list, unless they are 'precise' in which case flag
# them to be resolved after integration completes
@@ -384,7 +383,7 @@
# much less accurately determined)
if not breakwhile:
# only here if a terminal event hasn't just flagged
- for xi in xrange(self.dimension):
+ for xi in range(self.dimension):
if not self.contains(depdomains[xi],
solver.y[xi],
self.checklevel):
@@ -414,17 +413,17 @@
self.checklevel) \
for f in inputVarList]
except ValueError:
- print 'External input call caused value out of range error:',\
- 't = ', solver.t
+ print('External input call caused value out of range error:',\
+ 't = ', solver.t)
for f in inputVarList:
if f.diagnostics.hasWarnings():
- print 'External input variable %s out of range:'%f.name
- print ' t = ', repr(f.diagnostics.warnings[-1][0]), ', ', \
- f.name, ' = ', repr(f.diagnostics.warnings[-1][1])
+ print('External input variable %s out of range:'%f.name)
+ print(' t = ', repr(f.diagnostics.warnings[-1][0]), ', ', \
+ f.name, ' = ', repr(f.diagnostics.warnings[-1][1]))
raise
except AssertionError:
- print 'External input call caused t out of range error: t = ', \
- solver.t
+ print('External input call caused t out of range error: t = ', \
+ solver.t)
raise
solver.set_f_params(extralist)
breakwhile = not solver.successful()
@@ -437,8 +436,8 @@
try:
if self.diagnostics.warnings[-1][0] not in [W_TERMEVENT,
W_TERMSTATEBD]:
- print "t =", solver.t
- print "state =", dict(zip(xnames,solver.y))
+ print("t =", solver.t)
+ print("state =", dict(list(zip(xnames,solver.y))))
raise RuntimeError("Event finding code for terminal event "
"failed in Generator " + self.name + \
": try decreasing eventdelay or "
@@ -446,8 +445,8 @@
"atol and rtol parameters")
except IndexError:
info(self.diagnostics.outputStats, "Output statistics")
- print "t =", solver.t
- print "x =", solver.y
+ print("t =", solver.t)
+ print("x =", solver.y)
raise RuntimeError("Event finding failed in Generator " + \
self.name + ": try decreasing eventdelay "
"or eventinterval below eventtol")
@@ -485,18 +484,18 @@
interp = interp1d(alltData, xvals)
variables[x] = Variable(interp, 't', x, x)
else:
- print "Error in Generator:", self.name
- print "t = ", alltData
- print "x = ", allxDataDict
+ print("Error in Generator:", self.name)
+ print("t = ", alltData)
+ print("x = ", allxDataDict)
raise PyDSTool_ValueError("Fewer than 2 data points computed")
for a in anames:
if len(alltData) > 1:
variables[a] = Variable(interp1d(alltData, allaDataDict[a]),
't', a, a)
else:
- print "Error in Generator:", self.name
- print "t = ", alltData
- print "x = ", allxDataDict
+ print("Error in Generator:", self.name)
+ print("t = ", alltData)
+ print("x = ", allxDataDict)
raise PyDSTool_ValueError("Fewer than 2 data poRefactoringTool: Refactored ./PyDSTool/Generator/EmbeddedSysGen.py
ints computed")
self.diagnostics.outputStats = {'last_step': dt,
'num_fcns': num_points,
@@ -505,7 +504,7 @@
}
if solver.successful():
#self.validateSpec()
- for evname, evtlist in Evtimes.iteritems():
+ for evname, evtlist in Evtimes.items():
try:
self.eventstruct.Evtimes[evname].extend([et+self.globalt0 \
for et in evtlist])
@@ -526,7 +525,7 @@
'indepvararray': Evtimes[evname],
'indepvartype': float})
self.defined = True
- return Trajectory(trajname, variables.values(),
+ return Trajectory(trajname, list(variables.values()),
abseps=self._abseps, globalt0=self.globalt0,
checklevel=self.checklevel,
FScompatibleNames=self._FScompatibleNames,
@@ -540,7 +539,7 @@
self.diagnostics._errorcodes[errcode])))
except TypeError:
# e.g. when errcode has been used to return info list
- print "Error information: ", errcode
+ print("Error information: ", errcode)
self.diagnostics.errors.append((E_COMPUTFAIL, (solver.t,
self.diagnostics._errorcodes[0])))
self.defined = False
@@ -561,7 +560,7 @@
p = sortedDictValues(self._FScompatibleNames(pdict))
i = _pollInputs(sortedDictValues(self.inputs),
t, self.checklevel)
- return apply(getattr(self, self.funcspec.spec[1]), [t, x, p+i])
+ return getattr(self, self.funcspec.spec[1])(*[t, x, p+i])
def Jacobian(self, t, xdict, pdict=None, asarray=True):
@@ -579,8 +578,7 @@
p = sortedDictValues(self._FScompatibleNames(pdict))
i = _pollInputs(sortedDictValues(self.inputs),
t, self.checklevel)
- return apply(getattr(self, self.funcspec.auxfns["Jacobian"][1]), \
- [t, x, p+i])
+ return getattr(self, self.funcspec.auxfns["Jacobian"][1])(*[t, x, p+i])
else:
raise PyDSTool_ExistError("Jacobian not defined")
@@ -600,8 +598,7 @@
p = sortedDictValues(self._FScompatibleNames(pdict))
i = _pollInputs(sortedDictValues(self.inputs),
t, self.checklevel)
- return apply(getattr(self, self.funcspec.auxfns["Jacobian_pars"][1]), \
- [t, x, p+i])
+ return getattr(self, self.funcspec.auxfns["Jacobian_pars"][1])(*[t, x, p+i])
else:
raise PyDSTool_ExistError("Jacobian w.r.t. parameters not defined")
@@ -620,7 +617,7 @@
p = sortedDictValues(self._FScompatibleNames(pdict))
i = _pollInputs(sortedDictValues(self.inputs),
t, self.checklevel)
- return apply(getattr(self, self.funcspec.auxspec[1]), [t, x, p+i])
+ return getattr(self, self.funcspec.auxspec[1])(*[t, x, p+i])
def __del__(self):
--- ./PyDSTool/Generator/EmbeddedSysGen.py (original)
+++ ./PyDSTool/Generator/EmbeddedSysGen.py (refactored)
@@ -1,8 +1,8 @@
# Embedded dynamical system generator
-from __future__ import division
-
-from allimports import *
-from baseclasses import ctsGen, theGenSpecHelper
+
+
+from .allimports import *
+from .baseclasses import ctsGen, theGenSpecHelper
from PyDSTool.utils import *
from PyDSTool.common import *
from PyDSTool.Interval import uncertain
@@ -48,7 +48,7 @@
except (KeyError, AttributeError):
raise PyDSTool_KeyError("Model-type system must be provided")
self.funcspec = args(**self._kw_process_dispatch(dispatch_list, kw))
- self.funcspec.vars = kw['varspecs'].keys()
+ self.funcspec.vars = list(kw['varspecs'].keys())
self.funcspec.auxvars = []
# varspecs not specified by user and must be removed for checkArgs()
del kw['varspecs']
@@ -71,11 +71,11 @@
Interval('t', self.indepvartype, self.tdata,
self._abseps), 't')
self._register(self.indepvariable)
- for x in self.xdomain.keys():
+ for x in list(self.xdomain.keys()):
# aux vars?
try:
xinterval=Interval(x, self.xtype[x], self.xdomain[x], self._abseps)
- except KeyError, e:
+ except KeyError as e:
raise PyDSTool_KeyError('Mismatch between declared variables '
'and xspecs: ' + str(e))
# placeholder variable so that this class can be
@@ -103,7 +103,7 @@
try:
traj = self._embed_spec(self._solver)
except:
- print "Error in user-provided embedded system"
+ print("Error in user-provided embedded system")
raise
self.defined = True
traj.name = trajname
@@ -123,7 +123,7 @@
def set(self, **kw):
"""Set ExplicitFnGen parameters"""
- if remain(kw.keys(), self._validKeys) != []:
+ if remain(list(kw.keys()), self._validKeys) != []:
raise KeyError("Invalid keys in argument")
if 'globalt0' in kw:
# pass up to generic treatment for this
@@ -137,9 +137,9 @@
# optional keys for this call are
# ['pars', 'tdomain', 'xdomain', 'pdomain']
if 'xdomain' in kw:
- for k_temp, v in kw['xdomain'].iteritems():
- k = self._FScompatibleNames(k_temp)
- if k in self.xdomain.keys():
+ for k_temp, v in kw['xdomain'].items():
+ k = self._FScompatibleNames(k_temp)
+ if k in list(self.xdomain.keys()):
if isinstance(v, _seq_types):
assert len(v) == 2, \
"Invalid size of domain specification for "+k
@@ -162,9 +162,9 @@
' names -> valid interval 2-tuples or '
'singletons')
if 'pdomain' in kw:
- for k_temp, v in kw['pdomain'].iteritems():
- k = self._FScompatibleNames(k_temp)
- if k in self.pars.keys():
+ for k_temp, v in kw['pdomain'].items():
+ k = self._FScompatibleNames(k_temp)
+ if k in list(self.pars.keys()):
if isinstance(v, _seq_types):
assert len(v) == 2, \
"Invalid size of domain specification for "+k
@@ -197,29 +197,29 @@
self.diagnostics.warnings.append((W_UNCERTVAL,
(self.tdata[0],self.tdomain)))
else:
- print 'tdata cannot be specified below smallest '\
+ print('tdata cannot be specified below smallest '\
'value in tdomain\n (possibly due to uncertain bounding).'\
' It has been automatically adjusted from\n ', self.tdata[0], \
'to', self.tdomain[0], '(difference of', \
- self.tdomain[0]-self.tdata[0], ')'
+ self.tdomain[0]-self.tdata[0], ')')
self.tdata[0] = self.tdomain[0]
if self.tdomain[1] < self.tdata[1]:
if self.indepvariable.indepdomain.contains(self.tdata[1]) == uncertain:
self.diagnostics.warnings.append((W_UNCERTVAL,
(self.tdata[1],self.tdomain)))
else:
- print 'tdata cannot be specified above largest '\
+ print('tdata cannot be specified above largest '\
'value in tdomain\n (possibly due to uncertain bounding).'\
' It has been automatically adjusted from\n ', \
self.tdomain[1],RefactoringTool: Refactored ./PyDSTool/Generator/Dopri_ODEsystem.py
'to', \
self.tdomain[1], '(difference of', \
- self.tdata[1]-self.tdomain[1], ')'
+ self.tdata[1]-self.tdomain[1], ')')
self.tdata[1] = self.tdomain[1]
self.indepvariable.depdomain.set(self.tdata)
if 'ics' in kw:
- for k_temp, v in kw['ics'].iteritems():
- k = self._FScompatibleNames(k_temp)
- if k in self.xdomain.keys():
+ for k_temp, v in kw['ics'].items():
+ k = self._FScompatibleNames(k_temp)
+ if k in list(self.xdomain.keys()):
self._xdatadict[k] = ensurefloat(v)
else:
raise ValueError('Illegal variable name')
@@ -228,7 +228,7 @@
if not self.pars:
raise ValueError('No pars were declared for this object'
' at initialization.')
- for k_temp, v in kw['pars'].iteritems():
+ for k_temp, v in kw['pars'].items():
k = self._FScompatibleNames(k_temp)
if k in self.pars:
cval = self.parameterDomains[k].contains(v)
@@ -236,7 +236,7 @@
if cval is not notcontained:
self.pars[k] = ensurefloat(v)
if cval is uncertain and self.checklevel == 2:
- print 'Warning: Parameter value at bound'
+ print('Warning: Parameter value at bound')
else:
raise PyDSTool_ValueError('Parameter value out of '
'bounds')
@@ -256,11 +256,11 @@
def validateSpec(self):
ctsGen.validateSpec(self)
try:
- for v in self.variables.values():
+ for v in list(self.variables.values()):
assert isinstance(v, Variable)
assert not self.inputs
except AssertionError:
- print 'Invalid system specification'
+ print('Invalid system specification')
raise
--- ./PyDSTool/Generator/Dopri_ODEsystem.py (original)
+++ ./PyDSTool/Generator/Dopri_ODEsystem.py (refactored)
@@ -1,9 +1,9 @@
# Dopri ODE system
-from __future__ import division
-
-from allimports import *
+
+
+from .allimports import *
from PyDSTool.Generator import ODEsystem as ODEsystem
-from baseclasses import Generator, theGenSpecHelper, genDB, _pollInputs
+from .baseclasses import Generator, theGenSpecHelper, genDB, _pollInputs
from PyDSTool.utils import *
from PyDSTool.common import *
from PyDSTool.integrator import integrator
@@ -48,8 +48,8 @@
try:
self._integMod = __import__(modname, globals())
except:
- print "Error in importing compiled vector field and integrator."
- print "Did you compile the RHS C code?"
+ print("Error in importing compiled vector field and integrator.")
+ print("Did you compile the RHS C code?")
raise
# check module's directory
assert 'Integrate' in dir(self._integMod), \
@@ -358,23 +358,23 @@
'boundsCheckMaxSteps': 1000,
'checkBounds': self.checklevel
}
- for k, v in algparams_def.iteritems():
+ for k, v in algparams_def.items():
if k not in self.algparams:
self.algparams[k] = v
# verify that no additional keys are present in algparams, after
# defaults are added above
if len(self.algparams) != len(algparams_def):
raise ValueError("Invalid keys present in algparams argument: " \
- + str(remain(self.algparams.keys(),algparams_def.keys())))
+ + str(remain(list(self.algparams.keys()),list(algparams_def.keys()))))
thisplatform = platform.system()
if thisplatform == 'Windows':
self._dllext = ".pyd"
elif thisplatform in ['Linux', 'IRIX', 'Solaris', 'SunOS', 'MacOS', 'Darwin', 'FreeBSD']:
self._dllext = '.so'
else:
- print "Shared library extension not tested on this platform."
- print "If this process fails please report the errors to the"
- print "developers."
+ print("Shared library extension not tested on this platform.")
+ print("If this process fails please report the errors to the")
+ print("developers.")
self._dllext = '.so'
self._compilation_tempdir = os.path.join(os.getcwd(),
"dopri853_temp")
@@ -384,8 +384,8 @@
"A file already exists with the same name"
os.mkdir(self._compilation_tempdir)
except:
- print "Could not create compilation temp directory " + \
- self._compilation_tempdir
+ print("Could not create compilation temp directory " + \
+ self._compilation_tempdir)
raise
self._compilation_sourcedir = os.path.join(_pydstool_path,"integrator")
self._vf_file = self.name+"_vf.c"
@@ -399,8 +399,8 @@
self.makeLibSource()
self.compileLib()
else:
- print "Build the library using the makeLib method, or in "
- print "stages using the makeLibSource and compileLib methods."
+ print("Build the library using the makeLib method, or in ")
+ print("stages using the makeLibSource and compileLib methods.")
self._inputVarList = []
self._inputTimeList = []
@@ -432,9 +432,9 @@
## "_dop853"+self._vf_filename_ext+self._dllext)):
## os.remove(os.path.join(os.getcwd(),
## "_dop853"+self._vf_filename_ext+self._dllext))
- print "Cannot rebuild library without restarting session. Sorry."
- print "Try asking the Python developers to make a working module"
- print "unimport function!"
+ print("Cannot rebuild library without restarting session. Sorry.")
+ print("Try asking the Python developers to make a working module")
+ print("unimport function!")
## self.makeLibSource()
@@ -498,7 +498,7 @@
('stdlib.h', STDLIB), ('string.h', STDLIB), ('vfield.h', USERLIB),
('events.h', USERLIB), ('signum.h', USERLIB), ('maxmin.h', USERLIB)])
include_str = ''
- for libstr, libtype in libinclude.iteritems():
+ for libstr, libtype in libinclude.items():
if libtype == STDLIB:
quoteleft = '<'
quoteright = '>'
@@ -511,8 +511,8 @@
for libstr in include:
if libstr in libinclude:
# don't repeat libraries
- print "Warning: library '" + libstr + "' already appears in list"\
- + " of imported libraries"
+ print("Warning: library '" + libstr + "' already appears in list"\
+ + " of imported libraries")
else:
include_str += "#include " + '"' + libstr + '"\n'
allfilestr = "/* Vector field function and events for Dopri853 integrator.\n " \
@@ -552,17 +552,17 @@
inames = self.funcspec.inputs
pnames.sort()
inames.sort()
- for i in xrange(self.numpars):
+ for i in range(self.numpars):
p = pnames[i]
# add to defines
pardefines += self.funcspec._defstr+" "+p+"\tp_["+str(i)+"]\n"
- for i in xrange(self.dimension):
+ for i in range(self.dimension):
v = vnames[i]
# add to defines
vardefines += self.funcspec._defstr+" "+v+"\tY_["+str(i)+"]\n"
for i, v in enumerate(self.funcspec.auxvars):
auxvardefines += self.funcspec._defstr+" "+v+"\t("+self.funcspec._auxdefs_parsed[v]+")\n"
- for i in xrange(len(self.funcspec.inputs)):
+ for i in range(len(self.funcspec.inputs)):
inp = inames[i]
# add to defines
inpdefines += self.funcspec._defstr+" "+inp+"\txv_["+str(i)+"]\n"
@@ -588,7 +588,7 @@
# and add hidden p argument
if self.funcspec.auxfns:
fbody_parsed = addArgToCalls(fbody,
- self.funcspec.auxfns.keys(),
+ list(self.funcspec.auxfns.keys()),
"p_, wk_, xv_")
if 'initcond' in self.funcspec.auxfns:
# convert 'initcond(x)' to 'initcond("x")' for
@@ -603,7 +603,7 @@
# add signature for auxiliary functions
if self.funcspec.auxfns:
allfilestr += "\n"
- for finfo in self.funcspec.auxfns.values():
+ for finfo in list(self.funcspec.auxfns.values()):
allfilestr += finfo[1] + ";\n"
assignEvBody = ""
for evix in range(numevs):
@@ -627,11 +627,11 @@
+ ";\n\n\n"
allfilestr += self.funcspec.spec[0] + "\n\n"
if self.funcspec.auxfns:
- for fname, finfo in self.funcspec.auxfns.iteritems():
+ for fname, finfo in self.funcspec.auxfns.items():
fbody = finfo[0]
# subs _p into auxfn-to-auxfn calls (but not to the signature)
fbody_parsed = addArgToCalls(fbody,
- self.funcspec.auxfns.keys(),
+ list(self.funcspec.auxfns.keys()),
"p_, wk_, xv_", notFirst=fname)
if 'initcond' in self.funcspec.auxfns:
# convert 'initcond(x)' to 'initcond("x")' for
@@ -668,9 +668,9 @@
file = open(vffile, 'w')
file.write(allfilestr)
file.close()
- except IOError, e:
- print "Error opening file "+self._vf_file+" for writing"
- raise IOError, e
+ except IOError as e:
+ print("Error opening file "+self._vf_file+" for writing")
+ raise IOError(e)
def compileLib(self, libsources=[], libdirs=[]):
@@ -686,21 +686,21 @@
# then DLL file already exists and we can't overwrite it at this
# time
proceed = False
- print "\n"
- print "-----------------------------------------------------------"
- print "Present limitation of Python: Cannot rebuild library"
- print "without exiting Python and deleting the shared library"
- print " " + str(os.path.join(os.getcwd(),
- "_dop853"+self._vf_filename_ext+self._dllext))
- print "by hand! If you made any changes to the system you should"
- print "not proceed with running the integrator until you quit"
- print "and rebuild."
- print "-----------------------------------------------------------"
- print "\n"
+ print("\n")
+ print("-----------------------------------------------------------")
+ print("Present limitation of Python: Cannot rebuild library")
+ print("without exiting Python and deleting the shared library")
+ print(" " + str(os.path.join(os.getcwd(),
+ "_dop853"+self._vf_filename_ext+self._dllext)))
+ print("by hand! If you made any changes to the system you should")
+ print("not proceed with running the integrator until you quit")
+ print("and rebuild.")
+ print("-----------------------------------------------------------")
+ print("\n")
else:
proceed = True
if not proceed:
- print "Did not compile shared library."
+ print("Did not compile shared library.")
return
if self._solver is not None:
self.forceLibRefresh()
@@ -717,7 +717,7 @@
ifacefile_orig.close()
ifacefile_copy.close()
except IOError:
- print "dop853.i copying error in dopri853 compilation directory"
+ print("dop853.i copying error in dopri853 compilation directory")
raise
swigfile = os.path.join(self._compilation_tempdir,
"dop853"+self._vf_filename_ext+".i")
@@ -769,8 +769,8 @@
extra_compile_args=['-w', '-D__DOPRI__', '-m32'],
extra_link_args=['-w', '-m32'])])
except:
- print "\nError occurred in generating Dopri system..."
- print sys.exc_info()[0], sys.exc_info()[1]
+ print("\nError occurred in generating Dopri system...")
+ print(sys.exc_info()[0], sys.exc_info()[1])
raise RuntimeError
# Attempt to unload module through a shutdown() function being
# added to the SWIG module file. But it didn't work!
@@ -814,9 +814,9 @@
"dop853"+self._vf_filename_ext+".py"))
except:
rout.stop()
- print "\nError occurred in generating Dopri system"
- print "(while moving library extension modules to CWD)"
- print sys.exc_info()[0], sys.exc_info()[1]
+ print("\nError occurred in generating Dopri system")
+ print("(while moving library extension modules to CWD)")
+ print(sys.exc_info()[0], sys.exc_info()[1])
raise RuntimeError
rout.stop() # restore stdout
@@ -850,13 +850,13 @@
raise ValueError('rtol list must have same length as phase dimension')
else:
rtol = self.algparams['rtol']
- self.algparams['rtol'] = [rtol for dimix in xrange(self.dimension)]
+ self.algparams['rtol'] = [rtol for dimix in range(self.dimension)]
if isinstance(self.algparams['atol'], list):
if len(self.algparams['atol']) != self.dimension:
raise ValueError('atol list must have same length as phase dimension')
else:
atol = self.algparams['atol']
- self.algparams['atol'] = [atol for dimix in xrange(self.dimension)]
+ self.algparams['atol'] = [atol for dimix in range(self.dimension)]
anames = self.funcspec.auxvars
# Check i.c.'s are well defined (finite)
self.checkInitialConditions()
@@ -1035,12 +1035,12 @@
numevs = len(Evtimes[evix])
if self.algparams['eventTerm'][evix]:
if numevs > 1:
- print "Event info:", Evpoints, Evtimes
+ print("Event info:", Evpoints, Evtimes)
assert numevs <= 1, ("Internal error: more than one "
"terminal event of same type found")
# For safety, we should assert that this event
# also appears in termevents, but we don't
- if Evtimes[evix][0] in termevtimes.keys():
+ if Evtimes[evix][0] in list(termevtimes.keys()):
# append event name to this warning
warning_ix = termevtimes[Evtimes[evix][0]]
self.diagnostics.warnings[warning_ix][1][1].append(evname)
@@ -1052,7 +1052,7 @@
[self._eventNames[evix]])))
else:
for ev in range(numevs):
- if Evtimes[evix][ev] in nontermevtimes.keys():
+ if Evtimes[evix][ev] in list(nontermevtimes.keys()):
# append event name to this warning
warning_ix = nontermevtimes[Evtimes[evix][ev]]
self.diagnostics.warnings[warning_ix][1][1].append(evname)
@@ -1064,9 +1064,9 @@
(Evtimes[evix][ev],
[evname])))
except IndexError:
- print "Events returned from integrator are the wrong size."
- print " Did you change the system and not refresh the C " \
- + "library using the forcelibrefresh() method?"
+ print("Events returned from integrator are the wrong size.")
+ print(" Did you change the system and not refresh the C " \
+ + "library using the forcelibrefresh() method?")
raise
termcount = 0
for (w,i) in self.diagnostics.warnings:
@@ -1086,10 +1086,10 @@
last_t = Inf
if self.algparams['checkBounds'] > 0:
# temp storage for repeatedly used object attributes (for lookup efficiency)
- depdomains = dict(zip(range(self.dimension),
- [self.variables[xn].depdomain for xn in xnames]))
+ depdomains = dict(list(zip(list(range(self.dimension)),
+ [self.variables[xn].depdomain for xn in xnames])))
offender_ix = None
- for xi in xrange(self.dimension):
+ for xi in range(self.dimension):
if not any(depdomains[xi].isfinite()):
# no point in checking when the bounds are +/- infinity
continue
@@ -1106,7 +1106,7 @@
elif last_ix >= 0 and last_ix < highest_ix:
# truncate data
last_t = alltData[last_ix]
- print "Warning; domain bound reached (because algparams['checkBounds'] > 0)"
+ print("Warning; domain bound reached (because algparams['checkBounds'] > 0)")
self.diagnostics.warnings.append((W_TERMSTATEBD,
(last_t, xnames[offender_ix],
X[offender_ix, last_ix],
@@ -1158,11 +1158,11 @@
X = X[:, :last_ix]
alltData = alltData[:last_ix]
try:
- allxDataDict = dict(zip(xnames,X))
+ allxDataDict = dict(list(zip(xnames,X)))
except IndexError:
- print "Integration returned variable values of unexpected dimensions."
- print " Did you change the system and not refresh the C library" \
- + " using the forcelibrefresh() method?"
+ print("Integration returned variable values of unexpected dimensions.")
+ print(" Did you change the system and not refresh the C library" \
+ + " using the forcelibrefresh() method?")
raise
# storage of all auxiliary variable data
try:
@@ -1170,14 +1170,14 @@
if last_ix < highest_ix:
A = A[:, :last_ix]
try:
- allaDataDict = dict(zip(anames,A))
+ allaDataDict = dict(list(zip(anames,A)))
except TypeError:
- print "Internal error! Type of A: ", type(A)
+ print("Internal error! Type of A: ", type(A))
raise
except IndexError:
- print "Integration returned auxiliary values of unexpected dimensions."
- print " Did you change the system and not refresh the C library" \
- + " using the forcelibrefresh() method?"
+ print("Integration returned auxiliary values of unexpected dimensions.")
+ print(" Did you change the system and not refresh the C library" \
+ + " using the forcelibrefresh() method?")
raise
if int(Err) == 1 or (int(Err) == 2 and termcount == 1):
# output OK
@@ -1214,7 +1214,7 @@
# final checks
#self.validateSpec()
self.defined = True
- return Trajectory(trajname, variables.values(),
+ return Trajectory(trajname, list(variables.values()),
abseRefactoringTool: Refactored ./PyDSTool/Generator/DDEsystem.py
RefactoringTool: Refactored ./PyDSTool/Generator/ADMC_ODEsystem.py
ps=self._abseps, globalt0=self.globalt0,
checklevel=self.checklevel,
FScompatibleNames=self._FScompatibleNames,
@@ -1226,7 +1226,7 @@
diagnost_info = self.diagnostics._errorcodes[int(Err)]
except TypeError:
# errcode messed up from Dopri
- print "Error code: ", Err
+ print("Error code: ", Err)
diagnost_info = self.diagnostics._errorcodes[0]
if self._solver.verbose:
info(self.diagnostics.outputStats, "Output statistics")
@@ -1235,8 +1235,8 @@
if (len(alltData) == self.algparams['max_pts'] or \
self.diagnostics.outputStats['num_steps'] >= self.algparams['max_pts']) \
and alltData[-1] < tend:
- print "max_pts algorithmic parameter too small: current " + \
- "value is %i"%self.algparams['max_pts']
+ print("max_pts algorithmic parameter too small: current " + \
+ "value is %i"%self.algparams['max_pts'])
# avstep = (self.algparams['init_step']+self.diagnostics.outputStats['last_step'])/2.
if self.diagnostics.outputStats['last_time']-tbegin > 0:
ms = str(int(round(self.algparams['max_pts'] / \
@@ -1244,8 +1244,8 @@
tbegin)*(tend-tbegin))))
else:
ms = 'Inf'
- print "(recommended value for this trajectory segment is " + \
- "estimated to be %s (saved in diagnostics.errors attribute))"%str(ms)
+ print("(recommended value for this trajectory segment is " + \
+ "estimated to be %s (saved in diagnostics.errors attribute))"%str(ms))
diagnost_info += " -- recommended value is " + ms
self.diagnostics.errors.append((E_COMPUTFAIL,
(self._solver.lastTime, diagnost_info)))
--- ./PyDSTool/Generator/DDEsystem.py (original)
+++ ./PyDSTool/Generator/DDEsystem.py (refactored)
@@ -1,7 +1,7 @@
# Differential-delay system (incomplete)
-from allimports import *
-from baseclasses import ctsGen
+from .allimports import *
+from .baseclasses import ctsGen
from PyDSTool.utils import *
from PyDSTool.common import *
--- ./PyDSTool/Generator/ADMC_ODEsystem.py (original)
+++ ./PyDSTool/Generator/ADMC_ODEsystem.py (refactored)
@@ -1,9 +1,9 @@
# ADMC++ ODE system
-from __future__ import division
-
-from allimports import *
+
+
+from .allimports import *
from PyDSTool.Generator import ODEsystem as ODEsystem
-from baseclasses import Generator, theGenSpecHelper
+from .baseclasses import Generator, theGenSpecHelper
from PyDSTool.utils import *
from PyDSTool.common import *
from PyDSTool.integrator import integrator
@@ -62,7 +62,7 @@
algparams_def = {'evtols' : 0.0001, 'vftype' : 'vfieldts'}
# Remove this later
- for k, v in algparams_def.iteritems():
+ for k, v in algparams_def.items():
if k not in self.algparams:
self.algparams[k] = v
@@ -70,7 +70,7 @@
# defaults are added above
if len(self.algparams) != len(algparams_def):
raise ValueError("Invalid keys present in algparams argument: " \
- + str(remain(self.algparams.keys(),algparams_def.keys())))
+ + str(remain(list(self.algparams.keys()),list(algparams_def.keys()))))
thisplatform = platform.system()
@@ -82,8 +82,8 @@
"A file already exists with the same name"
os.mkdir(self._compilation_tempdir)
except:
- print "Could not create compilation temp directory " + \
- self._compilation_tempdir
+ print("Could not create compilation temp directory " + \
+ self._compilation_tempdir)
raise
# ADMC targets must go in their own directories with appropriate names
@@ -96,8 +96,8 @@
"A file already exists with the same name"
os.mkdir(self._target_dir)
except:
- print "Could not creat target ADMC model directory " + \
- self._target_dir
+ print("Could not creat target ADMC model directory " + \
+ self._target_dir)
raise
@@ -121,8 +121,8 @@
if not nobuild:
self.makeLibSource()
else:
- print "Build the library using the makeLib method, or in "
- print "stages using the makeLibSource and compileLib methods."
+ print("Build the library using the makeLib method, or in ")
+ print("stages using the makeLibSource and compileLib methods.")
def _prepareEventSpecs(self):
@@ -184,7 +184,7 @@
fbody += ev._LLfuncstr
if self.funcspec.auxfns:
- fbody_parsed = addArgToCalls(fbody, self.funcspec.auxfns.keys(), "p_")
+ fbody_parsed = addArgToCalls(fbody, list(self.funcspec.auxfns.keys()), "p_")
else:
fbody_parsed = fbody
@@ -253,11 +253,11 @@
pnames = self.funcspec.pars
pnames.sort()
- for i in xrange(self.numpars):
+ for i in range(self.numpars):
p = pnames[i]
pardefines += "\t" + p + " = p_(" + str(i+1) + ");\n"
- for i in xrange(self.dimension):
+ for i in range(self.dimension):
v = vnames[i]
vardefines += "\t" + v + " = x_(" + str(i+1) + ");\n"
@@ -288,11 +288,11 @@
allfilestr = ""
if self.funcspec.auxfns:
- for finfo in self.funcspec.auxfns.values():
+ for finfo in list(self.funcspec.auxfns.values()):
fbody = finfo[0]
# subs _p into auxfn-to-auxfn calls (but not to the signature)
fbody_parsed = addArgToCalls(fbody,
- self.funcspec.auxfns.keys(),
+ list(self.funcspec.auxfns.keys()),
"p_", notFirst=True)
allfilestr += "\n" + fbody_parsed + "\n\n"
@@ -337,7 +337,7 @@
bodystr = "ics_ = [ ...\n"
if self.initialconditions:
- icnames = self.initialconditions.keys()
+ icnames = list(self.initialconditions.keys())
icnames.sort()
for i in range(len(icnames)-1):
@@ -368,7 +368,7 @@
bodystr = "pars_ = [ ...\n"
if self.pars:
- pnames = self.pars.keys()
+ pnames = list(self.pars.keys())
pnames.sort()
for i in range(len(pnames)-1):
@@ -403,7 +403,7 @@
# NEED TO CHECK WHETHER THIS IS APPROPRIATELY DEFINED
# check for calls to user-defined functions and add hidden p_ argument
if self.funcspec.auxfns:
- fbody_parsed = addArgToCalls(fbody, self.funcspec.auxfns.keys(), "p_")
+ fbody_parsed = addArgToCalls(fbody, list(self.funcspec.auxfns.keys()), "p_")
if 'initcond' in self.funcspec.auxfns:
fbody_parsed = wrapArgInCall(fbody_parsed, 'initcond', ' ')
@@ -441,9 +441,9 @@
file = open(modelfile, 'w')
file.write(allfilestr)
file.close()
- except IOError, e:
- print "Error opening file "+self._model_file+" for writing"
- raise IOError, e
+ except IOError as e:
+ print("Error opening file "+self._model_file+" for writing")
+ raise IOError(e)
# Write the events.m file
if len(self._eventNames) > 0:
@@ -453,9 +453,9 @@
file = open(eventsfile, 'w')
file.write(allfilestr)
file.close()
- except IOError, e:
- print "Error opening file "+self._events_file+" for writing"
- raise IOError, e
+ except IOError as e:
+ RefactoringTool: Refactored ./PyDSTool/FuncSpec.py
print("Error opening file "+self._events_file+" for writing")
+ raise IOError(e)
# Write the initialconditions.m file
@@ -465,9 +465,9 @@
file = open(icfile, 'w')
file.write(allfilestr)
file.close()
- except IOError, e:
- print "Error opening file "+self._ic_file+" for writing"
- raise IOError, e
+ except IOError as e:
+ print("Error opening file "+self._ic_file+" for writing")
+ raise IOError(e)
# Write the pars.m file
allfilestr = self._prepareParamContents()
@@ -476,9 +476,9 @@
file = open(paramfile, 'w')
file.write(allfilestr)
file.close()
- except IOError, e:
- print "Error opening file "+self._param_file+" for writing"
- raise IOError, e
+ except IOError as e:
+ print("Error opening file "+self._param_file+" for writing")
+ raise IOError(e)
# Write the get.m file
allfilestr = self._prepareGetFileContents()
@@ -487,9 +487,9 @@
file = open(getfile, 'w')
file.write(allfilestr)
file.close()
- except IOError, e:
- print "Error opening file "+self._get_file+" for writing"
- raise IOError, e
+ except IOError as e:
+ print("Error opening file "+self._get_file+" for writing")
+ raise IOError(e)
# Write the set.m file
allfilestr = self._prepareSetFileContents()
@@ -498,9 +498,9 @@
file = open(setfile, 'w')
file.write(allfilestr)
file.close()
- except IOError, e:
- print "Error opening file "+self._set_file+" for writing"
- raise IOError, e
+ except IOError as e:
+ print("Error opening file "+self._set_file+" for writing")
+ raise IOError(e)
# Write the vfield.m file
# vfdefines = self._prepareVfieldDefines()
@@ -511,9 +511,9 @@
file = open(vffile, 'w')
file.write(allfilestr)
file.close()
- except IOError, e:
- print "Error opening file "+self._vfield_file+" for writing"
- raise IOError, e
+ except IOError as e:
+ print("Error opening file "+self._vfield_file+" for writing")
+ raise IOError(e)
# We have omitted methods: RHS, compute, etc. because this
--- ./PyDSTool/FuncSpec.py (original)
+++ ./PyDSTool/FuncSpec.py (refactored)
@@ -8,13 +8,13 @@
"""
# PyDSTool imports
-from __future__ import division
-from utils import *
-from common import *
-from parseUtils import *
-from errors import *
-from utils import info as utils_info
-from Symbolic import QuantSpec
+
+from .utils import *
+from .common import *
+from .parseUtils import *
+from .errors import *
+from .utils import info as utils_info
+from .Symbolic import QuantSpec
# Other imports
from copy import copy, deepcopy
@@ -146,7 +146,7 @@
raise ValueError('reuseterms must be a dictionary of strings ->'
' replacement strings')
ignore_list = []
- for term, repterm in self.reuseterms.iteritems():
+ for term, repterm in self.reuseterms.items():
assert isinstance(term, str), \
"terms in 'reuseterms' dictionary must be strings"
## if term[0] in num_chars+['.']:
@@ -159,32 +159,32 @@
# not sure about the next check any more...
# what is the point of not allowing subs terms to begin with op?
if term[0] in '+/*':
- print "Error in term:", term
+ print("Error in term:", term)
raise ValueError('terms to be substituted must not begin '
'with arithmetic operators')
if term[0] == '-':
term = '(' + term + ')'
if term[-1] in '+-/*':
- print "Error in term:", term
+ print("Error in term:", term)
raise ValueError('terms to be substituted must not end with '
'arithmetic operators')
for s in term:
if self.targetlang == 'python':
if s in '[]{}~@#$%&\|?^': # <>! now OK, e.g. for "if" statements
- print "Error in term:", term
+ print("Error in term:", term)
raise ValueError('terms to be substituted must be '
'alphanumeric or contain arithmetic operators '
'+ - / *')
else:
if s in '[]{}~!@#$%&\|?><': # removed ^ from this list
- print "Error in term:", term
+ print("Error in term:", term)
raise ValueError('terms to be substituted must be alphanumeric or contain arithmetic operators + - / *')
if repterm[0] in num_chars:
- print "Error in replacement term:", repterm
+ print("Error in replacement term:", repterm)
raise ValueError('replacement terms must not begin with numbers')
for s in repterm:
if s in '+-/*.()[]{}~!@#$%^&\|?><,':
- print "Error in replacement term:", repterm
+ print("Error in replacement term:", repterm)
raise ValueError('replacement terms must be alphanumeric')
for t in ignore_list:
del self.reuseterms[t]
@@ -235,9 +235,9 @@
num_varspecs = numaux + len(vars)
if len(kw['varspecs']) != len(self._varsbyforspec) and \
len(kw['varspecs']) != num_varspecs:
- print "# state variables: ", len(vars)
- print "# auxiliary variables: ", numaux
- print "# of variable specs: ", len(kw['varspecs'])
+ print("# state variables: ", len(vars))
+ print("# auxiliary variables: ", numaux)
+ print("# of variable specs: ", len(kw['varspecs']))
raise ValueError('Incorrect size of varspecs')
self.varspecs = deepcopy(kw['varspecs'])
foundKeys += 1 # for varspecs
@@ -280,8 +280,7 @@
# can be user-defined or generated from generateSpec
if 'spec' in kw:
if 'varspecs' in kw:
- raise PyDSTool_KeyError, \
- "Cannot provide both 'spec' and 'varspecs' keys"
+ raise PyDSTool_KeyError("Cannot provide both 'spec' and 'varspecs' keys")
assert isinstance(kw['spec'], tuple), ("'spec' must be a pair:"
" (spec body, spec name)")
assert len(kw['spec'])==2, ("'spec' must be a pair:"
@@ -303,7 +302,7 @@
if len(kw) > foundKeys:
raise PyDSTool_KeyError('Invalid keys passed in argument dict')
self.defined = False # initial value
- self.validateDef(vars, pars, inputs, auxvars, self._auxfnspecs.keys())
+ self.validateDef(vars, pars, inputs, auxvars, list(self._auxfnspecs.keys()))
# ... exception if not valid
# Fine to do the following if we get this far:
# sort for final order that will be used for determining array indices
@@ -354,10 +353,10 @@
new_args = deepcopy(self._initargs)
if self.codeinserts['start'] != '':
del new_args['codeinsert_start']
- print "Warning: code insert (start) ignored for new target"
+ print("Warning: code insert (start) ignored for new target")
if self.codeinserts['end'] != '':
del new_args['codeinsert_end']
- print "Warning: code insert (end) ignored for new target"
+ print("Warning: code insert (end) ignored for new target")
new_args['targetlang'] = targetlang
fs.__init__(new_args)
return fs
@@ -427,13 +426,13 @@
first_char_check = [alphabet_chars_RE.match(n[0]) \
is not None for n in allnames]
if not all(first_char_check):
- print "Offending names:", [n for i, n in enumerate(allnames) \
- if not first_char_check[i]]
+ print("Offending names:", [n for i, n in enumerate(allnames) \
+ if not first_char_check[i]])
raise ValueError('Variable, parameter, and input names must not '
'begin with non-alphabetic chars')
protected_overlap = intersect(allnames, allprotectednames)
if protected_overlap != []:
- print "Overlapping names:", protected_overlap
+ print("Overlapping names:", protected_overlap)
raise ValueError('Variable, parameter, and input names must not '
'overlap with protected math / aux function names')
## Not yet implemented ?
@@ -506,7 +505,7 @@
"""Pre-process any macro spec definitions (e.g. `for` loops)."""
assert self.varspecs != {}, 'varspecs attribute must be defined'
- specnames_unsorted = self.varspecs.keys()
+ specnames_unsorted = list(self.varspecs.keys())
_vbfs_inv = invertMap(self._varsbyforspec)
# Process state variable specifications
if len(_vbfs_inv) > 0:
@@ -580,7 +579,7 @@
expr = arglist[3]
# add macro text
varspecs = self._macroFor(rootstr, istr, ilo, ihi, expr)
- specnames_gen = varspecs.keys()
+ specnames_gen = list(varspecs.keys())
# now we update the dictionary of specnames with the
# processed, expanded versions
specnames.remove(specname)
@@ -628,7 +627,7 @@
eval_pieces[ix] = eval_str
# otherwise may be a different, embedded temp index for another
# sum, etc., so don't touch it
- keys = eval_pieces.keys()
+ keys = list(eval_pieces.keys())
keys.sort()
ranges = remove_indices_from_range(keys, len(q.parser.tokenized)-1)
# By virtue of this syntax, the first [] cannot be before some other text
@@ -663,7 +662,7 @@
def _macroSum(self, istr, ilo, ihi, expr_in_i):
def_dict = self._macroFor('', istr, int(ilo), int(ihi), expr_in_i)
- retstr = '(' + "+".join([term.strip() for term in def_dict.values()]) + ')'
+ retstr = '(' + "+".join([term.strip() for term in list(def_dict.values())]) + ')'
return retstr
# ----------------- Python specifications ----------------
@@ -672,7 +671,7 @@
if pytarget:
assert self.targetlang == 'python', \
'Wrong target language for this call'
- auxnames = self._auxfnspecs.keys()
+ auxnames = list(self._auxfnspecs.keys())
# User aux fn interface
uafi = {}
## protectednames = auxnames + self._protected_mathnames + \
@@ -765,8 +764,8 @@
# Process Jacobian functions, etc., specially, if present
if auxname == 'Jacobian':
if not compareList(auxinfo[0],['t']+self.vars):
- print ['t']+self.vars
- print "Auxinfo =", auxinfo[0]
+ print(['t']+self.vars)
+ print("Auxinfo =", auxinfo[0])
raise ValueError("Invalid argument list given in Jacobian.")
auxparlist = ["t","x","parsinps"]
# special symbols to allow in parsing function body
@@ -804,13 +803,13 @@
body_processed = ""
for row in range(m):
if specdict_check[specvars[row]] != n:
- print "Row %i: "%m, specdict[specvars[row]]
- print "Found length %i"%specdict_check[specvars[row]]
+ print("Row %i: "%m, specdict[specvars[row]])
+ print("Found length %i"%specdict_check[specvars[row]])
raise ValueError("Jacobian should be %sx%s"%(m,n))
elif auxname == 'Jacobian_pars':
if not compareList(auxinfo[0],['t']+self.vars):
- print ['t']+self.vars
- print "Auxinfo =", auxinfo[0]
+ print(['t']+self.vars)
+ print("Auxinfo =", auxinfo[0])
raise ValueError("Invalid argument list given in Jacobian.")
auxparlist = ["t","x","parsinps"]
# special symbols to allow in parsing function body
@@ -850,17 +849,17 @@
for row in range(m):
try:
if specdict_check[self.vars[row]] != n:
- print "Row %i: "%m, specdict[self.vars[row]]
- print "Found length %i"%specdict_check[self.vars[row]]
+ print("Row %i: "%m, specdict[self.vars[row]])
+ print("Found length %i"%specdict_check[self.vars[row]])
raise ValueError("Jacobian w.r.t. pars should be %sx%s"%(m,n))
except IndexError:
- print "\nFound:\n"
+ print("\nFound:\n")
info(specdict)
raise ValueError("Jacobian w.r.t. pars should be %sx%s"%(m,n))
elif auxname == 'massMatrix':
if not compareList(auxinfo[0],['t']+self.vars):
- print ['t']+self.vars
- print "Auxinfo =", auxinfo[0]
+ print(['t']+self.vars)
+ print("Auxinfo =", auxinfo[0])
raise ValueError("Invalid argument list given in Mass Matrix.")
auxparlist = ["t","x","parsinps"]
# special symbols to allow in parsing function body
@@ -876,7 +875,7 @@
"'[' character invalid in mass matrix for 1D system"
assert ']' not in auxstr, \
"']' character invalid in mass matrix for 1D system"
- specdict[specvars.values()[0]] = auxstr
+ specdict[list(specvars.values())[0]] = auxstr
else:
specdict = parseMatrixStrToDictStr(auxstr, specvars)
reusestr, body_processed_dict = self._processReusedPy(specvars,
@@ -897,8 +896,8 @@
body_processed = ""
for row in range(m):
if specdict_check[specvars[row]] != n:
- print "Row %i: "%m, specdict[specvars[row]]
- print "Found length %i"%specdict_check[specvars[row]]
+ print("Row %i: "%m, specdict[specvars[row]])
+ print("Found length %i"%specdict_check[specvars[row]])
raise ValueError("Mass matrix should be %sx%s"%(m,n))
else:
user_parstr = makeParList(auxinfo[0])
@@ -915,8 +914,8 @@
badparnames = intersect(auxparlist,
remain(protectednames,auxnames))
if badparnames != []:
- print "Bad parameter names in auxiliary function", \
- auxname, ":", badparnames
+ print("Bad parameter names in auxiliary function", \
+ auxname, ":", badparnames)
#print auxinfo[0]
#print auxparlist
raise ValueError("Cannot use protected names (including" \
@@ -947,7 +946,7 @@
auxfns[auxname] = makeUniqueFn(auxstr_py)
# Note: this automatically updates self._pyauxfns too
except:
- print 'Error in supplied auxiliary spec dictionary code'
+ print('Error in supplied auxiliary spec dictionary code')
raise
auxfn_namemap['ds.'+auxname] = 'ds.'+auxfns[auxname][1]
# prepare user-interface wrapper function (not method)
@@ -962,7 +961,7 @@
'(__parsinps__', fn_args, ')\n']
uafi[auxname] = ''.join(fn_elts)
# resolve inter-auxiliary function references
- for auxname, auxspec in auxfns.iteritems():
+ for auxname, auxspec in auxfns.items():
dummyQ = QuantSpec('dummy', auxspec[0], preserveSpace=True,
treatMultiRefs=False)
dummyQ.mapNames(auxfn_namemap)
@@ -1011,7 +1010,7 @@
retstr += _indentstr + 'return array([' + resname + '0])\n'
else:
retstr += _indentstr + 'return array([' \
- + makeParList(range(len(specnames)), resname) + '])\n'
+ + makeParList(list(range(len(specnames))), resname) + '])\n'
return retstr
@@ -1019,7 +1018,7 @@
assert self.targetlang == 'python', ('Wrong target language for this'
' call')
assert self.varspecs != {}, 'varspecs attribute must be defined'
- specnames_unsorted = self.varspecs.keys()
+ specnames_unsorted = list(self.varspecs.keys())
_vbfs_inv = invertMap(self._varsbyforspec)
# Process state variable specifications
if len(_vbfs_inv) > 0:
@@ -1039,7 +1038,7 @@
specname_vars = intersect(self.vars, specnames_unsorted)
specname_auxvars = intersect(self.auxvars, specnames_unsorted)
specname_vars.sort()
- for vn, vs in self.varspecs.items():
+ for vn, vs in list(self.varspecs.items()):
if any([pt in vs for pt in ('^', '**')]):
self.varspecs[vn] = convertPowers(vs, 'pow')
self.vars.sort()
@@ -1064,12 +1063,12 @@
try:
spec_info = makeUniqueFn(specstr_py)
except SyntaxError:
- print "Syntax error in specification:\n", specstr_py
+ print("Syntax error in specification:\n", specstr_py)
raise
try:
auxspec_info = makeUniqueFn(auxspecstr_py)
except SyntaxError:
- print "Syntax error in auxiliary spec:\n", auxspecstr_py
+ print("Syntax error in auxiliary spec:\n", auxspecstr_py)
raise
self.spec = spec_info
self.auxspec = auxspec_info
@@ -1090,10 +1089,10 @@
dopars=dopars, doinps=doinps,
illegal=illegal)
reusedefs = {}.fromkeys(new_protected)
- for vname, deflist in reusedParsed.iteritems():
+ for vname, deflist in reusedParsed.items():
for d in deflist:
reusedefs[d[2]] = d
- return (concatStrDict(reusedefs, intersect(order,reusedefs.keys())),
+ return (concatStrDict(reusedefs, intersect(order,list(reusedefs.keys()))),
specupdated)
@@ -1110,10 +1109,8 @@
+ self._protected_randomnames + self._protected_reusenames
allnames = remain(allnames, illegal)
if dovars:
- var_arrayixstr = dict(zip(self.vars, map(lambda i: str(i), \
- range(len(self.vars))) ))
- aux_arrayixstr = dict(zip(self.auxvars, map(lambda i: str(i), \
- range(len(self.auxvars))) ))
+ var_arrayixstr = dict(list(zip(self.vars, [str(i) for i in range(len(self.vars))] )))
+ aux_arrayixstr = dict(list(zip(self.auxvars, [str(i) for i in range(len(self.auxvars))] )))
else:
var_arrayixstr = {}
aux_arrayixstr = {}
@@ -1124,14 +1121,13 @@
parsinps_names = self.pars+self.inputs
else:
parsinps_names = self.pars
- parsinps_arrayixstr = dict(zip(parsinps_names,
- map(lambda i: str(i), \
- range(len(parsinps_names))) ))
+ parsinps_arrayixstr = dict(list(zip(parsinps_names,
+ [str(i) for i in range(len(parsinps_names))] )))
else:
parsinps_names = []
parsinps_arrayixstr = {}
specialtokens = remain(allnames,specials) + ['(', 't'] + specials
- for specname, itemlist in d.iteritems():
+ for specname, itemlist in d.items():
listix = -1
for strlist in itemlist:
listix += 1
@@ -1172,15 +1168,13 @@
allnames = remain(allnames, illegal)
if dovars:
if forexternal:
- var_arrayixstr = dict(zip(self.vars,
- ["'"+v+"'" for v in self.vars]))
- aux_arrayixstr = dict(zip(self.auxvars,
- ["'"+v+"'" for v in self.auxvars]))
- else:
- var_arrayixstr = dict(zip(self.vars, map(lambda i: str(i), \
- range(len(self.vars))) ))
- aux_arrayixstr = dict(zip(self.auxvars, map(lambda i: str(i),\
- range(len(self.auxvars))) ))
+ var_arrayixstr = dict(list(zip(self.vars,
+ ["'"+v+"'" for v in self.vars])))
+ aux_arrayixstr = dict(list(zip(self.auxvars,
+ ["'"+v+"'" for v in self.auxvars])))
+ else:
+ var_arrayixstr = dict(list(zip(self.vars, [str(i) for i in range(len(self.vars))] )))
+ aux_arrayixstr = dict(list(zip(self.auxvars, [str(i) for i in range(len(self.auxvars))] )))
else:
var_arrayixstr = {}
aux_arrayixstr = {}
@@ -1196,8 +1190,8 @@
else:
parsinps_names = self.pars
# for external calls we want parname -> 'parname'
- parsinps_arrayixstr = dict(zip(parsinps_names,
- ["'"+pn+"'" for pn in parsinps_names]))
+ parsinps_arrayixstr = dict(list(zip(parsinps_names,
+ ["'"+pn+"'" for pn in parsinps_names])))
else:
if doinps:
# parsinps_names is pars and inputs, each sorted
@@ -1205,9 +1199,8 @@
parsinps_names = self.pars+self.inputs
else:
parsinps_names = self.pars
- parsinps_arrayixstr = dict(zip(parsinps_names,
- map(lambda i: str(i), \
- range(len(parsinps_names))) ))
+ parsinps_arrayixstr = dict(list(zip(parsinps_names,
+ [str(i) for i in range(len(parsinps_names))] )))
else:
parsinps_names = []
parsinps_arrayixstr = {}
@@ -1268,8 +1261,8 @@
# adding allnames catches var names etc. that are valid
# in auxiliary functions but are not special tokens
# and must be left alone
- print "Error in specification `" + specname + \
- "` with token `"+s+"` :\n", specstr
+ print("Error in specification `" + specname + \
+ "` with token `"+s+"` :\n", specstr)
raise ValueError('Undeclared or illegal token `'+s+'` in'
' spec string `'+specname+'`')
if stemp == '^' and self.targetlang == 'python':
@@ -1336,9 +1329,9 @@
returnstr += "'"+s+"'"
strname_arg_imminent = False
else:
- print "Spec name:", specname
- print "Spec string:", specstr
- print "Problem symbol:", s
+ print("Spec name:", specname)
+ print("Spec string:", specstr)
+ print("Problem symbol:", s)
raise NameError('auxiliary variables cannot '
'appear on any right-hand side '
'except their initial value')
@@ -1390,8 +1383,8 @@
returnstr += 'scipy.'+s
elif s in self._protected_specialfns:
if self.targetlang != 'python':
- print "Function %s is currently not supported "%s, \
- "outside of python target language definitions"
+ print("Function %s is currently not supported "%s, \
+ "outside of python target language definitions")
raise ValueError("Invalid special function for "
"non-python target definition")
# replace the underscore in the name with a dot
@@ -1407,8 +1400,8 @@
# remove vars, auxs, inputs
to_remove = self.vars + self.auxvars + self.inputs
filtfunc = lambda n: n not in to_remove
- specialtokens_temp = filter(filtfunc,
- specialtokens+self._ignorespecial)
+ specialtokens_temp = list(filter(filtfunc,
+ specialtokens+self._ignorespecial))
else:
specialtokens_temp = specialtokens+self._ignorespecial
if s == 'if':
@@ -1512,7 +1505,7 @@
if self.auxfns:
def addParToCall(s):
return addArgToCalls(self._processSpecialC(s),
- self.auxfns.keys(), "p_, wk_, xv_")
+ list(self.auxfns.keys()), "p_, wk_, xv_")
parseFunc = addParToCall
else:
parseFunc = self._processSpecialC
@@ -1523,15 +1516,15 @@
parseFunc)
self._protected_reusenames = new_protected
reusedefs = {}.fromkeys(new_protected)
- for vname, deflist in reused.iteritems():
+ for vname, deflist in reused.items():
for d in deflist:
reusedefs[d[2]] = d
- return (concatStrDict(reusedefs, intersect(order, reusedefs.keys())),
+ return (concatStrDict(reusedefs, intersect(order, list(reusedefs.keys()))),
specupdated)
def _genAuxFnC(self):
- auxnames = self._auxfnspecs.keys()
+ auxnames = list(self._auxfnspecs.keys())
# parameter and variable definitions
# sorted version of var and par names sorted version of par
# names (vars not #define'd in aux functions unless Jacobian)
@@ -1553,21 +1546,21 @@
auxspec = self._auxfnspecs[auxname]
assert len(auxspec) == 2, 'auxspec tuple must be of length 2'
if not isinstance(auxspec[0], list):
- print "Found type ", type(auxspec[0])
- print "Containing: ", auxspec[0]
+ print("Found type ", type(auxspec[0]))
+ print("Containing: ", auxspec[0])
raise TypeError('aux function arguments '
'must be given as a list')
if not isinstance(auxspec[1], str):
- print "Found type ", type(auxspec[1])
- print "Containing: ", auxspec[1]
+ print("Found type ", type(auxspec[1]))
+ print("Containing: ", auxspec[1])
raise TypeError('aux function specification '
'must be a string of the function code')
# Process Jacobian functions specially, if present
if auxname == 'Jacobian':
sig = "void jacobian("
if not compareList(auxspec[0],['t']+self.vars):
- print ['t']+self.vars
- print "Auxspec =", auxspec[0]
+ print(['t']+self.vars)
+ print("Auxspec =", auxspec[0])
raise ValueError("Invalid argument list given in Jacobian.")
if any([pt in auxspec[1] for pt in ('^', '**')]):
auxstr = convertPowers(auxspec[1], 'pow')
@@ -1609,8 +1602,8 @@
elif auxname == 'Jacobian_pars':
sig = "void jacobianParam("
if not compareList(auxspec[0],['t']+self.vars):
- print ['t']+self.vars
- print "Auxspec =", auxspec[0]
+ print(['t']+self.vars)
+ print("Auxspec =", auxspec[0])
raise ValueError("Invalid argument list given in Jacobian.")
parlist = "unsigned n_, unsigned np_, double t, double *Y_,"
if any([pt in auxspec[1] for pt in ('^', '**')]):
@@ -1633,7 +1626,7 @@
"'[' character invalid in Jacobian for 1D system"
assert ']' not in auxstr, \
"']' character invalid in Jacobian for 1D system"
- specdict_temp[self.vars.values()[0]] = auxstr
+ specdict_temp[list(self.vars.values())[0]] = auxstr
else:
specdict_temp = parseMatrixStrToDictStr(auxstr, self.vars, m)
reusestr, body_processed_dict = self._processReusedC(self.vars,
@@ -1650,7 +1643,7 @@
body_processed += "f_[" + str(col) + "][" + str(row) \
+ "] = " + specdict[self.vars[row]][col] + ";\n"
except (IndexError, KeyError):
- print "\nFound matrix:\n"
+ print("\nFound matrix:\n")
info(specdict)
raise ValueError("Jacobian should be %sx%s"%(m,n))
body_processed += "\n"
@@ -1677,7 +1670,7 @@
"'[' character invalid in mass matrix for 1D system"
assert ']' not in auxstr, \
"']' character invalid in mass matrix for 1D system"
- specdict_temp[specvars.values()[0]] = auxstr
+ specdict_temp[list(specvars.values())[0]] = auxstr
else:
specdict_temp = parseMatrixStrToDictStr(auxstr, specvars, m)
reusestr, body_processed_dict = self._processReusedC(specvars,
@@ -1790,7 +1783,7 @@
# temporary placeholders for these built-ins...
cases_ic = ""
cases_index = ""
- for i in xrange(len(self.vars)):
+ for i in range(len(self.vars)):
if i == 0:
command = 'if'
else:
@@ -1801,7 +1794,7 @@
cases_index += " " + command + " (strcmp(name, " + '"' + vname + '"'\
+ ")==0)\n\treturn " + str(i) + ";\n"
# add remaining par names for getindex
- for i in xrange(len(self.pars)):
+ for i in range(len(self.pars)):
pname = self.pars[i]
cases_index += " else if" + " (strcmp(name, " + '"' + pname + '"'\
+")==0)\n\treturn " + str(i+len(self.vars)) + ";\n"
@@ -1828,7 +1821,7 @@
assert self.targetlang == 'c', ('Wrong target language for this'
' call')
assert self.varspecs != {}, 'varspecs attribute must be defined'
- specnames_unsorted = self.varspecs.keys()
+ specnames_unsorted = list(self.varspecs.keys())
_vbfs_inv = invertMap(self._varsbyforspec)
# Process state variable specifications
if len(_vbfs_inv) > 0:
@@ -1864,7 +1857,7 @@
assert self.vars == specname_vars, ('Mismatch between declared '
' variable names and varspecs keys')
valid_depTargNames = self.inputs+self.vars+self.auxvars
- for specname, specstr in self.varspecs.iteritems():
+ for specname, specstr in self.varspecs.items():
assert type(specstr)==str, "Specification for %s was not a string"%specname
if any([pt in specstr for pt in ('^', '**')]):
specstr = convertPowers(specstr, 'pow')
@@ -1921,13 +1914,13 @@
+ reusestr + "\n"
auxdefs_parsed = {}
# add function body
- for i in xrange(len(specnames)):
+ for i in range(len(specnames)):
xname = specnames[i]
fbody = self.varspecs[xname]
fbody_parsed = self._processSpecialC(fbody)
if self.auxfns:
fbody_parsed = addArgToCalls(fbody_parsed,
- self.auxfns.keys(),
+ list(self.auxfns.keys()),
"p_, wk_, xv_")
if 'initcond' in self.auxfns:
# convert 'initcond(x)' to 'initcond("x")' for
@@ -2024,7 +2017,7 @@
# ------------ Matlab code specifications -----------------------
def _genAuxFnMatlab(self):
- auxnames = self.auxfns.keys()
+ auxnames = list(self.auxfns.keys())
# parameter and variable definitions
# sorted version of var and par names sorted version of par
@@ -2044,16 +2037,16 @@
# else we add these extra pars automatically to
# every call found in the .c code (as is done currently.
# this is still an untidy solution, but there you go...)
- for auxname, auxspec in self._auxfnspecs.iteritems():
+ for auxname, auxspec in self._auxfnspecs.items():
assert len(auxspec) == 2, 'auxspec tuple must be of length 2'
if not isinstance(auxspec[0], list):
- print "Found type ", type(auxspec[0])
- print "Containing: ", auxspec[0]
+ print("Found type ", type(auxspec[0]))
+ print("Containing: ", auxspec[0])
raise TypeError('aux function arguments '
'must be given as a list')
if not isinstance(auxspec[1], str):
- print "Found type ", type(auxspec[1])
- print "Containing: ", auxspec[1]
+ print("Found type ", type(auxspec[1]))
+ print("Containing: ", auxspec[1])
raise TypeError('aux function specification '
'must be a string of the function code')
## assert auxspec[1].find('^') == -1, ('carat character ^ is not '
@@ -2105,7 +2098,7 @@
assert self.targetlang == 'matlab', ('Wrong target language for this'
' call')
assert self.varspecs != {}, 'varspecs attribute must be defined'
- specnames_unsorted = self.varspecs.keys()
+ specnames_unsorted = list(self.varspecs.keys())
specname_vars = intersect(self.vars, specnames_unsorted)
specname_vars.sort()
# parameter and variable definitions
@@ -2119,7 +2112,7 @@
assert self.vars == specname_vars, ('Mismatch between declared '
' variable names and varspecs keys')
valid_depTargNames = self.inputs+self.vars+self.auxvars
- for specname, specstr in self.varspecs.iteritems():
+ for specname, specstr in self.varspecs.items():
assert type(specstr)==str, "Specification for %s was not a string"%specname
if any([pt in specstr for pt in ('pow', '**')]):
specstr = convertPowers(specstr, '^')
@@ -2152,13 +2145,13 @@
specstr += (len(reusestr)>0)*"% reused term definitions \n" \
+ reusestr + "\n"
# add function body
- for i in xrange(len(specnames)):
+ for i in range(len(specnames)):
xname = specnames[i]
fbody = self.varspecs[xname]
fbody_parsed = self._processIfMatlab(fbody)
if self.auxfns:
fbody_parsed = addArgToCalls(fbody_parsed,
- self.auxfns.keys(),
+ list(self.auxfns.keys()),
"p_")
# if 'initcond' in self.auxfns:
# convert 'initcond(x)' to 'initcond("x")' for
@@ -2179,7 +2172,7 @@
if self.auxfns:
def addParToCall(s):
- return addArgToCalls(s, self.auxfns.keys(), "p_")
+ return addArgToCalls(s, list(self.auxfns.keys()), "p_")
parseFunc = addParToCall
else:
parseFunc = idfn
@@ -2190,10 +2183,10 @@
parseFunc)
self._protected_reusenames = new_protected
reusedefs = {}.fromkeys(new_protected)
- for vname, deflist in reused.iteritems():
+ for vname, deflist in reused.items():
for d in deflist:
reusedefs[d[2]] = d
- return (concatStrDict(reusedefs, intersect(order, reusedefs.keys())),
+ return (concatStrDict(reusedefs, intersect(order, list(reusedefs.keys()))),
specupdated)
# NEED TO CHECK WHETHER THIS IS NECESSARY AND WORKS
# IF STATEMENTS LOOK DIFFERENT IN MATLAB
@@ -2209,7 +2202,7 @@
def _prepareMatlabPDefines(self, pnames):
pardefines = ""
- for i in xrange(len(pnames)):
+ for i in range(len(pnames)):
p = pnames[i]
pardefines += "\t" + p + " = p_(" + str(i+1) + ");\n"
@@ -2219,7 +2212,7 @@
def _prepareMatlabVDefines(self, vnames):
vardefines = ""
- for i in xrange(len(vnames)):
+ for i in range(len(vnames)):
v = vnames[i]
vardefines += "\t" + v + " = x_(" + str(i+1) + ");\n"
alldefines = "\n% Variable definitions\n\n" + vardefines
@@ -2274,7 +2267,7 @@
return outputStr
def info(self, verbose=0):
- print self._infostr(verbose)
+ print(self._infostr(verbose))
def __repr__(self):
return self._infostr(verbose=0)
@@ -2332,8 +2325,8 @@
# establish order for reusable terms, in case of inter-dependencies
are_dependent = []
deps = {}
- for origterm, rterm in reuseterms.iteritems():
- for ot, rt in reuseterms.iteritems():
+ for origterm, rterm in reuseterms.items():
+ for ot, rt in reuseterms.items():
if proper_match(origterm, rt):
if rterm not in are_dependent:
are_dependent.append(rterm)
@@ -2342,12 +2335,12 @@
except KeyError:
# new list
deps[rterm] = [rt]
- order = remain(reuseterms.values(), are_dependent) + are_dependent
+ order = remain(list(reuseterms.values()), are_dependent) + are_dependent
for specname in specnames:
reused[specname] = []
specstr = specdict[specname]
repeatkeys = []
- for origterm, repterm in reuseterms.iteritems():
+ for origterm, repterm in reuseterms.items():
# only add definitions if string found
if proper_match(specstr, origterm):
specstr = specstr.replace(origterm, repterm)
@@ -2380,7 +2373,7 @@
# just log the definitions that will be needed without replacing
# any strings.
if reused[specname] == [] and len(reuseterms) > 0:
- for origterm, repterm in reuseterms.iteritems():
+ for origterm, repterm in reuseterms.items():
# add definition if *replacement* string found in specs
if proper_match(specstr, repterm) and repterm not in seenrepterms:
reused[specname].append([indentstr,
@@ -2471,10 +2464,10 @@
"""
changed_fns = []
new_fnspecs = {}
- for fname, (fargs, fRefactoringTool: Refactored ./PyDSTool/Events.py
spec) in fnspecs.iteritems():
+ for fname, (fargs, fspec) in fnspecs.items():
common_names = intersect(fargs, parnames)
if fname in parnames:
- print "Problem with function definition", fname
+ print("Problem with function definition", fname)
raise ValueError("Unrecoverable clash between parameter names and aux fn name")
if common_names == []:
new_fnspecs[fname] = (fargs, fspec)
@@ -2483,7 +2476,7 @@
new_fnspecs[fname] = (remain(fargs, parnames), fspec)
new_varspecs = {}
- for vname, vspec in varspecs.iteritems():
+ for vname, vspec in varspecs.items():
q = QuantSpec('__temp__', vspec)
# only update use of functions both changed and used in the varspecs
used_fns = intersect(q.parser.tokenized, changed_fns)
@@ -2507,7 +2500,7 @@
if any([p in qarg for p in parnames]):
# do not put raw parameter name arguments into new arg list
#raise ValueError("Cannot process argument to aux fn %s"%f)
- print "Warning: some auxiliary function parameters clash in function %s" %f
+ print("Warning: some auxiliary function parameters clash in function %s" %f)
new_args_list.append(arg)
elif arg not in parnames:
# do not put raw parameter name arguments into new arg list
@@ -2526,8 +2519,8 @@
try:
f = open(specfilename, 'r')
s = f.read()
- except IOError, e:
- print 'File error:', str(e)
+ except IOError as e:
+ print('File error:', str(e))
raise
f.close()
return s
--- ./PyDSTool/Events.py (original)
+++ ./PyDSTool/Events.py (refactored)
@@ -9,20 +9,21 @@
"""
# PyDSTool imports
-from Variable import *
-from utils import *
-from common import *
-from parseUtils import *
-from errors import *
-from Interval import *
-from utils import info as utils_info
-from Symbolic import QuantSpec, Var, ensureStrArgDict
-import FuncSpec
+from .Variable import *
+from .utils import *
+from .common import *
+from .parseUtils import *
+from .errors import *
+from .Interval import *
+from .utils import info as utils_info
+from .Symbolic import QuantSpec, Var, ensureStrArgDict
+from . import FuncSpec
# Other imports
import scipy, numpy, scipy, scipy.special
import math, random
import copy, types
+from functools import reduce
__all__ = ['EventStruct', 'Event',
'HighLevelEvent', 'LowLevelEvent', 'MatlabEvent',
@@ -110,7 +111,7 @@
if ev.name not in self.events:
self.events[ev.name] = ev
else:
- print self
+ print(self)
raise ValueError("Event name '"+ev.name+"' already present "
"in database")
elif isinstance(ev,list):
@@ -139,65 +140,65 @@
def getHighLevelEvents(self):
hlList = []
- for epair in self.events.items():
+ for epair in list(self.events.items()):
if isinstance(epair[1], HighLevelEvent):
hlList.append(epair)
return hlList
def getLowLevelEvents(self):
llList = []
- for epair in self.events.items():
+ for epair in list(self.events.items()):
if isinstance(epair[1], LowLevelEvent):
llList.append(epair)
return llList
def getAllEvents(self):
- return self.events.items()
+ return list(self.events.items())
def getTermEvents(self):
teList = []
- for epair in self.events.items():
+ for epair in list(self.events.items()):
if epair[1].termFlag:
teList.append(epair)
return teList
def getNonTermEvents(self):
neList = []
- for epair in self.events.items():
+ for epair in list(self.events.items()):
if not epair[1].termFlag:
neList.append(epair)
return neList
def getActiveEvents(self):
neList = []
- for epair in self.events.items():
+ for epair in list(self.events.items()):
if epair[1].activeFlag:
neList.append(epair)
return neList
def getNonActiveEvents(self):
neList = []
- for epair in self.events.items():
+ for epair in list(self.events.items()):
if not epair[1].activeFlag:
neList.append(epair)
return neList
def getNonPreciseEvents(self):
neList = []
- for epair in self.events.items():
+ for epair in list(self.events.items()):
if not epair[1].preciseFlag:
neList.append(epair)
return neList
def getPreciseEvents(self):
neList = []
- for epair in self.events.items():
+ for epair in list(self.events.items()):
if epair[1].preciseFlag:
neList.append(epair)
return neList
def setglobalt0(self, t0):
- for epair in self.events.items():
+ for epair in list(self.events.items()):
epair[1].globalt0 = t0
def query(self, keylist, eventlist=None):
@@ -216,11 +217,11 @@
if self.events == {}:
return []
else:
- eventlist = self.events.items()
+ eventlist = list(self.events.items())
if filterFuncs == []:
return []
for f in filterFuncs:
- eventlist = filter(f, eventlist)
+ eventlist = list(filter(f, eventlist))
return eventlist
@@ -235,7 +236,7 @@
utils_info(self.__dict__, "EventStruct",
recurseDepthLimit=1+verboselevel)
else:
- print self.__repr__()
+ print(self.__repr__())
def __contains__(self, evname):
@@ -250,8 +251,8 @@
eventlist=None):
if eventlist is None:
eventlist = self.query(['highlevel', 'active', 'notvarlinked'])
- return filter(lambda (n,e): e(t=tval, varDict=varDict,
- parDict=parDict), eventlist)
+ return [n_e for n_e in eventlist if n_e[1](t=tval, varDict=varDict,
+ parDict=parDict)]
def resetHighLevelEvents(self, t0, eventlist=None, state=None):
@@ -273,9 +274,9 @@
for ev in eventlist:
if isinstance(ev[1], HighLevelEvent):
if not reduce(bool.__and__, [key in database for key in \
- ev[1].vars.keys()]):
- ek = ev[1].vars.keys()
- print "Missing keys: ", remain(ek, database)
+ list(ev[1].vars.keys())]):
+ ek = list(ev[1].vars.keys())
+ print("Missing keys: ", remain(ek, database))
raise RuntimeError("Invalid keys in event '%s'" % ev[0])
#else:
# print "Warning: Low level events should not be passed to " \
@@ -286,10 +287,10 @@
def setTermFlag(self, eventTarget, flagval):
if isinstance(flagval, bool):
if isinstance(eventTarget, list):
- for evTarg in intersect(eventTarget, self.events.keys()):
+ for evTarg in intersect(eventTarget, list(self.events.keys())):
self.events[evTarg].termFlag = flagval
else:
- if eventTarget in self.events.keys():
+ if eventTarget in list(self.events.keys()):
self.events[eventTarget].termFlag = flagval
else:
raise TypeError("Invalid flag type")
@@ -298,10 +299,10 @@
def setActiveFlag(self, eventTarget, flagval):
if isinstance(flagval, bool):
if isinstance(eventTarget, list):
- for evTarg in intersect(eventTarget, self.events.keys()):
+ for evTarg in intersect(eventTarget, list(self.events.keys())):
self.events[evTarg].activeFlag = flagval
else:
- if eventTarget in self.events.keys():
+ if eventTarget in list(self.events.keys()):
self.events[eventTarget].activeFlag = flagval
else:
raise TypeError("Invalid flag type")
@@ -309,10 +310,10 @@
def setPreciseFlag(self, eventTarget, flagval):
if isinstance(flagval, bool):
if isinstance(eventTarget, list):
- for evTarg in intersect(eventTarget, self.events.keys()):
+ for evTarg in intersect(eventTarget, list(self.events.keys())):
self.events[evTarg].preciseFlag = flagval
else:
- if eventTarget in self.events.keys():
+ if eventTarget in list(self.events.keys()):
self.events[eventTarget].preciseFlag = flagval
else:
raise TypeError("Invalid flag type")
@@ -320,14 +321,14 @@
def setEventICs(self, eventTarget, val):
if isinstance(val, dict):
if isinstance(eventTarget, list):
- for evTarg in intersect(eventTarget, self.events.keys()):
- for name in val.keys():
- if name in self.events[evTarg].initialconditions.keys():
+ for evTarg in intersect(eventTarget, list(self.events.keys())):
+ for name in list(val.keys()):
+ if name in list(self.events[evTarg].initialconditions.keys()):
self.events[evTarg].initialconditions[name] = val[name]
else:
- if eventTarget in self.events.keys():
- for name in val.keys():
- if name in self.events[eventTarget].initialconditions.keys():
+ if eventTarget in list(self.events.keys()):
+ for name in list(val.keys()):
+ if name in list(self.events[eventTarget].initialconditions.keys()):
self.events[eventTarget].initialconditions[name] = val[name]
else:
raise TypeError("Invalid ICs type -- must be dict of varname, value pairs")
@@ -336,10 +337,10 @@
def setEventDelay(self, eventTarget, val):
if isinstance(val, int) or isinstance(val, float):
if isinstance(eventTarget, list):
- for evTarg in intersect(eventTarget, self.events.keys()):
+ for evTarg in intersect(eventTarget, list(self.events.keys())):
self.events[evTarg].eventdelay = val
else:
- if eventTarget in self.events.keys():
+ if eventTarget in list(self.events.keys()):
self.events[eventTarget].eventdelay = val
else:
raise TypeError("Invalid eventdelay type/value")
@@ -347,10 +348,10 @@
def setEventInterval(self, eventTarget, val):
if isinstance(val, int) or isinstance(val, float):
if isinstance(eventTarget, list):
- for evTarg in intersect(eventTarget, self.events.keys()):
+ for evTarg in intersect(eventTarget, list(self.events.keys())):
self.events[evTarg].eventinterval = val
else:
- if eventTarget in self.events.keys():
+ if eventTarget in list(self.events.keys()):
self.events[eventTarget].eventinterval = val
else:
raise TypeError("Invalid eventinterval type/value")
@@ -358,10 +359,10 @@
def setEventTol(self, eventTarget, val):
if val > 0:
if isinstance(eventTarget, list):
- for evTarg in intersect(eventTarget, self.events.keys()):
+ for evTarg in intersect(eventTarget, list(self.events.keys())):
self.events[evTarg].eventtol = val
else:
- if eventTarget in self.events.keys():
+ if eventTarget in list(self.events.keys()):
self.events[eventTarget].eventtol = val
else:
raise TypeError("Invalid eventtol type/value")
@@ -369,10 +370,10 @@
def setEventDir(self, eventTarget, val):
if val in [-1,0,1] and isinstance(val, int):
if isinstance(eventTarget, list):
- for evTarg in intersect(eventTarget, self.events.keys()):
+ for evTarg in intersect(eventTarget, list(self.events.keys())):
self.events[evTarg].dircode = val
else:
- if eventTarget in self.events.keys():
+ if eventTarget in list(self.events.keys()):
self.events[eventTarget].dircode = val
else:
raise TypeError("Invalid eventdir type/value")
@@ -380,10 +381,10 @@
def setStartTime(self, eventTarget, val):
if isinstance(val, int) or isinstance(val, float):
if isinstance(eventTarget, list):
- for evTarg in intersect(eventTarget, self.events.keys()):
+ for evTarg in intersect(eventTarget, list(self.events.keys())):
self.events[evTarg].starttime = val
else:
- if eventTarget in self.events.keys():
+ if eventTarget in list(self.events.keys()):
self.events[eventTarget].starttime = val
else:
raise TypeError("Invalid starttime type")
@@ -392,10 +393,10 @@
def setBisect(self, eventTarget, val):
if isinstance(val, int) and val > 0:
if isinstance(eventTarget, list):
- for evTarg in intersect(eventTarget, self.events.keys()):
+ for evTarg in intersect(eventTarget, list(self.events.keys())):
self.events[evTarg].bisectlimit = val
else:
- if eventTarget in self.events.keys():
+ if eventTarget in list(self.events.keys()):
self.events[eventTarget].bisectlimit = val
else:
raise TypeError("Invalid bisectlimit type/value")
@@ -463,7 +464,7 @@
self.dircode = kw['dircode']
assert self.dircode in [-1, 0, 1] # direction codes
except AssertionError:
- print 'invalid value for direction code -- must be -1, 0, or 1'
+ print('invalid value for direction code -- must be -1, 0, or 1')
raise
except KeyError:
self.dircode = 0
@@ -492,7 +493,7 @@
self.vars = kw['vars']
assert len(self.vars) > 0, 'vars dictionary must be non-empty'
if reduce(bool.__and__, [isinstance(var, Variable) for \
- var in self.vars.itervalues()]):
+ var in self.vars.values()]):
self.varlinked = True
# doesn't check that only argument is spec'd for _fn method
else:
@@ -605,7 +606,7 @@
def info(self, verboselevel=1):
- print self._infostr(verboselevel)
+ print(self._infostr(verboselevel))
def __repr__(self):
@@ -618,37 +619,37 @@
# clean up FuncSpec usage of parsinps and x for pars/inputs and
# variables
try:
- exec self._funcstr
+ exec(self._funcstr)
except:
- print 'Invalid event function definition:'
- print self._funcstr
+ print('Invalid event function definition:')
+ print(self._funcstr)
raise
try:
setattr(self, '_fn', types.MethodType(locals()[self._funcname],
self, self.__class__))
except KeyError:
- print 'Must pass objective function for event at initialization'
+ print('Must pass objective function for event at initialization')
raise
if '_fn' not in self._funcreg:
self._funcreg.append('_fn')
# _fnspecs keys are convenient, user-readable, short-hand names
# for the functions, whose actual function names are the second entry
# of the pair funcstr
- for funcpair in self._fnspecs.values():
+ for funcpair in list(self._fnspecs.values()):
# clean up FuncSpec usage of parsinps and x for pars/inputs and
# variables
try:
- exec funcpair[0]
+ exec(funcpair[0])
except:
- print 'Invalid auxiliary function definition:'
- print funcpair[0]
+ print('Invalid auxiliary function definition:')
+ print(funcpair[0])
raise
try:
setattr(self, funcpair[1], types.MethodType(locals()[funcpair[1]],
self,
self.__class__))
except KeyError:
- print 'Must pass objective function for event at initialization'
+ print('Must pass objective function for event at initialization')
raise
if funcpair[1] not in self._funcreg:
self._funcreg.append(funcpair[1])
@@ -690,7 +691,7 @@
try:
self.fval = self._fn(t, parDict)
except:
- print "Error in event", self.name
+ print("Error in event", self.name)
info(parDict, "Parameters")
raise
self.prevsign = scipy.sign(self.fval)
@@ -700,7 +701,7 @@
try:
self.fval = self._fn(t, parDict)
except:
- print "Error in event", self.name
+ print("Error in event", self.name)
info(parDict, "Parameters")
raise
sval = scipy.sign(self.fval)
@@ -729,9 +730,9 @@
try:
self.fval = self._fn(varDict_temp, parDict)
except:
- print "Error in event", self.name
+ print("Error in event", self.name)
info(parDict, "Parameters")
- print "\n"
+ print("\n")
info(varDict_temp, "Variables")
raise
self.prevsign = scipy.sign(self.fval)
@@ -741,9 +742,9 @@
try:
self.fval = self._fn(varDict_temp, parDict)
except:
- print "Error in event", self.name
+ print("Error in event", self.name)
info(parDict, "Parameters")
- print "\n"
+ print("\n")
info(varDict_temp, "Variables")
raise
sval = scipy.sign(self.fval)
@@ -790,7 +791,7 @@
varDict = vars
precise = self.preciseFlag
try:
- for var in varDict.itervalues():
+ for var in varDict.values():
if isdiscrete(var):
discretevars = True
elif iscontinuous(var):
@@ -798,23 +799,23 @@
else:
raise TypeError('varDict must consist of Variable objects')
except AttributeError:
- print 'event must contain a dictionary of vars'
+ print('event must contain a dictionary of vars')
raise
if discretevars and continuousvars:
raise TypeError('Cannot mix discrete and continuous Variable types')
if discretevars:
if precise:
- print 'argument precise cannot be used for discrete Variable objects'
+ print('argument precise cannot be used for discrete Variable objects')
precise = False
- varnames = varDict.keys()
+ varnames = list(varDict.keys())
if dt is not None:
- print 'argument dt is unused for discrete Variable objects'
+ print('argument dt is unused for discrete Variable objects')
if trange is not None:
# trange had better be contained in all var.indepdomain ranges
assert len(varDict) > 0, 'varDict was empty!'
if not reduce(bool.__and__, [trange[0] in var.indepdomain \
and trange[1] in var.indepdomain for var \
- in varDict.itervalues()]):
+ in varDict.values()]):
raise ValueError('trange not contained in all var ranges')
else:
raise ValueError('trange must be defined for discrete'
@@ -824,7 +825,7 @@
elif continuousvars:
# trange had better be contained in all var.indepdomain ranges
tlimits = None # initial value
- for var in varDict.itervalues():
+ for var in varDict.values():
if tlimits is None:
tlimits = var.indepdomain.get()
else:
@@ -863,7 +864,7 @@
pidict = copy.copy(ps)
try:
for t in ts:
- idict = dict([(n,i(t+globalt0)) for n,i in inputs.iteritems()])
+ idict = dict([(n,i(t+globalt0)) for n,i in inputs.items()])
pidict.update(idict)
fvals.append(self._fn(t, pidict))
except TypeError:
@@ -872,18 +873,18 @@
try:
tvals = array(ts)+globalt0
except:
- print "\n Found type", type(ts)
+ print("\n Found type", type(ts))
raise TypeError("t values invalid")
- idict = dict([(n,i(tvals)) for n,i in inputs.iteritems()])
+ idict = dict([(n,i(tvals)) for n,i in inputs.items()])
pidict.update(idict)
fvals = self._fn(ts, pidict)
return fvals
def self_caller(t=None, varDict=None, parDict=None):
if parDict is None:
- pidict = dict([(n,i(t+globalt0)) for n,i in inputs.iteritems()])
+ pidict = dict([(n,i(t+globalt0)) for n,i in inputs.items()])
else:
pidict = copy.copy(parDict)
- pidict.update(dict([(n,i(t+globalt0)) for n,i in inputs.iteritems()]))
+ pidict.update(dict([(n,i(t+globalt0)) for n,i in inputs.items()]))
return self(t, varDict=varDict, parDict=pidict)
# before search, check that start after 'eventdelay', if option set
if eventdelay:
@@ -928,11 +929,11 @@
restore_val = self.eventdelay
self.eventdelay = 0.
boollist = []
- for tix in xrange(len(tlist)):
+ for tix in range(len(tlist)):
boollist.append(self_caller(t=tlist[tix],
- varDict=dict(zip(varnames,
+ varDict=dict(list(zip(varnames,
[vallist[i][tix] for\
- i in range(len(vallist))])),
+ i in range(len(vallist))]))),
parDict=parDict))
# first bool may be True because event hasn't been called
# before and has prevsign unset (or mis-set)...
@@ -942,12 +943,12 @@
if not eventdelay:
# restore value for future use
self.eventdelay = restore_val
- except KeyError, e:
+ except KeyError as e:
# for discretevars if not all var.indepdomains equal over trange
if discretevars:
- print 'Note: All discrete Variables must have identical ' \
- 'independent variable domains over trange'
- print "Check that all variable references in events are legitimate"
+ print('Note: All discrete Variables must have identical ' \
+ 'independent variable domains over trange')
+ print("Check that all variable references in events are legitimate")
raise
# loop through boollist and find all events unless terminating at tpos!
tpos = -1
@@ -1045,7 +1046,7 @@
necessary temporary variable declarations and a return statement."""
def __init__(self, kw):
if 'vars' in kw:
- for v in kw['vars'].itervalues():
+ for v in kw['vars'].values():
if v is not None:
raise TypeError("Low level events cannot be linked to a"
" variable")
@@ -1056,8 +1057,8 @@
dummyQ = QuantSpec('dummy', LLfuncstr, preserveSpace=True)
dummyQ.mapNames({'abs': 'fabs', 'sign': 'signum', 'mod': 'fmod'})
if dummyQ[0] != 'return':
- print "Found: ", dummyQ[0]
- print "in event specification: ", dummyQ()
+ print("Found: ", dummyQ[0])
+ print("in event specification: ", dummyQ())
raise ValueError("'return' must be first token in low level "
"event specification")
# take out 'return' from tokenized because whitespace will be lost
@@ -1076,7 +1077,7 @@
necessary temporary variable declarations."""
def __init__(self, kw):
if 'vars' in kw:
- for v in kw['vars'].itervalues():
+ for v in kw['vars'].values():
if v is not None:
raise TypeError("Low level events cannot be linked to a variable")
kw['noHighLevel'] = True
@@ -1086,8 +1087,8 @@
LLfuncstr = kw['Matlabfuncspec']
dummyQ = QuantSpec('dummy', LLfuncstr, preserveSpace=True)
if dummyQ[0] != 'return':
- print "Found: ", dummyQ[0]
- print "in event specification: ", dummyQ()
+ print("Found: ", dummyQ[0])
+ print("in event specification: ", dummyQ())
raise ValueError("'return' must be first token in low level "
"event specification")
# take out 'return' from tokenized because whitespace will be lost
@@ -1337,8 +1338,8 @@
expr = dummyfuncspec._processSpecialC(expr)
for arg in newargs:
if arg in argDict:
- print 'Warning: `' + arg + '` already appears in argDict!'
- print ' This value will be overwritten.'
+ print('Warning: `' + arg + '` already appears in argDict!')
+ print(' This value will be overwritten.')
argDict_out = copy.copy(argDict)
funcname = "_f_"+exprname+"_ud"
if parnames == []:
@@ -1402,8 +1403,8 @@
newargs = ['dircode', 'funcspec', 'vars']
for arg in newargs:
if arg in argDict:
- print 'Warning: `' + arg + '` already appears in argDict!'
- print ' This value will be overwritten.'
+ print('Warning: `' + arg + '` already appears in argDict!')
+ print(' This value will be overwritten.')
if isinstance(varname, Var):
# supporting a Variable object
varname = varname.name
@@ -1491,10 +1492,10 @@
dopars=dopars, doinps=doinps,
illegal=illegal)
reusedefs = {}.fromkeys(new_protected)
- for vname, deflist in reusedParsed.iteritems():
+ for vname, deflist in reusedParsed.items():
for d in deflist:
reusedefs[d[2]] = d
- return (concatStrDict(reusedefs, intersect(order,reusedefs.keys())),
+ return (concatStrDict(reusedefs, intersect(order,list(reusedefs.keys()))),
specupdated)
@@ -1507,10 +1508,10 @@
reuseterms,
'', 'double', ';')
reusedefs = {}.fromkeys(new_protected)
- for vname, deflist in reused.iteritems():
+ for vname, deflist in reused.items():
for d in deflist:
reusedefs[d[2]] = d
- return (concatStrDict(reusedefs, intersect(order, reusedefs.keys())),
+ return (concatStrDict(reusedefs, intersect(order, list(reusedefs.keys()))),
specupdated)
@@ -1523,10 +1524,10 @@
reuseterms,
'', '', ';')
reusedefs = {}.fromkeys(new_protected)
- for vname, deflist in reused.iteritems():
+ for vname, deflist in reused.items():
for d in deflist:
reusedefs[d[2]] = d
- return (concatStrDict(reusedefs, intersect(order, reusedefs.keys())),
+ return (concatStrDict(reusedefs, intersect(order, list(reusedefs.keys()))),
specupdated)
@@ -1568,10 +1569,10 @@
else:
def test_fn(x, p):
if p is None:
- pidict = dict([(n,i(t+globalt0)) for n,i in inputs.iteritems()])
+ pidict = dict([(n,i(t+globalt0)) for n,i in inputs.items()])
else:
pidict = copy.copy(p)
- pidict.update(dict([(n,i(t+globalt0)) for n,i in inputs.iteritems()]))
+ pidict.update(dict([(n,i(t+globalt0)) for n,i in inputs.items()]))
return ev._fn(t, pidict)
else:
if quadratic_interp is not None:
@@ -1579,16 +1580,16 @@
else:
def test_fn(x, p):
if p is None:
- pidict = dict([(n,i(x['t']+globalt0)) for n,i in inputs.iteritems()])
+ pidict = dict([(n,i(x['t']+globalt0)) for n,i in inputs.items()])
else:
pidict = copy.copy(p)
- pidict.update(dict([(n,i(x['t']+globalt0)) for n,i in inputs.iteritems()]))
+ pidict.update(dict([(n,i(x['t']+globalt0)) for n,i in inputs.items()]))
return ev._fn(x, pidict)
if ev.varlinked:
assert vars is None, ("Only pass vars argument when event is not "
"linked to a variable")
assert reduce(bool.__and__, [iscontinuous(var) \
- for var in ev.vars.itervalues()]), \
+ for var in ev.vars.values()]), \
'Only pass continously-defined Variables in event'
elo = test_fn(tlo, parDict)
ehi = test_fn(thi, parDict)
@@ -1624,11 +1625,11 @@
assert vars is not None, ("vars argument is required when event is not"
" linked to a variable")
assert reduce(bool.__and__, [iscontinuous(var) \
- for var in vars.itervalues()]), \
+ for var in vars.values()]), \
'Only pass continously-defined Variables'
varnames = sortedDictKeys(vars)+['t']
- dlo = dict(zip(varnames, [v(tlo) for v in sortedDictValues(vars)]+[tlo]))
- dhi = dict(zip(varnames, [v(thi) for v in sortedDictValues(vars)]+[thi]))
+ dlo = dict(list(zip(varnames, [v(tlo) for v in sortedDictValues(vars)]+[tlo])))
+ dhi = dict(list(zip(varnames, [v(thi) for v in sortedDictValues(vars)]+[thi])))
elo = test_fn(dlo, parDict)
ehi = test_fn(dhi, parDict)
if elo == 0:
@@ -1641,14 +1642,14 @@
a = tlo
b = thi
i = 1
- da = dict(zip(varnames, [v(a) for v in sortedDictValues(vars)]+[a]))
- db = dict(zip(varnames, [v(b) for v in sortedDictValues(vars)]+[b]))
+ da = dict(list(zip(varnames, [v(a) for v in sortedDictValues(vars)]+[a])))
+ db = dict(list(zip(varnames, [v(b) for v in sortedDictValues(vars)]+[b])))
eva = test_fn(da, parDict)
rootival = (a,b)
while i <= ev.bisectlimit:
d = RefactoringTool: Files that were modified:
RefactoringTool: ./PyDSTool/utils.py
RefactoringTool: ./PyDSTool/tests/vode_withJac_test.py
RefactoringTool: ./PyDSTool/tests/vode_event_test2.py
RefactoringTool: ./PyDSTool/tests/vode_event_test1.py
RefactoringTool: ./PyDSTool/tests/traj_gt0_test.py
RefactoringTool: ./PyDSTool/tests/test_variable_traj.py
RefactoringTool: ./PyDSTool/tests/test_pointsets.py
RefactoringTool: ./PyDSTool/tests/test_interval.py
RefactoringTool: ./PyDSTool/tests/test_hybrid_extinputs_Cintegrator.py
RefactoringTool: ./PyDSTool/tests/test_hybrid_extinputs.py
RefactoringTool: ./PyDSTool/tests/test_find_nearby_ball.py
RefactoringTool: ./PyDSTool/tests/test_context_spikes.py
RefactoringTool: ./PyDSTool/tests/test_bd_containment.py
RefactoringTool: ./PyDSTool/tests/splinetest.py
RefactoringTool: ./PyDSTool/tests/sloppycell_example.py
RefactoringTool: ./PyDSTool/tests/saveload_test.py
RefactoringTool: ./PyDSTool/tests/run_all_tests.py
RefactoringTool: ./PyDSTool/tests/radau_event_test.py
RefactoringTool: ./PyDSTool/tests/poly_interp_test.py
RefactoringTool: ./PyDSTool/tests/phaseplane_HHtest.py
RefactoringTool: ./PyDSTool/tests/pest_test4_Cintegrator.py
RefactoringTool: ./PyDSTool/tests/pest_test3_Cintegrator.py
RefactoringTool: ./PyDSTool/tests/pest_test3.py
RefactoringTool: ./PyDSTool/tests/pest_test2.py
RefactoringTool: ./PyDSTool/tests/pest_test1.py
RefactoringTool: ./PyDSTool/tests/objectdelete_test.py
RefactoringTool: ./PyDSTool/tests/numeric_diff_test.py
RefactoringTool: ./PyDSTool/tests/mapsystem_test.py
RefactoringTool: ./PyDSTool/tests/joe_pest.py
RefactoringTool: ./PyDSTool/tests/interp_vode_test.py
RefactoringTool: ./PyDSTool/tests/interp_piecewise_test.py
RefactoringTool: ./PyDSTool/tests/interp_dopri_test.py
RefactoringTool: ./PyDSTool/tests/imprecise_event_test.py
RefactoringTool: ./PyDSTool/tests/impfn_test.py
RefactoringTool: ./PyDSTool/tests/imp_load_test.py
RefactoringTool: ./PyDSTool/tests/funcspec_tests.py
RefactoringTool: ./PyDSTool/tests/freefinger_noforce_radau.py
RefactoringTool: ./PyDSTool/tests/forced_spring.py
RefactoringTool: ./PyDSTool/tests/fingermodel_vode.py
RefactoringTool: ./PyDSTool/tests/fingermodel_auxvartest.py
RefactoringTool: ./PyDSTool/tests/expfn_test.py
RefactoringTool: ./PyDSTool/tests/embedded_map_test.py
RefactoringTool: ./PyDSTool/tests/dopri_event_test.py
RefactoringTool: ./PyDSTool/tests/basic_gen_tests_C.py
RefactoringTool: ./PyDSTool/tests/basic_gen_tests.py
RefactoringTool: ./PyDSTool/tests/Tutorial_linear.py
RefactoringTool: ./PyDSTool/tests/Tutorial_compneuro.py
RefactoringTool: ./PyDSTool/tests/Tutorial_VdP.py
RefactoringTool: ./PyDSTool/tests/Tutorial_SymbolicJac.py
RefactoringTool: ./PyDSTool/tests/Tutorial_PredatorPrey.py
RefactoringTool: ./PyDSTool/tests/Tutorial_LorenzMap.py
RefactoringTool: ./PyDSTool/tests/Tutorial_Calcium.py
RefactoringTool: ./PyDSTool/tests/Symbolic_test.py
RefactoringTool: ./PyDSTool/tests/Symbolic_Diff_test.py
RefactoringTool: ./PyDSTool/tests/SLIP_plot.py
RefactoringTool: ./PyDSTool/tests/SLIP_2D_pdc.py
RefactoringTool: ./PyDSTool/tests/SLIP_2D_maps.py
RefactoringTool: ./PyDSTool/tests/SLIP_2D.py
RefactoringTool: ./PyDSTool/tests/PySCes_import_test.py
RefactoringTool: ./PyDSTool/tests/PyCont_vanDerPol.py
RefactoringTool: ./PyDSTool/tests/PyCont_hybrid_osc.py
RefactoringTool: ./PyDSTool/tests/PyCont_SaddleNode.py
RefactoringTool: ./PyDSTool/tests/PyCont_PredPrey.py
RefactoringTool: ./PyDSTool/tests/PyCont_NewLorenz.py
RefactoringTool: ./PyDSTool/tests/PyCont_MorrisLecar_TypeII.py
RefactoringTool: ./PyDSTool/tests/PyCont_MorrisLecar_TypeI.py
RefactoringTool: ./PyDSTool/tests/PyCont_Lorenz.py
RefactoringTool: ./PyDSTool/tests/PyCont_Logistic.py
RefactoringTool: ./PyDSTool/tests/PyCont_LevelCurve.py
RefactoringTool: ./PyDSTool/tests/PyCont_LPNeuron.py
RefactoringTool: ./PyDSTool/tests/PyCont_Hopfield.py
RefactoringTool: ./PyDSTool/tests/PyCont_HindmarshRose.py
RefactoringTool: ./PyDSTool/tests/PyCont_Hamiltonian.py
RefactoringTool: ./PyDSTool/tests/PyCont_DiscPredPrey.py
RefactoringTool: ./PyDSTool/tests/PyCont_Catalytic_demo.py
RefactoringTool: ./PyDSTool/tests/PyCont_Catalytic.py
RefactoringTool: ./PyDSTool/tests/PyCont_Brusselator.py
RefactoringTool: ./PyDSTool/tests/PyCont_ABReaction.py
RefactoringTool: ./PyDSTool/tests/PyCont_ABCReaction.py
RefactoringTool: ./PyDSTool/tests/PointInfo_test.py
RefactoringTool: ./PyDSTool/tests/NineML_import_test.py
RefactoringTool: ./PyDSTool/tests/MultiCompartments2.py
RefactoringTool: ./PyDSTool/tests/MultiCompartments.py
RefactoringTool: ./PyDSTool/tests/ModelSpec_test.py
RefactoringTool: ./PyDSTool/tests/ML_adjointPRC.py
RefactoringTool: ./PyDSTool/tests/IF_squarespike_model.py
RefactoringTool: ./PyDSTool/tests/IF_model_test.py
RefactoringTool: ./PyDSTool/tests/IF_delaynet_syn.py
RefactoringTool: ./PyDSTool/tests/IF_delaynet.py
RefactoringTool: ./PyDSTool/tests/HH_model_testbounds.py
RefactoringTool: ./PyDSTool/tests/HH_model_Cintegrator_testbounds.py
RefactoringTool: ./PyDSTool/tests/HH_model_Cintegrator.py
RefactoringTool: ./PyDSTool/tests/HH_model.py
RefactoringTool: ./PyDSTool/tests/HH_loaded_Cintegrator.py
RefactoringTool: ./PyDSTool/tests/HH_loaded.py
RefactoringTool: ./PyDSTool/tests/HH_adjointPRC.py
RefactoringTool: ./PyDSTool/tests/HH_DSSRTtest.py
RefactoringTool: ./PyDSTool/tests/Dopri_backwards_test.py
RefactoringTool: ./PyDSTool/tests/DAE_example.py
RefactoringTool: ./PyDSTool/tests/CIN.py
RefactoringTool: ./PyDSTool/scipy_ode.py
RefactoringTool: ./PyDSTool/parseUtils.py
RefactoringTool: ./PyDSTool/matplotlib_import.py
RefactoringTool: ./PyDSTool/integrator.py
RefactoringTool: ./PyDSTool/fixedpickle.py
RefactoringTool: ./PyDSTool/errors.py
RefactoringTool: ./PyDSTool/conf.py
RefactoringTool: ./PyDSTool/common.py
RefactoringTool: ./PyDSTool/__init__.py
RefactoringTool: ./PyDSTool/Variable.py
RefactoringTool: ./PyDSTool/Trajectory.py
RefactoringTool: ./PyDSTool/Toolbox/syntheticdata.py
RefactoringTool: ./PyDSTool/Toolbox/synthetic_data.py
RefactoringTool: ./PyDSTool/Toolbox/prep_boxplot.py
RefactoringTool: ./PyDSTool/Toolbox/phaseplane.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/tests/test_rosenbrock.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/tests/test_quadratic.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/tests/test_powell.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/tests/test_restart_conjugate_gradient.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/tests/test_quasi_newton_step.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/tests/test_partial_step.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/tests/test_newton_step.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/tests/test_marquardt_step.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/tests/test_gradient_step.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/tests/test_goldstein_price_step.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/tests/test_conjugate_gradient_step.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/restart_conjugate_gradient.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/quasi_newton_step.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/partial_step.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/newton_step.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/marquardt_step.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/local_brute_force_1dstep.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/gradient_step.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/goldstein_price_step.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/goldfeld_step.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/conjugate_gradient_step.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/step/__init__.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/optimizer/standard_optimizer_modifying.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/optimizer/standard_optimizer.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/optimizer/optimizer.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/optimizer/__init__.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/wolfe_powell_rule.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/tests/test_wolfe_powell_rule.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/tests/test_strong_wolfe_powell_rule.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/tests/test_simple_line_search.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/tests/test_quadratic_interpolation.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/tests/test_goldstein_rule.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/tests/test_golden_section.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/tests/test_fixed_last_step_modifier.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/tests/test_fibonacci_section.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/tests/test_damped_line_search.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/tests/test_cubic_interpolation.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/tests/test_backtracking_search.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/tests/test_adaptive_last_step_modifier.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/strong_wolfe_powell_rule.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/simple_line_search.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/scaled_line_search.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/quadratic_interpolation.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/hyperbolic_line_search.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/goldstein_rule.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/golden_section.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/fixed_last_step_modifier.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/fibonacci_section.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/damped_line_search.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/cubic_interpolation.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_search.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_non_monotone_search.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/backtracking_search.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/adaptive_last_step_modifier.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/line_search/__init__.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/helpers/tests/test_quadratic.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/helpers/tests/test_levenberg_marquardt.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/helpers/tests/test_finite_difference.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/helpers/quadratic.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/helpers/levenberg_marquardt.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/helpers/finite_difference.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/helpers/__init__.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/defaults.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/criterion/tests/test_information_criteria.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/criterion/tests/test_facilities.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/criterion/tests/test_criteria.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/criterion/tests/test_composite_criteria.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/criterion/information_criteria.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/criterion/facilities.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/criterion/criteria.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/criterion/composite_criteria.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/criterion/__init__.py
RefactoringTool: ./PyDSTool/Toolbox/optimizers/__init__.py
RefactoringTool: ./PyDSTool/Toolbox/neuro_data.py
RefactoringTool: ./PyDSTool/Toolbox/neuralcomp.py
RefactoringTool: ./PyDSTool/Toolbox/model_primitives.py
RefactoringTool: ./PyDSTool/Toolbox/mechmatlib.py
RefactoringTool: ./PyDSTool/Toolbox/makeSloppyModel.py
RefactoringTool: ./PyDSTool/Toolbox/fracdim.py
RefactoringTool: ./PyDSTool/Toolbox/event_driven_simulator.py
RefactoringTool: ./PyDSTool/Toolbox/dssrt.py
RefactoringTool: ./PyDSTool/Toolbox/data_analysis.py
RefactoringTool: ./PyDSTool/Toolbox/adjointPRC.py
RefactoringTool: ./PyDSTool/Toolbox/__init__.py
RefactoringTool: ./PyDSTool/Toolbox/PySCes_SBML.py
RefactoringTool: ./PyDSTool/Toolbox/ParamEst.py
RefactoringTool: ./PyDSTool/Toolbox/PRCtools.py
RefactoringTool: ./PyDSTool/Toolbox/NineML.py
RefactoringTool: ./PyDSTool/Toolbox/ModelHelper.py
RefactoringTool: ./PyDSTool/Toolbox/ModelEst.py
RefactoringTool: ./PyDSTool/Toolbox/InputProfile.py
RefactoringTool: ./PyDSTool/Toolbox/FSM.py
RefactoringTool: ./PyDSTool/Toolbox/FR.py
RefactoringTool: ./PyDSTool/Toolbox/DSSRT_tools.py
RefactoringTool: ./PyDSTool/Symbolic.py
RefactoringTool: ./PyDSTool/Redirector.py
RefactoringTool: ./PyDSTool/PyCont/misc.py
RefactoringTool: ./PyDSTool/PyCont/auto/dev/setup.py
RefactoringTool: ./PyDSTool/PyCont/__init__.py
RefactoringTool: ./PyDSTool/PyCont/TestFunc.py
RefactoringTool: ./PyDSTool/PyCont/Plotting.py
RefactoringTool: ./PyDSTool/PyCont/Continuation.py
RefactoringTool: ./PyDSTool/PyCont/ContClass.py
RefactoringTool: ./PyDSTool/PyCont/BifPoint.py
RefactoringTool: ./PyDSTool/Points.py
RefactoringTool: ./PyDSTool/ModelSpec.py
RefactoringTool: ./PyDSTool/ModelConstructor.py
RefactoringTool: ./PyDSTool/Model.py
RefactoringTool: ./PyDSTool/MProject.py
RefactoringTool: ./PyDSTool/Interval.py
RefactoringTool: ./PyDSTool/Generator/messagecodes.py
RefactoringTool: ./PyDSTool/Generator/baseclasses.py
RefactoringTool: ./PyDSTool/Generator/allimports.py
RefactoringTool: ./PyDSTool/Generator/__init__.py
RefactoringTool: ./PyDSTool/Generator/Vode_ODEsystem.py
RefactoringTool: ./PyDSTool/Generator/Radau_ODEsystem.py
RefactoringTool: ./PyDSTool/Generator/ODEsystem.py
RefactoringTool: ./PyDSTool/Generator/MapSystem.py
RefactoringTool: ./PyDSTool/Generator/LookupTable.py
RefactoringTool: ./PyDSTool/Generator/InterpolateTable.py
RefactoringTool: ./PyDSTool/Generator/ImplicitFnGen.py
RefactoringTool: ./PyDSTool/Generator/ExtrapolateTable.py
RefactoringTool: ./PyDSTool/Generator/ExplicitFnGen.py
RefactoringTool: ./PyDSTool/Generator/Euler_ODEsystem.py
RefactoringTool: ./PyDSTool/Generator/EmbeddedSysGen.py
RefactoringTool: ./PyDSTool/Generator/Dopri_ODEsystem.py
RefactoringTool: ./PyDSTool/Generator/DDEsystem.py
RefactoringTool: ./PyDSTool/Generator/ADMC_ODEsystem.py
RefactoringTool: ./PyDSTool/FuncSpec.py
RefactoringTool: ./PyDSTool/Events.py
RefactoringTool: Warnings/messages while refactoring:
RefactoringTool: ### In file ./PyDSTool/tests/test_hybrid_extinputs.py ###
RefactoringTool: Line 35: could not convert: raise "Invalid target"
RefactoringTool: Python 3 does not support string exceptions
RefactoringTool: ### In file ./PyDSTool/Toolbox/fracdim.py ###
RefactoringTool: Line 1102: could not convert: raise "too many sample points specified"
RefactoringTool: Python 3 does not support string exceptions
RefactoringTool: Line 1118: could not convert: raise "invalid color source"
RefactoringTool: Python 3 does not support string exceptions
RefactoringTool: Line 1202: could not convert: raise "invalid color source"
RefactoringTool: Python 3 does not support string exceptions
RefactoringTool: ### In file ./PyDSTool/Toolbox/dssrt.py ###
RefactoringTool: Line 2107: could not convert: raise "Must specify at least one type of output"
RefactoringTool: Python 3 does not support string exceptions
RefactoringTool: Line 1622: could not convert: raise "Call make_pointsets first"
RefactoringTool: Python 3 does not support string exceptions
RefactoringTool: ### In file ./PyDSTool/Toolbox/ModelHelper.py ###
RefactoringTool: Line 25: could not convert: raise 'No modelName specified'
RefactoringTool: Python 3 does not support string exceptions
RefactoringTool: Line 30: could not convert: raise 'No modelDict specified'
RefactoringTool: Python 3 does not support string exceptions
RefactoringTool: ### In file ./PyDSTool/PyCont/misc.py ###
RefactoringTool: Line 84: could not convert: raise 'Number of indices must be larger than 1.'
RefactoringTool: Python 3 does not support string exceptions
RefactoringTool: ### In file ./PyDSTool/PyCont/Plotting.py ###
RefactoringTool: Line 89: could not convert: raise 'Object type must be point, text, cycle, or curve'
RefactoringTool: Python 3 does not support string exceptions
RefactoringTool: Line 636: could not convert: raise 'Please specify axes.'
RefactoringTool: Python 3 does not support string exceptions
RefactoringTool: Line 641: could not convert: raise 'Tuple must be of length 3'
RefactoringTool: Python 3 does not support string exceptions
RefactoringTool: ### In file ./PyDSTool/Generator/baseclasses.py ###
RefactoringTool: Line 1111: You should use a for loop here
RefactoringTool: ### In file ./PyDSTool/Generator/baseclasses.py ###
RefactoringTool: Line 157: could not convert: raise "Cannot access external input values using ixmap class"
RefactoringTool: Python 3 does not support string exceptions
RefactoringTool: ### In file ./PyDSTool/Generator/EmbeddedSysGen.py ###
RefactoringTool: Line 59: could not convert: raise "Must provide a function for the specification of this system"
RefactoringTool: Python 3 does not support string exceptions
(b-a)/2.0
p = a + d
- dp = dict(zip(varnames, [v(p) for v in sortedDictValues(vars)]+[p]))
+ dp = dict(list(zip(varnames, [v(p) for v in sortedDictValues(vars)]+[p])))
evp = test_fn(dp, parDict)
if abs(evp-eva) < ev.eventtol or evp == 0:
return (p, rootival)
+ install -p -m644 /usr/src/RPM/SOURCES/PyDSTool.pth .
+ popd
~/RPM/BUILD
+ find /usr/src/tmp/python-module-PyDSTool-buildroot '(' -name '*.DS_Store' -o -name '*.DS_Store.gz' ')' -print -delete
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/PyCont/.DS_Store
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/.DS_Store
+ /usr/lib/rpm/brp-alt
Cleaning files in /usr/src/tmp/python-module-PyDSTool-buildroot (auto)
Verifying and fixing files in /usr/src/tmp/python-module-PyDSTool-buildroot (binconfig,pkgconfig,libtool,desktop,gnuconfig)
Checking contents of files in /usr/src/tmp/python-module-PyDSTool-buildroot/ (default)
Compressing files in /usr/src/tmp/python-module-PyDSTool-buildroot (auto)
Adjusting library links in /usr/src/tmp/python-module-PyDSTool-buildroot
./usr/lib64:
Verifying ELF objects in /usr/src/tmp/python-module-PyDSTool-buildroot (arch=normal,fhs=normal,lfs=relaxed,lint=relaxed,rpath=normal,stack=normal,textrel=normal,unresolved=normal)
Bytecompiling python modules in /usr/src/tmp/python-module-PyDSTool-buildroot using /usr/bin/python
Can't list '/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib'
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/DDEsystem.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/EmbeddedSysGen.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Euler_ODEsystem.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ExplicitFnGen.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ExtrapolateTable.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ImplicitFnGen.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/InterpolateTable.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/LookupTable.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/MapSystem.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ODEsystem.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Radau_ODEsystem.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Vode_ODEsystem.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/__init__.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/allimports.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/baseclasses.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/messagecodes.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/auto/dev/setup.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/BifPoint.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Continuation.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Plotting.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/TestFunc.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/__init__.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/misc.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/tests/test_composite_criteria.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/tests/test_criteria.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/tests/test_facilities.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/tests/test_information_criteria.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/__init__.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/composite_criteria.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/criteria.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/facilities.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/information_criteria.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_finite_difference.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_levenberg_marquardt.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_quadratic.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/__init__.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/finite_difference.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/levenberg_marquardt.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/quadratic.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_adaptive_last_step_modifier.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_backtracking_search.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_cubic_interpolation.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_damped_line_search.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_fibonacci_section.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_fixed_last_step_modifier.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_golden_section.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_goldstein_rule.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_quadratic_interpolation.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_simple_line_search.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_strong_wolfe_powell_rule.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_wolfe_powell_rule.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/adaptive_last_step_modifier.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/backtracking_search.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_non_monotone_search.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_search.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/cubic_interpolation.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/damped_line_search.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/fibonacci_section.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/fixed_last_step_modifier.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/golden_section.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/goldstein_rule.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/hyperbolic_line_search.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/quadratic_interpolation.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/scaled_line_search.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/simple_line_search.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/strong_wolfe_powell_rule.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/wolfe_powell_rule.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/__init__.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/optimizer.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/standard_optimizer.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/standard_optimizer_modifying.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_conjugate_gradient_step.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_goldstein_price_step.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_gradient_step.py
compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_marquardt_step.py
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compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Toolbox/optimizers/step/goldfeld_step.py
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compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Toolbox/optimizers/step/gradient_step.py
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compile /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Toolbox/optimizers/step/partial_step.py
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'./usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_model_Cintegrator.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_model_Cintegrator.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_loaded_Cintegrator.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_loaded_Cintegrator.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_DSSRTtest.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_DSSRTtest.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/tests/Dopri_backwards_test.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/tests/Dopri_backwards_test.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/tests/DAE_example.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/tests/DAE_example.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/test_protocols.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/test_protocols.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/model_primitives.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/model_primitives.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/__init__.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/__init__.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/FSM.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/FSM.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/FR.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/FR.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ActivationFuncs.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ActivationFuncs.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/defaults.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/defaults.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/__init__.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/__init__.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/tests/test_rosenbrock.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/tests/test_rosenbrock.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/tests/test_quadratic.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/tests/test_quadratic.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/tests/test_powell.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/tests/test_powell.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/tests/__init__.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/tests/__init__.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/restart_conjugate_gradient.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/restart_conjugate_gradient.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/quasi_newton_step.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/quasi_newton_step.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/partial_step.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/partial_step.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/newton_step.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/newton_step.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/marquardt_step.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/marquardt_step.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/gradient_step.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/gradient_step.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/goldstein_price_step.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/goldstein_price_step.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/goldfeld_step.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/goldfeld_step.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/conjugate_gradient_step.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/conjugate_gradient_step.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/__init__.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/__init__.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_restart_conjugate_gradient.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_restart_conjugate_gradient.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_newton_step.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_newton_step.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_gradient_step.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_gradient_step.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_goldstein_price_step.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_goldstein_price_step.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/standard_optimizer_modifying.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/standard_optimizer_modifying.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/standard_optimizer.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/standard_optimizer.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/optimizer.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/optimizer.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/__init__.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/__init__.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/wolfe_powell_rule.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/wolfe_powell_rule.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/strong_wolfe_powell_rule.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/strong_wolfe_powell_rule.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/simple_line_search.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/simple_line_search.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/scaled_line_search.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/scaled_line_search.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/quadratic_interpolation.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/quadratic_interpolation.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/hyperbolic_line_search.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/hyperbolic_line_search.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/goldstein_rule.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/goldstein_rule.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/golden_section.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/golden_section.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/fixed_last_step_modifier.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/fixed_last_step_modifier.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/fibonacci_section.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/fibonacci_section.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/damped_line_search.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/damped_line_search.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/cubic_interpolation.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/cubic_interpolation.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_search.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_search.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_non_monotone_search.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_non_monotone_search.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/backtracking_search.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/backtracking_search.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/adaptive_last_step_modifier.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/adaptive_last_step_modifier.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_simple_line_search.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_simple_line_search.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_fibonacci_section.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_fibonacci_section.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_damped_line_search.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_damped_line_search.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/quadratic.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/quadratic.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/levenberg_marquardt.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/levenberg_marquardt.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/finite_difference.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/finite_difference.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/__init__.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/__init__.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_quadratic.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_quadratic.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_levenberg_marquardt.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_levenberg_marquardt.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_finite_difference.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_finite_difference.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/information_criteria.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/information_criteria.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/facilities.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/facilities.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/criteria.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/criteria.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/composite_criteria.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/composite_criteria.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/__init__.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/__init__.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/PyCont/__init__.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/PyCont/__init__.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/PyCont/TestFunc.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/PyCont/TestFunc.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Plotting.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Plotting.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/PyCont/BifPoint.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/PyCont/BifPoint.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/PyCont/auto/dev/setup.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/PyCont/auto/dev/setup.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Generator/messagecodes.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Generator/messagecodes.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Generator/allimports.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Generator/allimports.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Generator/Vode_ODEsystem.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Generator/Vode_ODEsystem.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Generator/Euler_ODEsystem.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Generator/Euler_ODEsystem.pyc'
'./usr/lib64/python2.7/site-packages/PyDSTool/Generator/DDEsystem.pyo' => './usr/lib64/python2.7/site-packages/PyDSTool/Generator/DDEsystem.pyc'
Processing files: python-module-PyDSTool-0.88.121202-alt3.bzr20130716.1.1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.FWsG0X
find-provides: running scripts (alternatives,debuginfo,lib,pam,perl,pkgconfig,python,python3,shell)
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.ckltFI
find-requires: running scripts (cpp,debuginfo,files,lib,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services)
In file included from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/memory.h:4:
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/integration.h:7:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
cpp.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/memory.h: cpp failed, trying c++ mode
x86_64-alt-linux-cpp: error trying to exec 'cc1plus': execvp: No such file or directory
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/memory.h: cpp failed
In file included from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/memory.h:4,
from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/dop853mod.h:9:
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/integration.h:7:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/dop853mod.h: cpp failed
In file included from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/memory.h:4,
from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/interface.h:8:
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/integration.h:7:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/interface.h: cpp failed
In file included from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/memory.h:4,
from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/radau5mod.h:9:
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/integration.h:7:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/radau5mod.h: cpp failed
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/integration.h:7:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/integration.h: cpp failed
In file included from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/eventFinding.h:6:
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/integration.h:7:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator/eventFinding.h: cpp failed
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/auto/module/include/automod.h:4:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/auto/module/include/automod.h: cpp failed
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/auto/module/include/interface.h:4:10: fatal error: auto_f2c.h: No such file or directory
#include "auto_f2c.h"
^~~~~~~~~~~~
compilation terminated.
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/auto/module/include/interface.h: cpp failed
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Events.py: hiding Variable, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Events.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Events.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Events.py: hiding parseUtils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Events.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Events.py: hiding Interval, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Events.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Events.py: hiding Symbolic, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Events.py: hiding FuncSpec, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Events.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Events.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Events.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/FuncSpec.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/FuncSpec.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/FuncSpec.py: hiding parseUtils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/FuncSpec.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/FuncSpec.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/FuncSpec.py: hiding Symbolic, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/FuncSpec.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/FuncSpec.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py: hiding allimports, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py: hiding baseclasses, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py: skipping gc
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/DDEsystem.py: hiding allimports, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/DDEsystem.py: hiding baseclasses, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/DDEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/DDEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/DDEsystem.py: line=14 IGNORE (for REQ=slight and deep=8) module=psyco
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: hiding allimports, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: hiding baseclasses, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: skipping gc
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/EmbeddedSysGen.py: hiding allimports, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/EmbeddedSysGen.py: hiding baseclasses, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/EmbeddedSysGen.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/EmbeddedSysGen.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/EmbeddedSysGen.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/EmbeddedSysGen.py: line=17 IGNORE (for REQ=slight and deep=8) module=psyco
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: hiding allimports, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: hiding baseclasses, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: line=15 IGNORE (for REQ=slight and deep=8) module=numpy
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: line=18 IGNORE (for REQ=slight and deep=8) module=numpy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: skipping gc
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: line=26 IGNORE (for REQ=slight and deep=8) module=psyco
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ExplicitFnGen.py: hiding allimports, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ExplicitFnGen.py: hiding baseclasses, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ExplicitFnGen.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ExplicitFnGen.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ExplicitFnGen.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ExplicitFnGen.py: line=18 IGNORE (for REQ=slight and deep=8) module=psyco
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ExtrapolateTable.py: hiding allimports, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ExtrapolateTable.py: hiding baseclasses, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ExtrapolateTable.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ExtrapolateTable.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ExtrapolateTable.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ImplicitFnGen.py: hiding allimports, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ImplicitFnGen.py: hiding baseclasses, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ImplicitFnGen.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ImplicitFnGen.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ImplicitFnGen.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ImplicitFnGen.py: line=17 IGNORE (for REQ=slight and deep=8) module=psyco
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/InterpolateTable.py: hiding allimports, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/InterpolateTable.py: hiding baseclasses, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/InterpolateTable.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/InterpolateTable.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/LookupTable.py: hiding allimports, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/LookupTable.py: hiding baseclasses, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/LookupTable.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/LookupTable.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/MapSystem.py: hiding allimports, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/MapSystem.py: hiding baseclasses, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/MapSystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/MapSystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/MapSystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/MapSystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/MapSystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/MapSystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/MapSystem.py: line=24 IGNORE (for REQ=slight and deep=8) module=psyco
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ODEsystem.py: hiding allimports, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ODEsystem.py: hiding baseclasses, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/ODEsystem.py: line=20 IGNORE (for REQ=slight and deep=8) module=psyco
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: hiding allimports, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: hiding baseclasses, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: skipping gc
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: hiding allimports, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: hiding baseclasses, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: line=17 IGNORE (for REQ=slight and deep=8) module=numpy
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: line=20 IGNORE (for REQ=slight and deep=8) module=numpy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: skipping gc
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/__init__.py: hiding baseclasses, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/__init__.py: hiding ODEsystem, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/__init__.py: hiding Euler_ODEsystem, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/__init__.py: hiding Vode_ODEsystem, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/__init__.py: hiding Dopri_ODEsystem, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/__init__.py: hiding Radau_ODEsystem, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/__init__.py: hiding ADMC_ODEsystem, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/__init__.py: hiding ExplicitFnGen, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/__init__.py: hiding ImplicitFnGen, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/__init__.py: hiding EmbeddedSysGen, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/__init__.py: hiding LookupTable, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/__init__.py: hiding InterpolateTable, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/__init__.py: hiding ExtrapolateTable, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/__init__.py: hiding MapSystem, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/allimports.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/allimports.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/allimports.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/allimports.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/allimports.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/allimports.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/allimports.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/allimports.py: hiding messagecodes, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/allimports.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/baseclasses.py: hiding allimports, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/baseclasses.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/baseclasses.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/baseclasses.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/baseclasses.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/baseclasses.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/baseclasses.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/baseclasses.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/baseclasses.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Generator/baseclasses.py: line=21 IGNORE (for REQ=slight and deep=8) module=psyco
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Interval.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Interval.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Interval.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/MProject.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/MProject.py: hiding Model, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/MProject.py: hiding Generator, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/MProject.py: hiding Events, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/MProject.py: hiding ModelSpec, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/MProject.py: hiding ModelConstructor, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/MProject.py: hiding Symbolic, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/MProject.py: hiding Trajectory, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/MProject.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/MProject.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/MProject.py: hiding parseUtils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/MProject.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Model.py: hiding Generator, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Model.py: hiding Events, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Model.py: hiding MProject, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Model.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Model.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Model.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Model.py: hiding Interval, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Model.py: hiding Trajectory, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Model.py: hiding Variable, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Model.py: hiding Points, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Model.py: hiding ModelSpec, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Model.py: hiding Symbolic, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Model.py: hiding parseUtils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Model.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelConstructor.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelConstructor.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelConstructor.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelConstructor.py: hiding Model, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelConstructor.py: hiding Generator, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelConstructor.py: hiding ModelSpec, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelConstructor.py: hiding Symbolic, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelConstructor.py: hiding Events, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelConstructor.py: hiding MProject, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelConstructor.py: hiding parseUtils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelConstructor.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelConstructor.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelSpec.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelSpec.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelSpec.py: hiding parseUtils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelSpec.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelSpec.py: hiding Symbolic, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/ModelSpec.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Points.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Points.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Points.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Points.py: hiding parseUtils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Points.py: skipping sys
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Points.py: line=2568 IGNORE (for REQ=slight and deep=8) module=csv
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/BifPoint.py: hiding misc, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/BifPoint.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/BifPoint.py: hiding TestFunc, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/BifPoint.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: hiding Continuation, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: hiding misc, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: hiding Plotting, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/ContClass.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Continuation.py: hiding misc, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Continuation.py: hiding TestFunc, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Continuation.py: hiding BifPoint, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Continuation.py: hiding Plotting, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Continuation.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Continuation.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Continuation.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Continuation.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Continuation.py: line=22 IGNORE (for REQ=slight and deep=8) module=PyDSTool
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Continuation.py: line=24 IGNORE (for REQ=slight and deep=8) module=PyDSTool
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Continuation.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Plotting.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/Plotting.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/TestFunc.py: hiding misc, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/TestFunc.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/TestFunc.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/__init__.py: hiding ContClass, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/misc.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/misc.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/misc.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/PyCont/misc.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Redirector.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Symbolic.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Symbolic.py: hiding Interval, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Symbolic.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Symbolic.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Symbolic.py: hiding parseUtils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Symbolic.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Symbolic.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Symbolic.py: line=423 IGNORE (for REQ=slight and deep=8) module=common
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ActivationFuncs.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ActivationFuncs.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/DSSRT_tools.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/DSSRT_tools.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/DSSRT_tools.py: hiding FR, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/FR.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/InputProfile.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ModelEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ModelEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ModelEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ModelEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ModelEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ModelEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ModelEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ModelEst.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ModelHelper.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/NineML.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/NineML.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/NineML.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/NineML.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/NineML.py: skipping sys
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/NineML.py: line=34 IGNORE (for REQ=slight and deep=8) module=nineml
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/PRCtools.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/PRCtools.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/PRCtools.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: line=22 IGNORE (for REQ=slight and deep=8) module=constraint
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: skipping sys
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/ParamEst.py: line=50 IGNORE (for REQ=slight and deep=8) module=psyco
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/PySCes_SBML.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/PySCes_SBML.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/PySCes_SBML.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/PySCes_SBML.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/PySCes_SBML.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/PySCes_SBML.py: skipping sys
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/PySCes_SBML.py: line=34 IGNORE (for REQ=slight and deep=8) module=pysces
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/adjointPRC.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/adjointPRC.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/data_analysis.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/data_analysis.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/data_analysis.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/data_analysis.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/data_analysis.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/data_analysis.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/data_analysis.py: skipping scipy
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/data_analysis.py: line=23 IGNORE (for REQ=slight and deep=8) module=mdp
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/data_analysis.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/dssrt.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/dssrt.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/dssrt.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/dssrt.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/dssrt.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/dssrt.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/dssrt.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/dssrt.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/dssrt.py: skipping scipy
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/dssrt.py: line=1897 IGNORE (for REQ=slight and deep=8) module=PyDSTool
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/event_driven_simulator.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/event_driven_simulator.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/event_driven_simulator.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/event_driven_simulator.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/event_driven_simulator.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/event_driven_simulator.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/fracdim.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/fracdim.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/fracdim.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/fracdim.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/fracdim.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/fracdim.py: skipping matplotlib
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/makeSloppyModel.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/model_primitives.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/model_primitives.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/model_primitives.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/neuralcomp.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/neuro_data.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/neuro_data.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/neuro_data.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/neuro_data.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/neuro_data.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/neuro_data.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/__init__.py: line=11 IGNORE (for REQ=slight and deep=8) module=sys
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/__init__.py: line=12 IGNORE (for REQ=slight and deep=8) module=os
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/__init__.py: hiding defaults, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/__init__.py: hiding criterion, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/__init__.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/__init__.py: hiding optimizer, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/__init__.py: hiding step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/__init__.py: hiding helpers, which SEEMS TO BE SELF-SATISFIED
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/__init__.py: line=27 IGNORE (for REQ=slight and deep=8) module=numpy
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/__init__.py: line=31 IGNORE (for REQ=slight and deep=8) module=numpy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/__init__.py: hiding criteria, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/__init__.py: hiding composite_criteria, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/__init__.py: hiding information_criteria, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/__init__.py: hiding facilities, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/composite_criteria.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/criteria.py: hiding defaults, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/facilities.py: hiding criteria, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/facilities.py: hiding composite_criteria, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/tests/test_composite_criteria.py: hiding criterion, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/tests/test_criteria.py: hiding criterion, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/tests/test_facilities.py: hiding criterion, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/criterion/tests/test_information_criteria.py: hiding criterion, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/__init__.py: hiding quadratic, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/__init__.py: hiding finite_difference, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/finite_difference.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/levenberg_marquardt.py: hiding quadratic, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_finite_difference.py: hiding criterion, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_finite_difference.py: hiding helpers, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_finite_difference.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_finite_difference.py: hiding optimizer, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_finite_difference.py: hiding step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_levenberg_marquardt.py: hiding criterion, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_levenberg_marquardt.py: hiding helpers, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_levenberg_marquardt.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_levenberg_marquardt.py: hiding optimizer, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_levenberg_marquardt.py: hiding step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_quadratic.py: hiding criterion, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_quadratic.py: hiding helpers, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_quadratic.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_quadratic.py: hiding optimizer, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_quadratic.py: hiding step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.py: hiding simple_line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.py: hiding hyperbolic_line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.py: hiding damped_line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.py: hiding backtracking_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.py: hiding wolfe_powell_rule, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.py: hiding strong_wolfe_powell_rule, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.py: hiding goldstein_rule, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.py: hiding golden_section, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.py: hiding fibonacci_section, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.py: hiding quadratic_interpolation, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.py: hiding cubic_interpolation, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.py: hiding adaptive_last_step_modifier, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.py: hiding fixed_last_step_modifier, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/__init__.py: hiding scaled_line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_non_monotone_search.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_non_monotone_search.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_search.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/barzilai_borwein_search.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_adaptive_last_step_modifier.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_backtracking_search.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_cubic_interpolation.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_damped_line_search.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_fibonacci_section.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_fixed_last_step_modifier.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_golden_section.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_goldstein_rule.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_quadratic_interpolation.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_simple_line_search.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_strong_wolfe_powell_rule.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/line_search/tests/test_wolfe_powell_rule.py: hiding line_search, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/__init__.py: hiding standard_optimizer, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/__init__.py: hiding standard_optimizer_modifying, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/standard_optimizer.py: hiding optimizer, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/optimizer/standard_optimizer_modifying.py: hiding optimizer, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/__init__.py: hiding gradient_step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/__init__.py: hiding conjugate_gradient_step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/__init__.py: hiding newton_step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/__init__.py: hiding marquardt_step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/__init__.py: hiding quasi_newton_step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/__init__.py: hiding goldfeld_step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/__init__.py: hiding goldstein_price_step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/__init__.py: hiding partial_step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/__init__.py: hiding restart_conjugate_gradient, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/__init__.py: hiding local_brute_force_1dstep, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/local_brute_force_1dstep.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_conjugate_gradient_step.py: hiding step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_goldstein_price_step.py: hiding step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_gradient_step.py: hiding step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_marquardt_step.py: hiding step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_newton_step.py: hiding step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_partial_step.py: hiding step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_quasi_newton_step.py: hiding step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/step/tests/test_restart_conjugate_gradient.py: hiding step, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/tests/test_powell.py: hiding optimizers, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/tests/test_quadratic.py: hiding optimizers, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/optimizers/tests/test_rosenbrock.py: hiding optimizers, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/phaseplane.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/phaseplane.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/phaseplane.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/phaseplane.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/phaseplane.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/phaseplane.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/phaseplane.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/phaseplane.py: line=32 IGNORE (for REQ=slight and deep=8) module=numpy
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/phaseplane.py: line=35 IGNORE (for REQ=slight and deep=8) module=numpy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/phaseplane.py: skipping matplotlib
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/phaseplane.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/phaseplane.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/phaseplane.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/phaseplane.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/phaseplane.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/prep_boxplot.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/prep_boxplot.py: skipping matplotlib
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/prep_boxplot.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/prep_boxplot.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/synthetic_data.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Toolbox/syntheticdata.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Trajectory.py: hiding Variable, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Trajectory.py: hiding Interval, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Trajectory.py: hiding Points, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Trajectory.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Trajectory.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Trajectory.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Trajectory.py: hiding parseUtils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Trajectory.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Trajectory.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Trajectory.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Variable.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Variable.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Variable.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Variable.py: hiding Points, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Variable.py: hiding Interval, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/Variable.py: hiding FuncSpec, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: skipping gc
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: line=53 IGNORE (for REQ=slight and deep=8) module=scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding Events, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding Interval, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding Points, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding Variable, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding Trajectory, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding FuncSpec, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding Generator, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding Generator, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding Generator, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding Model, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding Model, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding Model, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding ModelConstructor, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding Toolbox, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding Toolbox, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding MProject, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding Symbolic, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding ModelSpec, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding parseUtils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding PyCont, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: skipping matplotlib
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: skipping matplotlib
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/__init__.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/common.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/common.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/common.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/common.py: skipping scipy
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/common.py: line=25 IGNORE (for REQ=slight and deep=8) module=numpy
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/common.py: line=33 IGNORE (for REQ=slight and deep=8) module=numpy
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/common.py: line=45 IGNORE (for REQ=slight and deep=8) module=fixedpickle
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/common.py: line=47 IGNORE (for REQ=slight and deep=8) module=cPickle
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/conf.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/fixedpickle.py: skipping marshal
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/fixedpickle.py: skipping sys
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/fixedpickle.py: line=92 IGNORE (for REQ=slight and deep=8) module=org
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/fixedpickle.py: line=1398 IGNORE (for REQ=slight and deep=8) module=cStringIO
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/fixedpickle.py: line=1400 IGNORE (for REQ=slight and deep=8) module=StringIO
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/fixedpickle.py: line=1420 IGNORE (for REQ=slight and deep=8) module=doctest
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/integrator.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/matplotlib_import.py: skipping matplotlib
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/matplotlib_import.py: line=12 IGNORE (for REQ=slight and deep=12) module=matplotlib
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/matplotlib_import.py: line=13 IGNORE (for REQ=slight and deep=12) module=matplotlib
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/matplotlib_import.py: line=15 IGNORE (for REQ=slight and deep=12) module=matplotlib
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/matplotlib_import.py: line=16 IGNORE (for REQ=slight and deep=12) module=matplotlib
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/matplotlib_import.py: line=38 IGNORE (for REQ=slight and deep=8) module=os
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/matplotlib_import.py: line=39 IGNORE (for REQ=slight and deep=8) module=Trajectory
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/matplotlib_import.py: line=40 IGNORE (for REQ=slight and deep=8) module=common
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/parseUtils.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/parseUtils.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/scipy_ode.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/scipy_ode.py: skipping sys
/usr/lib/rpm/python.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/scipy_ode.py: line=253 IGNORE (for REQ=slight and deep=11) module=scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/CIN.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/CIN.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/DAE_example.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/Dopri_backwards_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_DSSRTtest.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_DSSRTtest.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_DSSRTtest.py: skipping sys
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_adjointPRC.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_adjointPRC.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_loaded.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_loaded_Cintegrator.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_model.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_model_Cintegrator.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_model_Cintegrator_testbounds.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/HH_model_testbounds.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/IF_delaynet.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/IF_delaynet_syn.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/IF_model_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/IF_squarespike_model.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/ML_adjointPRC.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/ML_adjointPRC.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/ModelSpec_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/ModelSpec_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/MultiCompartments.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PointInfo_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PointInfo_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_ABReaction.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_Brusselator.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_Catalytic.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_DiscPredPrey.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_Hamiltonian.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_HindmarshRose.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_Hopfield.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_LPNeuron.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_LevelCurve.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_Logistic.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_Lorenz.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_MorrisLecar_TypeI.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_MorrisLecar_TypeII.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_NewLorenz.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_PredPrey.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_SaddleNode.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_hybrid_osc.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_hybrid_osc.py: hiding IF_squarespike_model, which SEEMS TO BE SELF-SATISFIED
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/PyCont_vanDerPol.py: skipping sys
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/SLIP_2D_maps.py: skipping scipy
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/SLIP_2D_pdc.py: hiding SLIP_plot, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/SLIP_2D_pdc.py: hiding SLIP_2D, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/SLIP_2D_pdc.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/SLIP_plot.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/Symbolic_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/Symbolic_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/Tutorial_Calcium.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/Tutorial_Calcium.py: skipping matplotlib
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/Tutorial_LorenzMap.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/Tutorial_LorenzMap.py: skipping matplotlib
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/Tutorial_PredatorPrey.py: skipping matplotlib
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/Tutorial_PredatorPrey.py: skipping matplotlib
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/Tutorial_SymbolicJac.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/Tutorial_VdP.py: skipping matplotlib
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/Tutorial_linear.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/dopri_event_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/embedded_map_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/embedded_map_test.py: skipping scipy
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/freefinger_noforce_radau.py: skipping scipy
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/funcspec_tests.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/mapsystem_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/numeric_diff_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/pest_test2.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/pest_test2.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/pest_test2.py: hiding HH_model, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/pest_test2.py: hiding IF_squarespike_model, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/pest_test3.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/pest_test3.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/pest_test3.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/pest_test3.py: hiding HH_model, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/pest_test3_Cintegrator.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/pest_test3_Cintegrator.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/pest_test3_Cintegrator.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/pest_test3_Cintegrator.py: hiding HH_model_Cintegrator, which SEEMS TO BE SELF-SATISFIED
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/pest_test4_Cintegrator.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/pest_test4_Cintegrator.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/pest_test4_Cintegrator.py: hiding HH_model, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/phaseplane_HHtest.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/phaseplane_HHtest.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/poly_interp_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/radau_event_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/saveload_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/sloppycell_example.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/sloppycell_example.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/splinetest.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/splinetest.py: skipping sys
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python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/test_bd_containment.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/test_context_spikes.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/test_context_spikes.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/test_find_nearby_ball.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/test_find_nearby_ball.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/test_find_nearby_ball.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/test_hybrid_extinputs.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/test_hybrid_extinputs_Cintegrator.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/test_hybrid_extinputs_Cintegrator.py: hiding test_hybrid_extinputs, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/test_interval.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/test_pointsets.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/test_variable_traj.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/test_variable_traj.py: hiding utils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/traj_gt0_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/vode_event_test1.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/vode_event_test2.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/tests/vode_withJac_test.py: hiding PyDSTool, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/utils.py: hiding errors, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/utils.py: hiding common, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/utils.py: hiding Redirector, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/utils.py: hiding parseUtils, which SEEMS TO BE SELF-SATISFIED
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/utils.py: skipping scipy
python.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python2.7/site-packages/PyDSTool/utils.py: skipping sys
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find-requires: FINDPACKAGE-COMMANDS: dos2unix
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python2.7(Toolbox.optimizers.defaults), python2.7(Toolbox.optimizers.helpers), python2.7(Toolbox.optimizers.helpers.finite_difference), python2.7(Toolbox.optimizers.helpers.levenberg_marquardt), python2.7(Toolbox.optimizers.helpers.quadratic), python2.7(Toolbox.optimizers.line_search), python2.7(Toolbox.optimizers.line_search.adaptive_last_step_modifier), python2.7(Toolbox.optimizers.line_search.backtracking_search), python2.7(Toolbox.optimizers.line_search.barzilai_borwein_non_monotone_search), python2.7(Toolbox.optimizers.line_search.barzilai_borwein_search), python2.7(Toolbox.optimizers.line_search.cubic_interpolation), python2.7(Toolbox.optimizers.line_search.damped_line_search), python2.7(Toolbox.optimizers.line_search.fibonacci_section), python2.7(Toolbox.optimizers.line_search.fixed_last_step_modifier), python2.7(Toolbox.optimizers.line_search.golden_section), python2.7(Toolbox.optimizers.line_search.goldstein_rule), python2.7(Toolbox.optimizers.line_search.hyperbolic_line_search), python2.7(Toolbox.optimizers.line_search.quadratic_interpolation), python2.7(Toolbox.optimizers.line_search.scaled_line_search), python2.7(Toolbox.optimizers.line_search.simple_line_search), python2.7(Toolbox.optimizers.line_search.strong_wolfe_powell_rule), python2.7(Toolbox.optimizers.line_search.wolfe_powell_rule), python2.7(Toolbox.optimizers.optimizer), python2.7(Toolbox.optimizers.optimizer.optimizer), python2.7(Toolbox.optimizers.optimizer.standard_optimizer), python2.7(Toolbox.optimizers.optimizer.standard_optimizer_modifying), python2.7(Toolbox.optimizers.step), python2.7(Toolbox.optimizers.step.conjugate_gradient_step), python2.7(Toolbox.optimizers.step.goldfeld_step), python2.7(Toolbox.optimizers.step.goldstein_price_step), python2.7(Toolbox.optimizers.step.gradient_step), python2.7(Toolbox.optimizers.step.local_brute_force_1dstep), python2.7(Toolbox.optimizers.step.marquardt_step), python2.7(Toolbox.optimizers.step.newton_step), python2.7(Toolbox.optimizers.step.partial_step), python2.7(Toolbox.optimizers.step.quasi_newton_step), python2.7(Toolbox.optimizers.step.restart_conjugate_gradient), python2.7(Toolbox.optimizers.tests), python2.7(Toolbox.optimizers.tests.test_powell), python2.7(Toolbox.optimizers.tests.test_quadratic), python2.7(Toolbox.optimizers.tests.test_rosenbrock), python2.7(Toolbox.phaseplane), python2.7(Toolbox.prep_boxplot), python2.7(Toolbox.synthetic_data), python2.7(Toolbox.syntheticdata), python2.7(Toolbox.test_protocols), python2.7(Trajectory), python2.7(Variable), python2.7(common), python2.7(conf), python2.7(errors), python2.7(fixedpickle), python2.7(integrator), python2.7(matplotlib_import), python2.7(parseUtils), python2.7(scipy_ode), python2.7(utils)
Requires: /bin/sh, /usr/bin/dos2unix, /usr/lib64/python2.7/site-packages, python-modules, python2.7(distutils), python2.7(mpl_toolkits), python2.7(nineml), python2.7(numpy), python2.7(unittest)
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.dtg4wX
Processing files: python3-module-PyDSTool-0.88.121202-alt3.bzr20130716.1.1
Finding Provides (using /usr/lib/rpm/find-provides)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.eiRFCg
find-provides: running scripts (alternatives,debuginfo,lib,pam,perl,pkgconfig,python,python3,shell)
Finding Requires (using /usr/lib/rpm/find-requires)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.L9WnrG
find-requires: running scripts (cpp,debuginfo,files,lib,pam,perl,pkgconfig,pkgconfiglib,python,python3,rpmlib,shebang,shell,static,symlinks,systemd-services)
In file included from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/memory.h:4:
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/integration.h:7:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
cpp.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/memory.h: cpp failed, trying c++ mode
x86_64-alt-linux-cpp: error trying to exec 'cc1plus': execvp: No such file or directory
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/memory.h: cpp failed
In file included from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/memory.h:4,
from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/dop853mod.h:9:
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/integration.h:7:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/dop853mod.h: cpp failed
In file included from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/memory.h:4,
from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/interface.h:8:
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/integration.h:7:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/interface.h: cpp failed
In file included from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/memory.h:4,
from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/radau5mod.h:9:
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/integration.h:7:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/radau5mod.h: cpp failed
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/integration.h:7:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/integration.h: cpp failed
In file included from /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/eventFinding.h:6:
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/integration.h:7:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator/eventFinding.h: cpp failed
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/PyCont/auto/module/include/automod.h:4:10: fatal error: Python.h: No such file or directory
#include "Python.h"
^~~~~~~~~~
compilation terminated.
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/PyCont/auto/module/include/automod.h: cpp failed
/usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/PyCont/auto/module/include/interface.h:4:10: fatal error: auto_f2c.h: No such file or directory
#include "auto_f2c.h"
^~~~~~~~~~~~
compilation terminated.
cpp.req: WARNING: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/PyCont/auto/module/include/interface.h: cpp failed
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Events.py: line=12 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Events.py: line=13 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Events.py: line=14 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Events.py: line=15 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Events.py: line=16 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Events.py: line=17 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Events.py: line=18 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Events.py: line=19 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Events.py: line=20 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Events.py: skipping scipy
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Events.py: skipping scipy
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/FuncSpec.py: line=12 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/FuncSpec.py: line=13 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/FuncSpec.py: line=14 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/FuncSpec.py: line=15 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/FuncSpec.py: line=16 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/FuncSpec.py: line=17 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/FuncSpec.py: skipping scipy
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py: line=4 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py: line=6 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py: skipping sys
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py: skipping gc
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ADMC_ODEsystem.py: skipping time
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/DDEsystem.py: line=3 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/DDEsystem.py: line=4 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/DDEsystem.py: line=14 IGNORE (for REQ=slight and deep=8) module=psyco
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=4 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=6 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: skipping sys
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: skipping gc
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: skipping time
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [274, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Dopri_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/EmbeddedSysGen.py: line=4 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/EmbeddedSysGen.py: line=5 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/EmbeddedSysGen.py: line=17 IGNORE (for REQ=slight and deep=8) module=psyco
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: line=5 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: line=7 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: line=15 IGNORE (for REQ=slight and deep=8) module=numpy
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: line=18 IGNORE (for REQ=slight and deep=8) module=numpy
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: skipping sys
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: skipping gc
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Euler_ODEsystem.py: line=26 IGNORE (for REQ=slight and deep=8) module=psyco
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ExplicitFnGen.py: line=4 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ExplicitFnGen.py: line=5 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ExplicitFnGen.py: line=18 IGNORE (for REQ=slight and deep=8) module=psyco
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ExtrapolateTable.py: line=4 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ExtrapolateTable.py: line=5 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ExtrapolateTable.py: skipping scipy
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ImplicitFnGen.py: line=4 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ImplicitFnGen.py: line=5 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ImplicitFnGen.py: line=17 IGNORE (for REQ=slight and deep=8) module=psyco
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/InterpolateTable.py: line=4 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/InterpolateTable.py: line=5 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/LookupTable.py: line=4 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/LookupTable.py: line=5 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/MapSystem.py: line=8 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/MapSystem.py: line=9 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/MapSystem.py: line=24 IGNORE (for REQ=slight and deep=8) module=psyco
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ODEsystem.py: line=3 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ODEsystem.py: line=4 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/ODEsystem.py: line=20 IGNORE (for REQ=slight and deep=8) module=psyco
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=4 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=6 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: skipping sys
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: skipping gc
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [274, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [319, [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [320, [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [321, [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [322, [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 UNABLE to determine the imported name at parse-time: modname
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Radau_ODEsystem.py: line=49 a form of __import__ was read which gave no deps: [323, [324, [1, '__import__', 49]], [326, [7, '(', 49], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'modname', 49]]]]]]]]]]]]]]]]], [12, ',', 49], [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'globals', 49]], [326, [7, '(', 49], [8, ')', 49]]]]]]]]]]]]]]]]]], [8, ')', 49]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: line=6 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: line=8 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: line=17 IGNORE (for REQ=slight and deep=8) module=numpy
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: line=20 IGNORE (for REQ=slight and deep=8) module=numpy
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: skipping sys
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/Vode_ODEsystem.py: skipping gc
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/__init__.py: line=6 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/__init__.py: line=7 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/__init__.py: line=8 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/__init__.py: line=9 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/__init__.py: line=10 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/__init__.py: line=11 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/__init__.py: line=12 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/__init__.py: line=13 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/__init__.py: line=14 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/__init__.py: line=15 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/__init__.py: line=16 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/__init__.py: line=17 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/__init__.py: line=18 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/__init__.py: line=19 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/allimports.py: line=13 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/allimports.py: skipping scipy
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/baseclasses.py: line=4 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Generator/baseclasses.py: line=21 IGNORE (for REQ=slight and deep=8) module=psyco
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Interval.py: line=20 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Interval.py: line=21 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Interval.py: line=22 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/MProject.py: skipping sys
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/MProject.py: line=13 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/MProject.py: line=15 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/MProject.py: line=16 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Model.py: line=39 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Model.py: line=40 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Model.py: line=41 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Model.py: line=42 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Model.py: line=43 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Model.py: line=44 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Model.py: line=45 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Model.py: line=46 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Model.py: line=47 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Model.py: line=48 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Model.py: line=49 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Model.py: skipping sys
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Model.py: skipping time
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/ModelConstructor.py: line=36 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/ModelConstructor.py: line=37 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/ModelConstructor.py: line=38 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/ModelConstructor.py: line=39 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/ModelConstructor.py: line=40 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/ModelConstructor.py: skipping scipy
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/ModelConstructor.py: skipping sys
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/ModelSpec.py: line=16 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/ModelSpec.py: line=17 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/ModelSpec.py: line=18 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/ModelSpec.py: line=19 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/ModelSpec.py: line=20 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/ModelSpec.py: line=23 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Points.py: line=13 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Points.py: line=14 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Points.py: line=15 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Points.py: line=16 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Points.py: skipping sys
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Points.py: line=2568 IGNORE (for REQ=slight and deep=8) module=csv
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/PyCont/BifPoint.py: line=6 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/PyCont/BifPoint.py: line=8 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/PyCont/BifPoint.py: skipping scipy
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/PyCont/ContClass.py: line=6 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/PyCont/ContClass.py: line=8 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/PyCont/ContClass.py: line=9 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/PyCont/ContClass.py: skipping scipy
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python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Toolbox/phaseplane.py: skipping itertools
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Toolbox/phaseplane.py: line=32 IGNORE (for REQ=slight and deep=8) module=numpy
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Toolbox/phaseplane.py: line=35 IGNORE (for REQ=slight and deep=8) module=numpy
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Toolbox/phaseplane.py: skipping scipy
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Toolbox/phaseplane.py: skipping sys
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Toolbox/prep_boxplot.py: skipping scipy
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Trajectory.py: line=9 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Trajectory.py: line=10 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Trajectory.py: line=11 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Trajectory.py: line=12 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Trajectory.py: line=13 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Trajectory.py: line=14 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Trajectory.py: line=15 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Trajectory.py: line=16 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Trajectory.py: skipping sys
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Variable.py: line=9 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Variable.py: line=10 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Variable.py: line=11 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Variable.py: line=12 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Variable.py: line=13 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Variable.py: line=14 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: skipping sys
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: skipping gc
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=53 IGNORE (for REQ=slight and deep=8) module=scipy
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: skipping time
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=86 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=87 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=88 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=89 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=90 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=91 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=93 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=94 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=95 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=97 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=98 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=99 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=102 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=103 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=104 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=105 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=106 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=107 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=108 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=110 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: skipping scipy
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: skipping matplotlib
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=128 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: skipping scipy
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/__init__.py: line=134 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/common.py: line=7 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/common.py: skipping sys
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/common.py: skipping scipy
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/common.py: line=25 IGNORE (for REQ=slight and deep=8) module=numpy
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/common.py: line=33 IGNORE (for REQ=slight and deep=8) module=numpy
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/common.py: skipping time
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/common.py: line=45 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/common.py: line=47 IGNORE (for REQ=slight and deep=8) module=pickle
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/conf.py: skipping sys
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: skipping marshal
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: skipping sys
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=92 IGNORE (for REQ=slight and deep=8) module=org.python.core
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [269, [270, [271, [272, [274, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]]]]]]]]]]]]]], [4, '', 764]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [270, [271, [272, [274, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]]]]]]]]]]]]]], [4, '', 764]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [271, [272, [274, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [272, [274, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [274, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [319, [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [320, [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [321, [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [322, [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=764 a form of __import__ was read which gave no deps: [323, [324, [1, '__import__', 764]], [326, [7, '(', 764], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 764]]]]]]]]]]]]]]]]]], [8, ')', 764]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [269, [270, [271, [272, [274, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]]]]]]]]]]]]]], [4, '', 1159]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [270, [271, [272, [274, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]]]]]]]]]]]]]], [4, '', 1159]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [271, [272, [274, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [272, [274, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [274, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [317, [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [318, [319, [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [319, [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [320, [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [321, [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [322, [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 UNABLE to determine the imported name at parse-time: module
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1159 a form of __import__ was read which gave no deps: [323, [324, [1, '__import__', 1159]], [326, [7, '(', 1159], [334, [335, [305, [309, [310, [311, [312, [315, [316, [317, [318, [319, [320, [321, [322, [323, [324, [1, 'module', 1159]]]]]]]]]]]]]]]]]], [8, ')', 1159]]]
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1398 IGNORE (for REQ=slight and deep=8) module=io
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1400 IGNORE (for REQ=slight and deep=8) module=io
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/fixedpickle.py: line=1420 IGNORE (for REQ=slight and deep=8) module=doctest
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator.py: line=5 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator.py: line=6 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator.py: line=7 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/integrator.py: skipping sys
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/matplotlib_import.py: skipping matplotlib
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/matplotlib_import.py: line=12 IGNORE (for REQ=slight and deep=12) module=matplotlib.matlab
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/matplotlib_import.py: line=13 IGNORE (for REQ=slight and deep=12) module=matplotlib.matlab
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/matplotlib_import.py: line=15 IGNORE (for REQ=slight and deep=12) module=matplotlib.pyplot
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/matplotlib_import.py: line=16 IGNORE (for REQ=slight and deep=12) module=matplotlib.pyplot
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/matplotlib_import.py: line=38 IGNORE (for REQ=slight and deep=8) module=os
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/matplotlib_import.py: line=39 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/matplotlib_import.py: line=40 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/parseUtils.py: line=12 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/parseUtils.py: line=13 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/scipy_ode.py: skipping scipy
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/scipy_ode.py: skipping sys
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/scipy_ode.py: line=252 IGNORE (for REQ=slight and deep=11) module=scipy.integrate.vode
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/CIN.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/Dopri_backwards_test.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/HH_DSSRTtest.py: skipping sys
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/HH_model.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/HH_model_Cintegrator.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/HH_model_Cintegrator_testbounds.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/HH_model_testbounds.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/IF_delaynet.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/IF_delaynet_syn.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/IF_model_test.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/IF_squarespike_model.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/PyCont_vanDerPol.py: skipping sys
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/SLIP_2D_pdc.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/Tutorial_Calcium.py: skipping matplotlib
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/Tutorial_LorenzMap.py: skipping matplotlib
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/Tutorial_PredatorPrey.py: skipping matplotlib
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/Tutorial_PredatorPrey.py: skipping matplotlib
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/Tutorial_VdP.py: skipping matplotlib
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/freefinger_noforce_radau.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/imprecise_event_test.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/interp_dopri_test.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/interp_vode_test.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/joe_pest.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/mapsystem_test.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/pest_test1.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/pest_test3.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/pest_test3_Cintegrator.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/pest_test4_Cintegrator.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/phaseplane_HHtest.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/run_all_tests.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/sloppycell_example.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/tests/splinetest.py: skipping sys
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/utils.py: line=5 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/utils.py: line=6 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/utils.py: line=7 possible relative import from ., UNIMPLEMENTED
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/utils.py: line=8 possible relative import from ., UNIMPLEMENTED
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/utils.py: skipping time
python3.req: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/utils.py: skipping sys
/usr/lib/rpm/python3.req.py: /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/utils.py: line=748 IGNORE (for REQ=slight and deep=8) module=scipy
shebang.req.files: executable script /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/PyCont/auto/dev/setup.py is not executable
shebang.req.files: executable script /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/PyCont/auto/dev/setup.py.lib is not executable
shebang.req.files: executable script /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/PyCont/auto/dev/setup.py.works is not executable
shebang.req.files: executable script /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_finite_difference.py is not executable
shebang.req.files: executable script /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_levenberg_marquardt.py is not executable
shebang.req.files: executable script /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Toolbox/optimizers/helpers/tests/test_quadratic.py is not executable
shebang.req.files: executable script /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Toolbox/optimizers/tests/test_powell.py is not executable
shebang.req.files: executable script /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Toolbox/optimizers/tests/test_quadratic.py is not executable
shebang.req.files: executable script /usr/src/tmp/python-module-PyDSTool-buildroot/usr/lib64/python3/site-packages/PyDSTool/Toolbox/optimizers/tests/test_rosenbrock.py is not executable
find-requires: FINDPACKAGE-COMMANDS: dos2unix
Provides: python3(Events), python3(FuncSpec), python3(Generator), python3(Generator.ADMC_ODEsystem), python3(Generator.DDEsystem), python3(Generator.Dopri_ODEsystem), python3(Generator.EmbeddedSysGen), python3(Generator.Euler_ODEsystem), python3(Generator.ExplicitFnGen), python3(Generator.ExtrapolateTable), python3(Generator.ImplicitFnGen), python3(Generator.InterpolateTable), python3(Generator.LookupTable), python3(Generator.MapSystem), python3(Generator.ODEsystem), python3(Generator.Radau_ODEsystem), python3(Generator.Vode_ODEsystem), python3(Generator.allimports), python3(Generator.baseclasses), python3(Generator.messagecodes), python3(Interval), python3(MProject), python3(Model), python3(ModelConstructor), python3(ModelSpec), python3(Points), python3(PyCont), python3(PyCont.BifPoint), python3(PyCont.ContClass), python3(PyCont.Continuation), python3(PyCont.Plotting), python3(PyCont.TestFunc), python3(PyCont.misc), python3(PyDSTool), python3(PyDSTool.Events), python3(PyDSTool.FuncSpec), python3(PyDSTool.Generator), python3(PyDSTool.Generator.ADMC_ODEsystem), python3(PyDSTool.Generator.DDEsystem), python3(PyDSTool.Generator.Dopri_ODEsystem), python3(PyDSTool.Generator.EmbeddedSysGen), python3(PyDSTool.Generator.Euler_ODEsystem), python3(PyDSTool.Generator.ExplicitFnGen), python3(PyDSTool.Generator.ExtrapolateTable), python3(PyDSTool.Generator.ImplicitFnGen), python3(PyDSTool.Generator.InterpolateTable), python3(PyDSTool.Generator.LookupTable), python3(PyDSTool.Generator.MapSystem), python3(PyDSTool.Generator.ODEsystem), python3(PyDSTool.Generator.Radau_ODEsystem), python3(PyDSTool.Generator.Vode_ODEsystem), python3(PyDSTool.Generator.allimports), python3(PyDSTool.Generator.baseclasses), python3(PyDSTool.Generator.messagecodes), python3(PyDSTool.Interval), python3(PyDSTool.MProject), python3(PyDSTool.Model), python3(PyDSTool.ModelConstructor), python3(PyDSTool.ModelSpec), python3(PyDSTool.Points), python3(PyDSTool.PyCont), python3(PyDSTool.PyCont.BifPoint), python3(PyDSTool.PyCont.ContClass), python3(PyDSTool.PyCont.Continuation), python3(PyDSTool.PyCont.Plotting), python3(PyDSTool.PyCont.TestFunc), python3(PyDSTool.PyCont.misc), python3(PyDSTool.Redirector), python3(PyDSTool.Symbolic), python3(PyDSTool.Toolbox), python3(PyDSTool.Toolbox.ActivationFuncs), python3(PyDSTool.Toolbox.DSSRT_tools), python3(PyDSTool.Toolbox.FR), python3(PyDSTool.Toolbox.FSM), python3(PyDSTool.Toolbox.InputProfile), python3(PyDSTool.Toolbox.ModelEst), python3(PyDSTool.Toolbox.ModelHelper), python3(PyDSTool.Toolbox.NineML), python3(PyDSTool.Toolbox.PRCtools), python3(PyDSTool.Toolbox.ParamEst), python3(PyDSTool.Toolbox.PySCes_SBML), python3(PyDSTool.Toolbox.adjointPRC), python3(PyDSTool.Toolbox.data_analysis), python3(PyDSTool.Toolbox.dssrt), python3(PyDSTool.Toolbox.event_driven_simulator), python3(PyDSTool.Toolbox.fracdim), python3(PyDSTool.Toolbox.makeSloppyModel), python3(PyDSTool.Toolbox.mechmatlib), python3(PyDSTool.Toolbox.model_primitives), python3(PyDSTool.Toolbox.neuralcomp), python3(PyDSTool.Toolbox.neuro_data), python3(PyDSTool.Toolbox.optimizers), python3(PyDSTool.Toolbox.optimizers.criterion), python3(PyDSTool.Toolbox.optimizers.criterion.composite_criteria), python3(PyDSTool.Toolbox.optimizers.criterion.criteria), python3(PyDSTool.Toolbox.optimizers.criterion.facilities), python3(PyDSTool.Toolbox.optimizers.criterion.information_criteria), python3(PyDSTool.Toolbox.optimizers.defaults), python3(PyDSTool.Toolbox.optimizers.helpers), python3(PyDSTool.Toolbox.optimizers.helpers.finite_difference), python3(PyDSTool.Toolbox.optimizers.helpers.levenberg_marquardt), python3(PyDSTool.Toolbox.optimizers.helpers.quadratic), python3(PyDSTool.Toolbox.optimizers.line_search), python3(PyDSTool.Toolbox.optimizers.line_search.adaptive_last_step_modifier), python3(PyDSTool.Toolbox.optimizers.line_search.backtracking_search), python3(PyDSTool.Toolbox.optimizers.line_search.barzilai_borwein_non_monotone_search), python3(PyDSTool.Toolbox.optimizers.line_search.barzilai_borwein_search), python3(PyDSTool.Toolbox.optimizers.line_search.cubic_interpolation), python3(PyDSTool.Toolbox.optimizers.line_search.damped_line_search), python3(PyDSTool.Toolbox.optimizers.line_search.fibonacci_section), python3(PyDSTool.Toolbox.optimizers.line_search.fixed_last_step_modifier), python3(PyDSTool.Toolbox.optimizers.line_search.golden_section), python3(PyDSTool.Toolbox.optimizers.line_search.goldstein_rule), python3(PyDSTool.Toolbox.optimizers.line_search.hyperbolic_line_search), python3(PyDSTool.Toolbox.optimizers.line_search.quadratic_interpolation), python3(PyDSTool.Toolbox.optimizers.line_search.scaled_line_search), python3(PyDSTool.Toolbox.optimizers.line_search.simple_line_search), python3(PyDSTool.Toolbox.optimizers.line_search.strong_wolfe_powell_rule), python3(PyDSTool.Toolbox.optimizers.line_search.wolfe_powell_rule), python3(PyDSTool.Toolbox.optimizers.optimizer), python3(PyDSTool.Toolbox.optimizers.optimizer.optimizer), python3(PyDSTool.Toolbox.optimizers.optimizer.standard_optimizer), python3(PyDSTool.Toolbox.optimizers.optimizer.standard_optimizer_modifying), python3(PyDSTool.Toolbox.optimizers.step), python3(PyDSTool.Toolbox.optimizers.step.conjugate_gradient_step), python3(PyDSTool.Toolbox.optimizers.step.goldfeld_step), python3(PyDSTool.Toolbox.optimizers.step.goldstein_price_step), python3(PyDSTool.Toolbox.optimizers.step.gradient_step), python3(PyDSTool.Toolbox.optimizers.step.local_brute_force_1dstep), python3(PyDSTool.Toolbox.optimizers.step.marquardt_step), python3(PyDSTool.Toolbox.optimizers.step.newton_step), python3(PyDSTool.Toolbox.optimizers.step.partial_step), python3(PyDSTool.Toolbox.optimizers.step.quasi_newton_step), python3(PyDSTool.Toolbox.optimizers.step.restart_conjugate_gradient), python3(PyDSTool.Toolbox.optimizers.tests), python3(PyDSTool.Toolbox.optimizers.tests.test_powell), python3(PyDSTool.Toolbox.optimizers.tests.test_quadratic), python3(PyDSTool.Toolbox.optimizers.tests.test_rosenbrock), python3(PyDSTool.Toolbox.phaseplane), python3(PyDSTool.Toolbox.prep_boxplot), python3(PyDSTool.Toolbox.synthetic_data), python3(PyDSTool.Toolbox.syntheticdata), python3(PyDSTool.Toolbox.test_protocols), python3(PyDSTool.Trajectory), python3(PyDSTool.Variable), python3(PyDSTool.common), python3(PyDSTool.conf), python3(PyDSTool.errors), python3(PyDSTool.fixedpickle), python3(PyDSTool.integrator), python3(PyDSTool.matplotlib_import), python3(PyDSTool.parseUtils), python3(PyDSTool.scipy_ode), python3(PyDSTool.utils), python3(Redirector), python3(Symbolic), python3(Toolbox), python3(Toolbox.ActivationFuncs), python3(Toolbox.DSSRT_tools), python3(Toolbox.FR), python3(Toolbox.FSM), python3(Toolbox.InputProfile), python3(Toolbox.ModelEst), python3(Toolbox.ModelHelper), python3(Toolbox.NineML), python3(Toolbox.PRCtools), python3(Toolbox.ParamEst), python3(Toolbox.PySCes_SBML), python3(Toolbox.adjointPRC), python3(Toolbox.data_analysis), python3(Toolbox.dssrt), python3(Toolbox.event_driven_simulator), python3(Toolbox.fracdim), python3(Toolbox.makeSloppyModel), python3(Toolbox.mechmatlib), python3(Toolbox.model_primitives), python3(Toolbox.neuralcomp), python3(Toolbox.neuro_data), python3(Toolbox.optimizers), python3(Toolbox.optimizers.criterion), python3(Toolbox.optimizers.criterion.composite_criteria), python3(Toolbox.optimizers.criterion.criteria), python3(Toolbox.optimizers.criterion.facilities), python3(Toolbox.optimizers.criterion.information_criteria), python3(Toolbox.optimizers.defaults), python3(Toolbox.optimizers.helpers), python3(Toolbox.optimizers.helpers.finite_difference), python3(Toolbox.optimizers.helpers.levenberg_marquardt), python3(Toolbox.optimizers.helpers.quadratic), python3(Toolbox.optimizers.line_search), python3(Toolbox.optimizers.line_search.adaptive_last_step_modifier), python3(Toolbox.optimizers.line_search.backtracking_search), python3(Toolbox.optimizers.line_search.barzilai_borwein_non_monotone_search), python3(Toolbox.optimizers.line_search.barzilai_borwein_search), python3(Toolbox.optimizers.line_search.cubic_interpolation), python3(Toolbox.optimizers.line_search.damped_line_search), python3(Toolbox.optimizers.line_search.fibonacci_section), python3(Toolbox.optimizers.line_search.fixed_last_step_modifier), python3(Toolbox.optimizers.line_search.golden_section), python3(Toolbox.optimizers.line_search.goldstein_rule), python3(Toolbox.optimizers.line_search.hyperbolic_line_search), python3(Toolbox.optimizers.line_search.quadratic_interpolation), python3(Toolbox.optimizers.line_search.scaled_line_search), python3(Toolbox.optimizers.line_search.simple_line_search), python3(Toolbox.optimizers.line_search.strong_wolfe_powell_rule), python3(Toolbox.optimizers.line_search.wolfe_powell_rule), python3(Toolbox.optimizers.optimizer), python3(Toolbox.optimizers.optimizer.optimizer), python3(Toolbox.optimizers.optimizer.standard_optimizer), python3(Toolbox.optimizers.optimizer.standard_optimizer_modifying), python3(Toolbox.optimizers.step), python3(Toolbox.optimizers.step.conjugate_gradient_step), python3(Toolbox.optimizers.step.goldfeld_step), python3(Toolbox.optimizers.step.goldstein_price_step), python3(Toolbox.optimizers.step.gradient_step), python3(Toolbox.optimizers.step.local_brute_force_1dstep), python3(Toolbox.optimizers.step.marquardt_step), python3(Toolbox.optimizers.step.newton_step), python3(Toolbox.optimizers.step.partial_step), python3(Toolbox.optimizers.step.quasi_newton_step), python3(Toolbox.optimizers.step.restart_conjugate_gradient), python3(Toolbox.optimizers.tests), python3(Toolbox.optimizers.tests.test_powell), python3(Toolbox.optimizers.tests.test_quadratic), python3(Toolbox.optimizers.tests.test_rosenbrock), python3(Toolbox.phaseplane), python3(Toolbox.prep_boxplot), python3(Toolbox.synthetic_data), python3(Toolbox.syntheticdata), python3(Toolbox.test_protocols), python3(Trajectory), python3(Variable), python3(common), python3(conf), python3(errors), python3(fixedpickle), python3(integrator), python3(matplotlib_import), python3(parseUtils), python3(scipy_ode), python3(utils)
Requires: /bin/sh, /usr/bin/dos2unix, /usr/lib64/python3/site-packages, python3(binascii) < 0, python3(copy) < 0, python3(copyreg) < 0, python3(distutils) < 0, python3(distutils.core) < 0, python3(distutils.sysconfig) < 0, python3(functools) < 0, python3(io) < 0, python3(math) < 0, python3(matplotlib.font_manager) < 0, python3(matplotlib.pyplot) < 0, python3(mpl_toolkits.mplot3d) < 0, python3(nineml.abstraction_layer) < 0, python3(numpy) < 0, python3(numpy.distutils.core) < 0, python3(numpy.linalg) < 0, python3(numpy.random) < 0, python3(numpy.testing) < 0, python3(numpy.testing.utils) < 0, python3(operator) < 0, python3(os) < 0, python3(os.path) < 0, python3(parser) < 0, python3(pickle) < 0, python3(platform) < 0, python3(pprint) < 0, python3(random) < 0, python3(re) < 0, python3(scipy.interpolate) < 0, python3(scipy.io) < 0, python3(scipy.linalg) < 0, python3(scipy.optimize) < 0, python3(scipy.signal) < 0, python3(scipy.special) < 0, python3(shutil) < 0, python3(struct) < 0, python3(symbol) < 0, python3(tempfile) < 0, python3(token) < 0, python3(traceback) < 0, python3(types) < 0, python3(unittest) < 0, python3(warnings) < 0
Finding debuginfo files (using /usr/lib/rpm/find-debuginfo-files)
Executing: /bin/sh -e /usr/src/tmp/rpm-tmp.exEs32
Wrote: /usr/src/RPM/RPMS/x86_64/python-module-PyDSTool-0.88.121202-alt3.bzr20130716.1.1.x86_64.rpm (w2T8.xzdio)
Wrote: /usr/src/RPM/RPMS/x86_64/python3-module-PyDSTool-0.88.121202-alt3.bzr20130716.1.1.x86_64.rpm (w2T8.xzdio)
132.09user 9.92system 2:20.77elapsed 100%CPU (0avgtext+0avgdata 210672maxresident)k
0inputs+0outputs (0major+1858309minor)pagefaults 0swaps
6.01user 1.86system 2:35.09elapsed 5%CPU (0avgtext+0avgdata 134576maxresident)k
0inputs+0outputs (0major+275967minor)pagefaults 0swaps
--- python3-module-PyDSTool-0.88.121202-alt3.bzr20130716.1.1.x86_64.rpm.repo 2019-04-22 01:33:20.000000000 +0000
+++ python3-module-PyDSTool-0.88.121202-alt3.bzr20130716.1.1.x86_64.rpm.hasher 2024-02-11 17:11:45.370871052 +0000
@@ -2913,5 +2913,5 @@
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-File: /usr/lib64/python3/site-packages/PyDSTool/__pycache__/fixedpickle.cpython-37.pyc 100644 root:root e176104b1da2dab9f7937deff66c2de9
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+File: /usr/lib64/python3/site-packages/PyDSTool/__pycache__/fixedpickle.cpython-37.opt-2.pyc 100644 root:root d0f0d36cdc18bcb7396ef91023720690
+File: /usr/lib64/python3/site-packages/PyDSTool/__pycache__/fixedpickle.cpython-37.pyc 100644 root:root 630ae54f76e1cd9b7c882c2cd934ddf2
File: /usr/lib64/python3/site-packages/PyDSTool/__pycache__/integrator.cpython-37.opt-1.pyc 100644 root:root 622e974dbc8f4c7983c2f84949e52fe9
@@ -4163,2 +4163,2 @@
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