[med-svn] [Git][med-team/microbegps][master] 8 commits: Use 2to3 to port to Python3
Andreas Tille
gitlab at salsa.debian.org
Thu Sep 5 16:11:31 BST 2019
Andreas Tille pushed to branch master at Debian Med / microbegps
Commits:
dd2de3d5 by Andreas Tille at 2019-09-05T14:25:04Z
Use 2to3 to port to Python3
- - - - -
18ffadf3 by Andreas Tille at 2019-09-05T14:56:11Z
Fix linking of data dir
- - - - -
12da5071 by Andreas Tille at 2019-09-05T14:56:36Z
debhelper-compat 12
- - - - -
59132893 by Andreas Tille at 2019-09-05T14:56:39Z
Standards-Version: 4.4.0
- - - - -
8a3a4409 by Andreas Tille at 2019-09-05T14:56:39Z
Secure URI in copyright format
- - - - -
481aa88e by Andreas Tille at 2019-09-05T14:56:46Z
Use secure URI in debian/watch.
Fixes lintian: debian-watch-uses-insecure-uri
See https://lintian.debian.org/tags/debian-watch-uses-insecure-uri.html for more details.
- - - - -
6210c0d9 by Andreas Tille at 2019-09-05T14:56:52Z
Set upstream metadata fields: Archive.
- - - - -
c456bd2a by Andreas Tille at 2019-09-05T15:00:14Z
Upload to unstable
- - - - -
9 changed files:
- debian/changelog
- − debian/compat
- debian/control
- debian/copyright
- debian/patches/2to3.patch
- debian/patches/series
- debian/rules
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+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 at debian.org> Thu, 05 Sep 2019 16:56:54 +0200
+
microbegps (1.0.0-3) unstable; urgency=medium
* debhelper 11
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,12 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at 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
=====================================
@@ -1,4 +1,4 @@
-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 at rki.de>
Source: http://sourceforge.net/projects/microbegps/files/
=====================================
debian/patches/2to3.patch
=====================================
@@ -1,7 +1,56 @@
+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/937043
Author: Andreas Tille <tille at 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
=====================================
@@ -1 +1 @@
-# 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
=====================================
@@ -1,19 +1,20 @@
Reference:
- - Author: Martin S. Lindner and Bernhard Y. Renard
- Title: Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS
- Journal: PLoS One
- Year: 2015
- Volume: 10
- Number: 2
- Pages: e0117711
- DOI: 10.1371/journal.pone.0117711
- PMID: 25643362
- URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117711
- eprint: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0117711&representation=PDF
+- Author: Martin S. Lindner and Bernhard Y. Renard
+ Title: Metagenomic Profiling of Known and Unknown Microbes with MicrobeGPS
+ Journal: PLoS One
+ Year: 2015
+ Volume: 10
+ Number: 2
+ Pages: e0117711
+ DOI: 10.1371/journal.pone.0117711
+ PMID: 25643362
+ URL: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0117711
+ eprint: http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0117711&representation=PDF
Registry:
- - Name: OMICtools
- Entry: OMICS_17085
- - Name: bio.tools
- Entry: MicrobeGPS
- - Name: SciCrunch
- Entry: NA
+- Name: OMICtools
+ Entry: OMICS_17085
+- Name: bio.tools
+ Entry: MicrobeGPS
+- Name: SciCrunch
+ Entry: NA
+Archive: SourceForge
=====================================
debian/watch
=====================================
@@ -1,3 +1,3 @@
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)))
View it on GitLab: https://salsa.debian.org/med-team/microbegps/compare/5d830c7bffc06ac365ce3aba1185e83ffc359bdd...c456bd2a0ead992c8bf434f1bf8cf1a64408970c
--
View it on GitLab: https://salsa.debian.org/med-team/microbegps/compare/5d830c7bffc06ac365ce3aba1185e83ffc359bdd...c456bd2a0ead992c8bf434f1bf8cf1a64408970c
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