[med-svn] r16371 - trunk/packages/python-biopython/trunk/debian
Andreas Tille
tille at moszumanska.debian.org
Tue Mar 4 12:44:49 UTC 2014
Author: tille
Date: 2014-03-04 12:44:48 +0000 (Tue, 04 Mar 2014)
New Revision: 16371
Added:
trunk/packages/python-biopython/trunk/debian/python3-biopython-sql.install
trunk/packages/python-biopython/trunk/debian/python3-biopython.install
Modified:
trunk/packages/python-biopython/trunk/debian/changelog
trunk/packages/python-biopython/trunk/debian/control
trunk/packages/python-biopython/trunk/debian/python-biopython-sql.install
trunk/packages/python-biopython/trunk/debian/python-biopython.install
trunk/packages/python-biopython/trunk/debian/rules
Log:
Commit current but non-working status of packaging to ask for help on debian-python list
Modified: trunk/packages/python-biopython/trunk/debian/changelog
===================================================================
--- trunk/packages/python-biopython/trunk/debian/changelog 2014-03-04 12:43:18 UTC (rev 16370)
+++ trunk/packages/python-biopython/trunk/debian/changelog 2014-03-04 12:44:48 UTC (rev 16371)
@@ -1,6 +1,8 @@
python-biopython (1.63-1) UNRELEASED; urgency=medium
* New upstream version
+ * Enable Python3
+ TODO: Fixing dh_install files which are totally broken
-- Andreas Tille <tille at debian.org> Tue, 04 Mar 2014 11:16:02 +0100
Modified: trunk/packages/python-biopython/trunk/debian/control
===================================================================
--- trunk/packages/python-biopython/trunk/debian/control 2014-03-04 12:43:18 UTC (rev 16370)
+++ trunk/packages/python-biopython/trunk/debian/control 2014-03-04 12:44:48 UTC (rev 16371)
@@ -7,13 +7,14 @@
Priority: optional
Build-Depends: debhelper (>= 9),
dpkg-dev (>= 1.16.1~),
- cdbs (>= 0.4.90~),
- python-all,
python-all-dev,
+ python3-all-dev,
flex,
python-reportlab,
python-numpy,
python-mysqldb,
+ python3-reportlab,
+ python3-numpy,
wise
Standards-Version: 3.9.5
Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/python-biopython/trunk/
@@ -27,7 +28,6 @@
Depends: ${python:Depends},
${shlibs:Depends},
${misc:Depends},
- python-numpy,
python-reportlab
Recommends: python-biopython-doc (= ${source:Version})
Suggests: python-tk,
@@ -40,7 +40,7 @@
python-psycopg2,
probcons
Provides: ${python:Provides}
-Description: Python library for bioinformatics
+Description: Python library for bioinformatics (implemented in Python 2)
The Biopython Project is an international association
of developers of freely available Python tools for
computational molecular biology.
@@ -49,11 +49,46 @@
libraries and applications which address the needs of
current and future work in bioinformatics. The source code
is made available under the Biopython License, which is
- extremely liberal and compatible with almost every license
- in the world. We work along with the Open Bioinformatics
+ extremely liberal and compatible with almost every license in
+ the world. The project works along with the Open Bioinformatics
Foundation, who generously provide web and CVS space for
the project.
+ .
+ This package is targeting Python version 2.
+Package: python3-biopython
+Architecture: any
+Depends: ${python:Depends},
+ ${shlibs:Depends},
+ ${misc:Depends},
+ python3-reportlab
+Recommends: python-biopython-doc (= ${source:Version})
+Suggests: python3-tk,
+ wise,
+ muscle,
+ clustalw,
+ mafft,
+ emboss,
+ blast2,
+ python3-psycopg2,
+ probcons
+Provides: ${python:Provides}
+Description: Python library for bioinformatics (implemented in Python 3)
+ The Biopython Project is an international association
+ of developers of freely available Python tools for
+ computational molecular biology.
+ .
+ It is a distributed collaborative effort to develop Python
+ libraries and applications which address the needs of
+ current and future work in bioinformatics. The source code
+ is made available under the Biopython License, which is
+ extremely liberal and compatible with almost every license in
+ the world. The project works along with the Open Bioinformatics
+ Foundation, who generously provide web and CVS space for
+ the project.
+ .
+ This package is targeting Python version 3.
+
Package: python-biopython-doc
Architecture: all
Section: doc
@@ -71,7 +106,23 @@
python-mysqldb,
python-biopython
Provides: ${python:Provides}
-Description: Biopython support for the BioSQL database schema
+Description: Biopython support for the BioSQL database schema (Python 2)
This is the Biopython interface to a BioSQL database (see www.biosql.org
for details). BioPerl, BioJava and BioRuby also provide their own BioSQL
interfaces onto the same shared SQL schema.
+ .
+ This package is targeting Python version 2.
+
+Package: python3-biopython-sql
+# Todo: add www.biosql.org as "External Ressource" on packages.debian.org when the infrastructure will provide a way to do so.
+Architecture: all
+Depends: ${python:Depends},
+ ${misc:Depends},
+ python3-biopython
+Provides: ${python:Provides}
+Description: Biopython support for the BioSQL database schema (Python 3)
+ This is the Biopython interface to a BioSQL database (see www.biosql.org
+ for details). BioPerl, BioJava and BioRuby also provide their own BioSQL
+ interfaces onto the same shared SQL schema.
+ .
+ This package is targeting Python version 3.
Modified: trunk/packages/python-biopython/trunk/debian/python-biopython-sql.install
===================================================================
--- trunk/packages/python-biopython/trunk/debian/python-biopython-sql.install 2014-03-04 12:43:18 UTC (rev 16370)
+++ trunk/packages/python-biopython/trunk/debian/python-biopython-sql.install 2014-03-04 12:44:48 UTC (rev 16371)
@@ -1 +1 @@
-usr/lib/python*/*-packages/BioSQL
+usr/lib/python[^3]*/*-packages/BioSQL
Modified: trunk/packages/python-biopython/trunk/debian/python-biopython.install
===================================================================
--- trunk/packages/python-biopython/trunk/debian/python-biopython.install 2014-03-04 12:43:18 UTC (rev 16370)
+++ trunk/packages/python-biopython/trunk/debian/python-biopython.install 2014-03-04 12:44:48 UTC (rev 16371)
@@ -1 +1 @@
-usr/lib/python*/*-packages/Bio
+usr/lib/python[^3]*/*-packages/Bio
Added: trunk/packages/python-biopython/trunk/debian/python3-biopython-sql.install
===================================================================
--- trunk/packages/python-biopython/trunk/debian/python3-biopython-sql.install (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/python3-biopython-sql.install 2014-03-04 12:44:48 UTC (rev 16371)
@@ -0,0 +1 @@
+usr/lib/python3*/*-packages/BioSQL
Added: trunk/packages/python-biopython/trunk/debian/python3-biopython.install
===================================================================
--- trunk/packages/python-biopython/trunk/debian/python3-biopython.install (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/python3-biopython.install 2014-03-04 12:44:48 UTC (rev 16371)
@@ -0,0 +1 @@
+usr/lib/python3*/*-packages/Bio
Modified: trunk/packages/python-biopython/trunk/debian/rules
===================================================================
--- trunk/packages/python-biopython/trunk/debian/rules 2014-03-04 12:43:18 UTC (rev 16370)
+++ trunk/packages/python-biopython/trunk/debian/rules 2014-03-04 12:44:48 UTC (rev 16371)
@@ -1,11 +1,17 @@
#!/usr/bin/make -f
-# hardening flags
-DPKG_EXPORT_BUILDFLAGS = 1
-include /usr/share/dpkg/buildflags.mk
+# Uncomment this to turn on verbose mode.
+export DH_VERBOSE=1
-include /usr/share/cdbs/1/rules/debhelper.mk
-include /usr/share/cdbs/1/class/python-distutils.mk
+#PACKAGE_NAME := python_biopython
+#export PYBUILD_DESTDIR_python2=debian/python-biopython/
+#export PYBUILD_DESTDIR_python3=debian/python3-biopython/
-binary-post-install/python-biopython::
+%:
+ dh $@ --with python2,python3 --buildsystem=pybuild
+
+override_dh_auto_install:
+ dh_auto_install
dh_numpy -ppython-biopython
+ dh_numpy3 -ppython3-biopython
+
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