debian/changelog

+microbegps (1.0.0-4) unstable; urgency=medium
+
+  * Use 2to3 to port to Python3
+    Closes: #937043
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Secure URI in copyright format
+  * Use secure URI in debian/watch.
+  * Set upstream metadata fields: Archive.
+
+ -- Andreas Tille <tille@debian.org>  Thu, 05 Sep 2019 16:56:54 +0200
+
 microbegps (1.0.0-3) unstable; urgency=medium
 
   * debhelper 11

debian/compat

-11

debian/control

@@ -3,12 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
-               python,
-               python-setuptools,
-               python-qt4
-Standards-Version: 4.1.4
+               python3,
+               python3-setuptools,
+               python3-pyqt4
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/microbegps
 Vcs-Git: https://salsa.debian.org/med-team/microbegps.git
 Homepage: http://sourceforge.net/projects/microbegps/
@@ -16,9 +16,9 @@ Homepage: http://sourceforge.net/projects/microbegps/
 Package: microbegps
 Architecture: all
 Depends: ${misc:Depends},
-         ${python:Depends},
-         python-matplotlib-venn,
-         python-qt4
+         ${python3:Depends},
+         python3-matplotlib-venn,
+         python3-pyqt4
 Description: explorative taxonomic profiling tool for metagenomic data
  MicrobeGPS is a bioinformatics tool for the analysis of metagenomic
  sequencing data. The goal is to profile the composition of metagenomic

debian/copyright

-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: MicrobeGPS
 Upstream-Contact: Martin S. Lindner <LindnerM@rki.de>
 Source: http://sourceforge.net/projects/microbegps/files/

debian/patches/2to3.patch

+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/937043
 Author: Andreas Tille <tille@debian.org>
-Last-Update: Wed, 06 May 2015 15:53:45 +0200
-Description: Patch created by 2to3 to run with Python3
-
+Last-Update: Thu, 05 Sep 2019 16:17:31 +0200
+
+--- a/README
++++ b/README
+@@ -52,7 +52,7 @@ Installation
+ 
+   * Source distribution
+     Download the MicrobeGPS source file from the project home page. This method
+-    requires you to have Python (>= 2.7), PyQt4 and pip installed. To install 
++    requires you to have Python3 (>= 3.3), PyQt4 and pip installed. To install 
+     MicrobeGPS, run the following command from your command line:
+     > pip install MicrobeGPS-X.X.tax.gz
+     Now you can run the program by typing MicrobeGPS on the command line.
+@@ -61,9 +61,9 @@ Installation
+     Check out a current development snapshot from the MicrobeGPS project page.
+     Navigate to the MicrobeGPS directory. Now you can directly run MicrobeGPS  
+     from the command line with:
+-    > python run.py
++    > python3 run.py
+     Install MicrobeGPS using the provided setup.py script:
+-    > python setup.py install
++    > python3 setup.py install
+     Now you can run the program by typing MicrobeGPS on the command line.
+ 
+ 
+@@ -77,13 +77,13 @@ If you want to use the source distributi
+ following dependencies.
+ 
+ Software:
+-  * Python (2.7)
++  * Python3 (3.3)
+ Python packages:
+   * setuptools (1.3)
+   * PyQt4 (4.9)
+ 
+-The following Python packages must be installed manually, if the tool is not
+-installed as a python egg or via the setup.py script:
++The following Python3 packages must be installed manually, if the tool is not
++installed as a python3 egg or via the setup.py script:
+   * numpy (1.8.0)
+   * scipy (0.13.0)
+   * matplotlib (1.3.1)
+--- a/microbegps/__init__.py
++++ b/microbegps/__init__.py
+@@ -1,3 +1,3 @@
+-from __version__ import __version__,__url__
++from .__version__ import __version__,__url__
+ #__version__='1.0.0'
+ #__url__='https://sourceforge.net/p/microbegps'
+\ No newline at end of file
 --- a/microbegps/gps.py
 +++ b/microbegps/gps.py
 @@ -5,11 +5,11 @@ Analysis tools used by MicrobeGPS
@@ -236,6 +285,15 @@ Description: Patch created by 2to3 to run with Python3
  				pool.close()
  				#GpsTools.calculate_valcov(p.ref_table,printer)
  				def custom_filt2(ref):
+@@ -879,7 +879,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
+ 		self.load_modules()
+ 
+ 	def load_modules(self):
+-		""" Loads all python modules located in 'modules'. This function was 
++		""" Loads all python3 modules located in 'modules'. This function was 
+ 		inspired by Luca Invernizzi on http://stackoverflow.com/a/8556471"""
+ 		modules_d = dict()
+ 		for importer, mod_name, _ in pkgutil.iter_modules(modules.__path__):
 @@ -892,7 +892,7 @@ class GPSAnalyzer(QtGui.QMainWindow):
  				self.pr('<b><font color="DarkRed">Failed loading module %s</font></b><br>Message: <i>%s</i>'%(mod_name,e.message))			
  		self.modules = modules_d
@@ -394,14 +452,13 @@ Description: Patch created by 2to3 to run with Python3
  					assert type(settings) == dict
  					try:
  						sgroups = settings['candidates']
---- a/microbegps/__init__.py
-+++ b/microbegps/__init__.py
-@@ -1,3 +1,3 @@
--from __version__ import __version__,__url__
-+from .__version__ import __version__,__url__
- #__version__='1.0.0'
- #__url__='https://sourceforge.net/p/microbegps'
+@@ -1739,4 +1739,4 @@ def main():
+ 	app.exec_()	
+ 
+ if __name__ == '__main__':
+-	main()
 \ No newline at end of file
++	main()
 --- a/microbegps/modules/composition_analysis.py
 +++ b/microbegps/modules/composition_analysis.py
 @@ -79,15 +79,15 @@ class GPSModule:

debian/patches/series

-# 2to3.patch
+2to3.patch

debian/rules

@@ -2,13 +2,16 @@
 
 export DH_VERBOSE := 1
 export PYBUILD_NAME=microbegps
-INTERPRETER=python2.7
+INTERPRETER=python3
 
 %:
-	dh $@ --with python2 --buildsystem=pybuild
+	dh $@ --with python3 --buildsystem=pybuild
 
 override_dh_install:
 	dh_install
 	mkdir -p debian/$(PYBUILD_NAME)/usr/share/$(PYBUILD_NAME)
-	mv debian/$(PYBUILD_NAME)/usr/lib/$(INTERPRETER)/dist-packages/microbegps/data debian/$(PYBUILD_NAME)/usr/share/$(PYBUILD_NAME)
-	ln -s ../../../../share/$(PYBUILD_NAME)/data debian/$(PYBUILD_NAME)/usr/lib/$(INTERPRETER)/dist-packages/microbegps/
+	mv debian/$(PYBUILD_NAME)/usr/lib/$(INTERPRETER)*/dist-packages/microbegps/data debian/$(PYBUILD_NAME)/usr/share/$(PYBUILD_NAME)
+
+override_dh_link:
+	dh_link
+	dh_link /usr/share/$(PYBUILD_NAME)/data /usr/lib/$(INTERPRETER)/dist-packages/$(PYBUILD_NAME)/data

debian/upstream/metadata

@@ -17,3 +17,4 @@ Registry:
   Entry: MicrobeGPS
 - Name: SciCrunch
   Entry: NA
+Archive: SourceForge

debian/watch

 version=3
 
-http://sf.net/microbegps/MicrobeGPS-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))
+https://sf.net/microbegps/MicrobeGPS-(\d[\d\.]+)\.(?:tgz|tbz|txz|(?:tar\.(?:gz|bz2|xz)))