debian/bin/cain

 #!/bin/sh
 mkdir -p ~/.cain
-python /usr/share/cain/Cain.py
+python3 /usr/share/cain/Cain.py

debian/changelog

@@ -8,6 +8,11 @@ cain (1.10+dfsg-4) UNRELEASED; urgency=medium
   * Build-Depends: dh-python
   * Use 2to3 to port to Python3
     Closes: #936261
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Respect DEB_BUILD_OPTIONS in override_dh_auto_test target
+  * Do not parse d/changelog
+  * Use secure URI in debian/watch.
 
  -- Andreas Tille <tille@debian.org>  Tue, 10 Sep 2019 20:29:13 +0200
 

debian/compat

-11

debian/control

@@ -4,28 +4,28 @@ Uploaders: Ivo Maintz <ivo@maintz.de>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
-               python-all-dev,
-               python (<< 3.0),
+               python3-all-dev,
+               python3,
                libeigen3-dev,
                zip
-Standards-Version: 4.1.5
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/cain
 Vcs-Git: https://salsa.debian.org/med-team/cain.git
 Homepage: http://cain.sourceforge.net
 
 Package: cain
 Architecture: all
-Depends: ${python:Depends},
+Depends: ${python3:Depends},
          ${shlibs:Depends},
          ${misc:Depends},
-         python (<< 3.0),
-         python-wxgtk3.0,
-         python-matplotlib,
-         python-numpy,
-         python-scipy,
-         python-sympy,
+         python3,
+         python3-wxgtk4.0,
+         python3-matplotlib,
+         python3-numpy,
+         python3-scipy,
+         python3-sympy,
          cain-solvers
 Recommends: cain-examples
 Description: simulations of chemical reactions
@@ -36,7 +36,7 @@ Description: simulations of chemical reactions
  exported. The models and methods can be read from input files or edited
  within the program.
  .
- The GUI (Graphical User Interface) is written in Python and uses the wxPython
+ The GUI (Graphical User Interface) is written in Python3 and uses the wxPython
  toolkit. Most of the solvers are implemented as command line executables,
  written in C++, which are driven by Cain. This makes it easy to launch batch
  jobs. It also simplifies the process of adding new solvers. Cain offers a
@@ -63,7 +63,7 @@ Description: solvers for cain
  exported. The models and methods can be read from input files or edited
  within the program.
  .
- The GUI (Graphical User Interface) is written in Python and uses the wxPython
+ The GUI (Graphical User Interface) is written in Python3 and uses the wxPython
  toolkit. Most of the solvers are implemented as command line executables,
  written in C++, which are driven by Cain. This makes it easy to launch batch
  jobs. It also simplifies the process of adding new solvers. Cain offers a
@@ -90,7 +90,7 @@ Description: examples for cain
  exported. The models and methods can be read from input files or edited
  within the program.
  .
- The GUI (Graphical User Interface) is written in Python and uses the wxPython
+ The GUI (Graphical User Interface) is written in Python3 and uses the wxPython
  toolkit. Most of the solvers are implemented as command line executables,
  written in C++, which are driven by Cain. This makes it easy to launch batch
  jobs. It also simplifies the process of adding new solvers. Cain offers a

debian/patches/2to3.patch

@@ -5,7 +5,13 @@ Last-Update: Tue, 10 Sep 2019 20:29:13 +0200
 
 --- a/Cain.py
 +++ b/Cain.py
-@@ -32,24 +32,24 @@ def main():
+@@ -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:
@@ -24,10 +30,8 @@ Last-Update: Tue, 10 Sep 2019 20:29:13 +0200
 +            tkinter.messagebox.showwarning('Error', '\n'.join(errors))
              root.mainloop()
          else:
--            print('\n'.join(errors))
-+            print(('\n'.join(errors)))
-         sys.exit(1)
- 
+             print('\n'.join(errors))
+@@ -49,7 +49,7 @@ def main():
      # Launch the application.
      from gui.Application import Application
      if len(sys.argv) > 2:
@@ -602,7 +606,12 @@ Last-Update: Tue, 10 Sep 2019 20:29:13 +0200
      main()
 --- a/fio/SbmlReader.py
 +++ b/fio/SbmlReader.py
-@@ -17,15 +17,15 @@ def readSbmlFile(fileName):
+@@ -1,3 +1,4 @@
++#!/usr/bin/python3
+ """SBML reader.
+ This code is currently not used. I cannot get libsbml and wxPython to work
+ together. Thus I wrote my own SBML parser in ContentHandlerSbml."""
+@@ -17,15 +18,15 @@ def readSbmlFile(fileName):
      # Create an empty model.
      model = Model()
      # Read the SBML file.
@@ -621,14 +630,14 @@ Last-Update: Tue, 10 Sep 2019 20:29:13 +0200
      #sbmlModel = document.getModel()
      sbmlModel = libsbml.SBMLReader().readSBML(fileName).getModel()
      # Model identifier.
-@@ -77,8 +77,8 @@ def readSbmlFile(fileName):
+@@ -77,8 +78,8 @@ def readSbmlFile(fileName):
  
  if __name__ == '__main__':
      if (len(sys.argv) != 2):
 -        print 'Usage:'
 -        print 'python SbmlReader.py file.xml'
 +        print('Usage:')
-+        print('python SbmlReader.py file.xml')
++        print('python3 SbmlReader.py file.xml')
          raise 'Bad command line arguments.'
 -    print sys.argv[1]
 +    print(sys.argv[1])
@@ -2532,3 +2541,26 @@ Last-Update: Tue, 10 Sep 2019 20:29:13 +0200
          if not 'expression' in keys:
              return 'Missing expression attribute in parameter or compartment.\n'
          self.expression = attributes['expression']
+--- a/gui/Application.py
++++ b/gui/Application.py
+@@ -1,4 +1,4 @@
+-#! /usr/bin/env python
++#!/usr/bin/python3
+ 
+ """The script that launches Cain."""
+ 
+--- a/fio/SbmlLevel1To2.py
++++ b/fio/SbmlLevel1To2.py
+@@ -1,10 +1,11 @@
++#!/usr/bin/python3
+ """SbmlLevel1To2.py."""
+ 
+ import sys, re
+ 
+ if len(sys.argv) != 3:
+     print("""Usage:
+-python SbmlLevel1To2.py input.xml output.xml
++python3 SbmlLevel1To2.py input.xml output.xml
+ Bad command line arguments. Exiting...""")
+     sys.exit()
+ 

debian/rules

@@ -6,13 +6,13 @@ SRC_TMP=$(CURDIR)/SRC_TMP
 debtmp := $(CURDIR)/debian/tmp
 
 include /usr/share/dpkg/default.mk
-BUILD_DATE := $(shell dpkg-parsechangelog | grep Date: | cut -d' ' -f2-7)
+BUILD_DATE := $(shell TZ=UTC LC_ALL=C date --date="@$(SOURCE_DATE_EPOCH)" +'%b %d %Y')
 
 export TZ=UTC
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
 
 %:
-	dh $@ --with python2
+	dh $@ --with python3
 
 override_dh_auto_clean:
 	dh_auto_clean
@@ -37,4 +37,6 @@ override_dh_install-indep:
 	fi
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	echo "no tests implemented"
+endif

debian/watch

 version=3
 opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,uversionmangle=s/_/./" \
-  http://sf.net/cain/[cC]ain-(\d[\d\._]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))|zip)
+  https://sf.net/cain/[cC]ain-(\d[\d\._]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz))|zip)