[med-svn] r13712 - in trunk/packages/python-cogent/trunk/debian: . patches

Sun May 26 16:51:10 UTC 2013

Author: alteholz
Date: 2013-05-26 16:51:09 +0000 (Sun, 26 May 2013)
New Revision: 13712

Added:
   trunk/packages/python-cogent/trunk/debian/python-cogent-doc.doc-base
   trunk/packages/python-cogent/trunk/debian/python-cogent-doc.install
Modified:
   trunk/packages/python-cogent/trunk/debian/changelog
   trunk/packages/python-cogent/trunk/debian/compat
   trunk/packages/python-cogent/trunk/debian/control
   trunk/packages/python-cogent/trunk/debian/patches/fix_python_shebang_line.patch
   trunk/packages/python-cogent/trunk/debian/rules
Log:
new upstream version

Modified: trunk/packages/python-cogent/trunk/debian/changelog
===================================================================

--- trunk/packages/python-cogent/trunk/debian/changelog	2013-05-25 08:19:49 UTC (rev 13711)
+++ trunk/packages/python-cogent/trunk/debian/changelog	2013-05-26 16:51:09 UTC (rev 13712)
@@ -1,11 +1,17 @@
-python-cogent (1.5.3-1) precise; urgency=low
+python-cogent (1.5.3-1) unstable; urgency=low
 
   * New upstream
+  * debian/control: use dh 9
+  * debian/control: set standard to 3.9.4 (no changes)
+  * debian/rules: add get-orig-source target
+  * debian/rules: remove some superfluous files
+
+  [ Tim Booth ]
   * Added back python2 helper and invoked dh_numpy to sort deps
   * Split out docs into separate package
   * Added extra cleanup to dh_clean
 
- -- Tim Booth <tbooth at ceh.ac.uk>  Tue, 13 Nov 2012 15:26:47 +0000
+ -- Thorsten Alteholz <debian at alteholz.de>  Sun, 16 May 2013 18:00:00 +0200
 
 python-cogent (1.5.1-3) UNRELEASED; urgency=low
 

Modified: trunk/packages/python-cogent/trunk/debian/compat
===================================================================
--- trunk/packages/python-cogent/trunk/debian/compat	2013-05-25 08:19:49 UTC (rev 13711)
+++ trunk/packages/python-cogent/trunk/debian/compat	2013-05-26 16:51:09 UTC (rev 13712)
@@ -1 +1 @@
-8
+9

Modified: trunk/packages/python-cogent/trunk/debian/control
===================================================================
--- trunk/packages/python-cogent/trunk/debian/control	2013-05-25 08:19:49 UTC (rev 13711)
+++ trunk/packages/python-cogent/trunk/debian/control	2013-05-26 16:51:09 UTC (rev 13712)
@@ -3,10 +3,11 @@
 Priority: extra
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Steffen Moeller <moeller at debian.org>,
- Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 8), python-all-dev (>= 2.6), python-support, python-numpy (>= 1.3.0),
+ Andreas Tille <tille at debian.org>,
+ Thorsten Alteholz <debian at alteholz.de>
+Build-Depends: debhelper (>= 9), python-all-dev (>= 2.6), python-support, python-numpy (>= 1.3.0),
  python-sphinx, cython
-Standards-Version: 3.9.3
+Standards-Version: 3.9.4
 Homepage: http://pycogent.sourceforge.net/
 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/python-cogent/trunk/
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/python-cogent/trunk/
@@ -32,6 +33,12 @@
 Section: debug
 Depends: python-cogent (= ${binary:Version}), ${misc:Depends}
 Description: debug information for pycogent
+ PyCogent is a software library for genomic biology.
+ .
+ It is distinguished by many unique built-in capabilities (such as true codon
+ alignment) and the frequent addition of entirely new methods for the analysis
+ of genomic data.
+ .
  This package is needed to improve significantly the bug reports
  that users may feel inclined to send.
 
@@ -41,4 +48,10 @@
 Depends: ${misc:Depends}, libjs-jquery, libjs-underscore
 Suggests: python-cogent (= ${binary:Version})
 Description: docs for python-cogent
- Documentation and examples for python-cogent
+ PyCogent is a software library for genomic biology.
+ .
+ It is distinguished by many unique built-in capabilities (such as true codon
+ alignment) and the frequent addition of entirely new methods for the analysis
+ of genomic data.
+ .
+ This package contains documentation and examples.

Modified: trunk/packages/python-cogent/trunk/debian/patches/fix_python_shebang_line.patch
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/fix_python_shebang_line.patch	2013-05-25 08:19:49 UTC (rev 13711)
+++ trunk/packages/python-cogent/trunk/debian/patches/fix_python_shebang_line.patch	2013-05-26 16:51:09 UTC (rev 13712)
@@ -1,3 +1,5 @@
+Author: Steffen Moeller <moeller at debian.org>
+Description: fix path to python interpreter
 Index: PyCogent-1.5.1/cogent/align/dp_calculation.py
 ===================================================================
 --- PyCogent-1.5.1.orig/cogent/align/dp_calculation.py	2011-06-06 18:10:17.000000000 +0200

Added: trunk/packages/python-cogent/trunk/debian/python-cogent-doc.doc-base
===================================================================
--- trunk/packages/python-cogent/trunk/debian/python-cogent-doc.doc-base	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/python-cogent-doc.doc-base	2013-05-26 16:51:09 UTC (rev 13712)
@@ -0,0 +1,28 @@
+Document: python-cogent-doc
+Title: PyCogent documentation
+Author: PyCogent Team
+Abstract: PyCogent is a software library for genomic biology. 
+ It is a fully integrated and thoroughly tested framework for: 
+  * controlling third-party applications; 
+  * devising workflows; 
+  * querying databases; 
+  * conducting novel probabilistic analyses of biological sequence 
+    evolution; 
+  * and generating publication quality graphics. 
+ It is distinguished by many unique built-in capabilities (such as 
+ true codon alignment) and the frequent addition of entirely new 
+ methods for the analysis of genomic data.
+ .
+ Our primary goal is to provide a collection of rigourously validated 
+ tools for the manipulation and analysis of genome biology data sets. 
+ The project is routinely employed in numerous labs across the world 
+ and has provided essential capabilities for many high profile 
+ publications, e.g. Nature 2009 457:480-4, PNAS 2008 105:17994-9, 
+ Science 2008 320:1647-51, Nature 2008 453: 175-83 and 
+ Nat Genet 2007 39: 1261-5.
+Section: Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/python-cogent-doc/html/index.html
+Files: /usr/share/doc/python-cogent-doc/html/*.html
+

Added: trunk/packages/python-cogent/trunk/debian/python-cogent-doc.install
===================================================================
--- trunk/packages/python-cogent/trunk/debian/python-cogent-doc.install	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/python-cogent-doc.install	2013-05-26 16:51:09 UTC (rev 13712)
@@ -0,0 +1 @@
+doc/_build/* usr/share/doc/python-cogent-doc/

Modified: trunk/packages/python-cogent/trunk/debian/rules
===================================================================
--- trunk/packages/python-cogent/trunk/debian/rules	2013-05-25 08:19:49 UTC (rev 13711)
+++ trunk/packages/python-cogent/trunk/debian/rules	2013-05-26 16:51:09 UTC (rev 13712)
@@ -21,6 +21,12 @@
 override_dh_auto_build:
 	dh_auto_build
 	cd doc; $(MAKE) html
+	# remove superfluous files and dirs
+	rm doc/_build/doctrees/COGENT_LICENSE.doctree
+	rm doc/_build/html/_sources/COGENT_LICENSE.txt
+	rm doc/_build/html/_static/jquery.js
+	rm doc/_build/html/_static/underscore.js
+	rmdir doc/_build/html/_images/math/
 
 override_dh_shlibdeps:
 	dh_shlibdeps
@@ -35,3 +41,8 @@
 
 override_dh_strip:
 	dh_strip --dbg-package=python-cogent-dbg
+
+get-orig-source:
+	mkdir -p ../tarballs
+	uscan --verbose --force-download --destdir=../tarballs
+


