[med-svn] r12533 - trunk/packages/python-cogent/trunk/debian

[Timothy Booth]

Author: tbooth-guest
Date: 2012-11-14 10:09:03 +0000 (Wed, 14 Nov 2012)
New Revision: 12533

Removed:
   trunk/packages/python-cogent/trunk/debian/docs
   trunk/packages/python-cogent/trunk/debian/links
   trunk/packages/python-cogent/trunk/debian/python-cogent.doc-base
Modified:
   trunk/packages/python-cogent/trunk/debian/changelog
   trunk/packages/python-cogent/trunk/debian/control
   trunk/packages/python-cogent/trunk/debian/rules
Log:
New upstream, and I needed the new python-cogent to support the latest QIIME
Some small changes to the build for 1.5.3


Modified: trunk/packages/python-cogent/trunk/debian/changelog
===================================================================
--- trunk/packages/python-cogent/trunk/debian/changelog	2012-11-13 10:06:28 UTC (rev 12532)
+++ trunk/packages/python-cogent/trunk/debian/changelog	2012-11-14 10:09:03 UTC (rev 12533)
@@ -1,3 +1,12 @@
+python-cogent (1.5.3-1) precise; urgency=low
+
+  * New upstream
+  * 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
+
 python-cogent (1.5.1-3) UNRELEASED; urgency=low
 
   * debian/upstream: Added citations

Modified: trunk/packages/python-cogent/trunk/debian/control
===================================================================
--- trunk/packages/python-cogent/trunk/debian/control	2012-11-13 10:06:28 UTC (rev 12532)
+++ trunk/packages/python-cogent/trunk/debian/control	2012-11-14 10:09:03 UTC (rev 12533)
@@ -6,14 +6,15 @@
  Andreas Tille <tille at debian.org>
 Build-Depends: debhelper (>= 8), python-all-dev (>= 2.6), python-support, python-numpy (>= 1.3.0),
  python-sphinx, cython
-Standards-Version: 3.9.2
+Standards-Version: 3.9.3
 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/
 
 Package: python-cogent
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, libjs-jquery, libjs-underscore, python-numpy (>= 1.3.0)
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}
+Suggests: python-cogent-doc
 Description: framework for genomic biology
  PyCogent is a software library for genomic biology. It is a fully
  integrated and thoroughly tested framework for:
@@ -33,3 +34,11 @@
 Description: debug information for pycogent
  This package is needed to improve significantly the bug reports
  that users may feel inclined to send.
+
+Package: python-cogent-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends}, libjs-jquery, libjs-underscore
+Suggests: python-cogent (= ${binary:Version})
+Description: docs for python-cogent
+ Documentation and examples for python-cogent

Deleted: trunk/packages/python-cogent/trunk/debian/docs
===================================================================
--- trunk/packages/python-cogent/trunk/debian/docs	2012-11-13 10:06:28 UTC (rev 12532)
+++ trunk/packages/python-cogent/trunk/debian/docs	2012-11-14 10:09:03 UTC (rev 12533)
@@ -1,3 +0,0 @@
-NumpyPortingNotes.txt
-README
-doc/_build/html

Deleted: trunk/packages/python-cogent/trunk/debian/links
===================================================================
--- trunk/packages/python-cogent/trunk/debian/links	2012-11-13 10:06:28 UTC (rev 12532)
+++ trunk/packages/python-cogent/trunk/debian/links	2012-11-14 10:09:03 UTC (rev 12533)
@@ -1,2 +0,0 @@
-usr/share/javascript/jquery/jquery.js	usr/share/doc/python-cogent/html/_static/jquery.js
-usr/share/javascript/underscore/underscore.js	usr/share/doc/python-cogent/html/_static/underscore.js

Deleted: trunk/packages/python-cogent/trunk/debian/python-cogent.doc-base
===================================================================
--- trunk/packages/python-cogent/trunk/debian/python-cogent.doc-base	2012-11-13 10:06:28 UTC (rev 12532)
+++ trunk/packages/python-cogent/trunk/debian/python-cogent.doc-base	2012-11-14 10:09:03 UTC (rev 12533)
@@ -1,16 +0,0 @@
-Document: python-cogent
-Title: Debian python-cogent Manual
-Author: The Cogent Project
-Abstract: PyCogent documentation
- 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.
-Section: Science/Biology
-
-Format: html
-Files: /usr/share/doc/python-cogent/html/*
-Index: /usr/share/doc/python-cogent/html/index.html

Modified: trunk/packages/python-cogent/trunk/debian/rules
===================================================================
--- trunk/packages/python-cogent/trunk/debian/rules	2012-11-13 10:06:28 UTC (rev 12532)
+++ trunk/packages/python-cogent/trunk/debian/rules	2012-11-14 10:09:03 UTC (rev 12533)
@@ -10,13 +10,22 @@
 	dh $@ --with python2
 
 override_dh_clean:
+	#These files are rebuilt on-the-fly
+	for f in `find -name '*.c'` ; do \
+	    head -n 1 "$$f" | grep -q '^/\* Generated by Cython' && rm "$$f" ; \
+	done
 	rm -rf build build-stamp
 	rm -rf doc/_build
 	dh_clean
 
 override_dh_auto_build:
+	dh_auto_build
 	cd doc; $(MAKE) html
 
+override_dh_shlibdeps:
+	dh_shlibdeps
+	dh_numpy
+
 override_dh_compress:
 	dh_compress --exclude=.js --exclude=.fasta --exclude=.txt --exclude=.pdb