Another chunk of manual 2to3 re-runs

 def main():

--- a/Cain.py

+++ b/Cain.py

@@ -1,4 +1,4 @@

-#! /usr/bin/env python

+#! /usr/bin/python3

 """The script that launches Cain."""

@@ -32,15 +32,15 @@ def main():

         errors.append('Consult the documentation available at http://cain.sourceforge.net/.')

         hasTk = True

         try:

-            import Tkinter

+            import tkinter

         except:

             hasTk = False

         if hasTk:

-            import tkMessageBox

-            root = Tkinter.Tk()

+            import tkinter.messagebox

+            root = tkinter.Tk()

             #Tkinter.Label(root, text='\n'.join(errors)).pack()

             #root.title('Error')

-            tkMessageBox.showwarning('Error', '\n'.join(errors))

+            tkinter.messagebox.showwarning('Error', '\n'.join(errors))

             root.mainloop()

         else:

             print('\n'.join(errors))

@@ -49,7 +49,7 @@ def main():

     # Launch the application.

     from gui.Application import Application

     if len(sys.argv) > 2:

-        print "Warning: Unmatched command line arguments."

+        print("Warning: Unmatched command line arguments.")

     app = Application()

     if len(sys.argv) == 2:

         #app.readInitialFile(sys.argv[1])

--- a/gui/Preferences.py

+++ b/gui/Preferences.py

@@ -1,6 +1,6 @@

 """Implements the preferences."""

-from PreferencesDialog import PreferencesDialog

+from .PreferencesDialog import PreferencesDialog

 from copy import copy

 import wx

 import sys

@@ -63,9 +63,9 @@ def main():

     preferences.openDialog()

     app.MainLoop()

     for category in preferences.data:

-        print category

+        print(category)

         for field in preferences.data[category]:

-            print '    ', preferences.data[category][field]

+            print('    ', preferences.data[category][field])

 if __name__ == '__main__':

     main()

--- a/gui/Launcher.py

+++ b/gui/Launcher.py

@@ -24,7 +24,7 @@ def cpuCount():

         # http://codeliberates.blogspot.com/2008/05/detecting-cpuscores-in-python.html

         # Linux, Unix and MacOS:

         if hasattr(os, "sysconf"):

-            if os.sysconf_names.has_key("SC_NPROCESSORS_ONLN"):

+            if "SC_NPROCESSORS_ONLN" in os.sysconf_names:

                 # Linux & Unix:

                 count = os.sysconf("SC_NPROCESSORS_ONLN")

                 if isinstance(count, int) and count > 0:

@@ -32,7 +32,7 @@ def cpuCount():

             else: # OS X:

                 return int(os.popen2("sysctl -n hw.ncpu")[1].read())

         # Windows:

-        if os.environ.has_key("NUMBER_OF_PROCESSORS"):

+        if "NUMBER_OF_PROCESSORS" in os.environ:

             count = int(os.environ["NUMBER_OF_PROCESSORS"]);

             if count > 0:

                 return count

@@ -362,28 +362,28 @@ class LauncherFrame(wx.Frame):

                             self.importTrajectories)

     def launch(self):

-        print 'launch'

+        print('launch')

     def compile(self):

-        print 'compile'

+        print('compile')

     def stop(self):

-        print 'stop'

+        print('stop')

     def kill(self):

-        print 'kill'

+        print('kill')

     def saveExecutable(self):

-        print 'saveExecutable'

+        print('saveExecutable')

     def exportJobs(self):

-        print 'exportJobs'

+        print('exportJobs')

     def importTrajectories(self):

-        print 'importTrajectories'

+        print('importTrajectories')

     def exportMathematica(self):

-        print 'exportMathematica'

+        print('exportMathematica')

     def getSelectedModelId(self):

         return '1'

--- a/fio/ValueTextParser.py

+++ b/fio/ValueTextParser.py

@@ -77,21 +77,21 @@ def main():

     assert not parser.parse('a', '', '', [])

     assert not parser.parse('a', 'expression', '', ['a'])

-    print parser.parseTable([['a', 'expression', '']], [])

+    print(parser.parseTable([['a', 'expression', '']], []))

     assert not parser.errorMessage

-    print parser.parseTable([['', 'expression', '']], [])

+    print(parser.parseTable([['', 'expression', '']], []))

     assert parser.errorMessage

-    print parser.errorMessage

+    print(parser.errorMessage)

-    print parser.parseTable([['a', '', '']], [])

+    print(parser.parseTable([['a', '', '']], []))

     assert parser.errorMessage

-    print parser.errorMessage

+    print(parser.errorMessage)

-    print parser.parseTable([['a', 'expression', ''], ['a', 'expression', '']],

-                            [])

+    print(parser.parseTable([['a', 'expression', ''], ['a', 'expression', '']],

+                            []))

     assert parser.errorMessage

-    print parser.errorMessage

+    print(parser.errorMessage)

 if __name__ == '__main__':

     main()

--- a/fio/TriggerEventTextParser.py

+++ b/fio/TriggerEventTextParser.py

@@ -89,28 +89,28 @@ def main():

     assert not parser.parse('1', 't>1', 's1=2', '0', '', 'name', [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     assert not parser.parse('e1', '', 's1=2', '0', '', 'name', [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     assert not parser.parse('e1', 't>1', '', '0', '', 'name', [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     assert not parser.parse('e1', 't>1', 's1=2', 'a', '', 'name', [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     assert not parser.parse('e1', 't>1', 's1=2', '-1', '', 'name', [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     identifiers = []

     assert parser.parseTable([['e1', 't>1', 's1=2', '0', '', 'name']],

@@ -118,8 +118,8 @@ def main():

     assert not parser.parseTable([['e1', 't>1', 's1=2', '0', '', 'name']],

                                  identifiers)

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

 if __name__ == '__main__':

     main()

--- a/fio/ReactionTextParser.py

+++ b/fio/ReactionTextParser.py

@@ -161,38 +161,38 @@ def main():

     assert not parser.parse('1', 's1 + 2 s2', 's3', '1', '2.5', 'reaction 1',

                             ['s1', 's2', 's3'], [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     assert not parser.parse('r1', '1 + 2 s2', 's3', '1', '2.5', 'reaction 1',

                             ['s1', 's2', 's3'], [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     assert not parser.parse('r1', 's1 - 2 s2', 's3', '1', '2.5', 'reaction 1',

                             ['s1', 's2', 's3'], [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     assert not parser.parse('r1', 's1 + 2 s2', '3', '1', '2.5', 'reaction 1',

                             ['s1', 's2', 's3'], [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     assert not parser.parse('r1', 's1 + 2 s2', 's3 + s4', '1', 'reaction 1',

                             '2.5', ['s1', 's2', 's3'], [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     assert not parser.parse('r1', 's1 + 2 s2', 's3', '1', '', 'reaction 1',

                             ['s1', 's2', 's3'], [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     # Does not check for negative numbers.

     assert parser.parse('r1', 's1 + 2 s2', 's3', '1', '-2.5', 'reaction 1',

@@ -201,8 +201,8 @@ def main():

     assert not parser.parse('r1', 's1 + 2 s2', 's3', '1', '2.5', 'reaction 1',

                             ['s1', 's2', 's3'], ['r1'])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     assert parser.parseTable(

         [['r1', 's1 + 2 s2', 's3', '1', '2.5', 'reaction 1']],

@@ -219,16 +219,16 @@ def main():

         [['1', 's1 + 2 s2', 's3', '1', '2.5', 'reaction 1']],

         ['s1', 's2', 's3'], [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     assert not parser.parseTable(

         [['r1', 's1 + 2 s2', 's3', '1', '2.5', 'reaction 1'],

          ['r1', 's1 + s2', 's3', '1', '2.5', 'reaction 2']],

         ['s1', 's2', 's3'], [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

 if __name__ == '__main__':

     main()

--- a/fio/TimeEventTextParser.py

+++ b/fio/TimeEventTextParser.py

@@ -88,35 +88,35 @@ def main():

     assert not parser.parse('1', '1', 's1=2', 'name', [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     assert not parser.parse('e1', '1', 's1=2', 'name', ['e1'])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     assert not parser.parse('e1', 'a', 's1=2', 'name', [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     assert not parser.parse('e1', '[a]', 's1=2', 'name', [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     assert not parser.parse('e1', '1', '', 'name', [])

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

     identifiers = []

     assert parser.parseTable([['e1', '1', 's1=2', 'name']], identifiers)

     assert not parser.parseTable([['e1', '1', 's1=2', 'name']], identifiers)

     assert parser.errorMessage

-    print parser.errorMessage

-    print ''

+    print(parser.errorMessage)

+    print('')

 if __name__ == '__main__':

     main()

--- a/fio/SpeciesTextParser.py

+++ b/fio/SpeciesTextParser.py

@@ -101,23 +101,23 @@ def main():

     assert not parser.parse('a', '', '', 'c1', [])

     assert not parser.parse('a', '1', '', 'c1', ['a'])

-    print parser.parseTable([['s1', '100', 'species 1', 'c1']], [])

+    print(parser.parseTable([['s1', '100', 'species 1', 'c1']], []))

     assert not parser.errorMessage

-    print parser.parseTable([['s1', '100', 'species 1', 'c1'],

-                             ['s2', '200', 'species 2', 'c1']], [])

+    print(parser.parseTable([['s1', '100', 'species 1', 'c1'],

+                             ['s2', '200', 'species 2', 'c1']], []))

     assert not parser.errorMessage

-    print parser.parseTable([['1', '100', 'species 1', 'c1']], [])

+    print(parser.parseTable([['1', '100', 'species 1', 'c1']], []))

     assert parser.errorMessage

-    print parser.errorMessage

+    print(parser.errorMessage)

-    print parser.parseTable([['s1', '100', 'species 1', 'c1'],

-                             ['s1', '200', 'species 2', 'c1']], [])

+    print(parser.parseTable([['s1', '100', 'species 1', 'c1'],

+                             ['s1', '200', 'species 2', 'c1']], []))

     assert parser.errorMessage

-    print parser.errorMessage

+    print(parser.errorMessage)

-    print parser.parseTable([['s1', '100', 'species 1', 'c1']], [])

+    print(parser.parseTable([['s1', '100', 'species 1', 'c1']], []))

     assert not parser.errorMessage

 if __name__ == '__main__':

--- a/fio/readModelText.py

+++ b/fio/readModelText.py

@@ -48,7 +48,7 @@ def readModelText(input):

         for n in range(numberOfSpecies):

             model.species[sid[n]] = Species('', '', initialAmounts[n])

         # Read the packed reactions into a list of integers.

-        data = map(int, input.readline().rstrip().split())

+        data = list(map(int, input.readline().rstrip().split()))

         # The propensity factors.

         propensityFactors = input.readline().rstrip().split()

         # Add the reactions.

@@ -82,7 +82,7 @@ def readModelText(input):

                                             True, propensityFactors[i]))

         # Return the model.

         return model

-    except Exception, error:

+    except Exception as error:

         print(error)

         return None

--- a/gui/MainFrame.py

+++ b/gui/MainFrame.py

@@ -17,19 +17,19 @@ import threading

 import webbrowser

 import platform

 import tempfile

-import urllib2

+import urllib.request, urllib.error, urllib.parse

-from About import About

-from IdentifierListEditor import IdentifierListEditor

-from ModelEditor import ModelEditor, EVT_SPECIES_OR_REACTIONS_MODIFIED

-from Record import Record

-from MethodEditor import MethodEditor

-from Launcher import Launcher

-from TrajectoriesList import TrajectoriesList

-from PlotTimeSeries import closeAll

+from .About import About

+from .IdentifierListEditor import IdentifierListEditor

+from .ModelEditor import ModelEditor, EVT_SPECIES_OR_REACTIONS_MODIFIED

+from .Record import Record

+from .MethodEditor import MethodEditor

+from .Launcher import Launcher

+from .TrajectoriesList import TrajectoriesList

+from .PlotTimeSeries import closeAll

 from resourcePath import resourcePath

-from DuplicateDialog import DuplicateDialog

-from StateModified import EVT_STATE_MODIFIED

+from .DuplicateDialog import DuplicateDialog

+from .StateModified import EVT_STATE_MODIFIED

 from fio.SpeciesTextParser import SpeciesTextParser

 from fio.ReactionTextParser import ReactionTextParser

 from fio.TimeEventTextParser import TimeEventTextParser

@@ -38,7 +38,7 @@ from fio.ParameterTextParser import Para

 from fio.CompartmentTextParser import CompartmentTextParser

 from state.State import State

 import state.simulationMethods as simulationMethods

-from messages import UpdateVersionFrame, ScrolledMessageFrame,\

+from .messages import UpdateVersionFrame, ScrolledMessageFrame,\

      CompilationError, CompilingMessage, truncatedMessageBox,\

      truncatedErrorBox, openWrite

@@ -200,7 +200,7 @@ class MainFrame(wx.Frame):

     def checkVersion(self):

         try:

             url = 'http://cain.sourceforge.net/version.txt'

-            currentVersion = urllib2.urlopen(url, timeout=2).read()

+            currentVersion = urllib.request.urlopen(url, timeout=2).read()

             c = currentVersion.split('.')

             t = self.state.version.split('.')

             if int(t[0]) < int(c[0]) or \

@@ -1026,7 +1026,7 @@ class MainFrame(wx.Frame):

                 self.state.importStatistics(filename, self.modelId, 

                                             self.methodId, recordedSpecies)

                 self.updateSimulations()

-            except Exception, exception:

+            except Exception as exception:

                 truncatedErrorBox("Problem in importing %s.\n" % filename +

                                   str(exception))

                 self.deleteOutput(self.modelId, self.methodId)

@@ -1059,7 +1059,7 @@ class MainFrame(wx.Frame):

                 self.state.importSuiteOfTrajectories(dialog.GetPaths(),

                                                      self.modelId,

                                                      self.methodId)

-            except Exception, exception:

+            except Exception as exception:

                 truncatedErrorBox("Problem in importing trajectories.\n" +

                                   str(exception))

             self.updateSimulations()

@@ -1088,7 +1088,7 @@ class MainFrame(wx.Frame):

             if re.search('<sbml', open(filename, 'r').read()):

                 self.importSbml(filename, useMessageBox)

                 return

-        except Exception, exception:

+        except Exception as exception:

             if useMessageBox:

                 truncatedErrorBox('Problem in determining the file type for ' +

                                   filename + '.\n' + str(exception))

@@ -1119,7 +1119,7 @@ class MainFrame(wx.Frame):

             self.filename = filename

             self.SetTitle(self.title + ' -- ' + self.filename)

             self.isModified = False

-        except Exception, exception:

+        except Exception as exception:

             if useMessageBox:

                 truncatedErrorBox("Problem in reading %s.\n" % filename +

                                   errors + '\n' + str(exception))

@@ -1146,7 +1146,7 @@ class MainFrame(wx.Frame):

                 # Select the model.

                 self.modelsList.selectLast()

             self.isModified = True

-        except Exception, exception:

+        except Exception as exception:

             if useMessageBox:

                 truncatedErrorBox("Problem in importing %s.\n" % filename +

                                   errors + '\n' + str(exception))

@@ -1170,7 +1170,7 @@ class MainFrame(wx.Frame):

             # Select the model.

             self.modelsList.selectLast()

             self.isModified = True

-        except Exception, exception:

+        except Exception as exception:

             if useMessageBox:

                 truncatedErrorBox("Problem in importing text model %s.\n"

                                   % filename + '\n' + str(exception))