[med-svn] r2996 - in trunk/packages/python-biopython/trunk/debian: . patches

plessy at alioth.debian.org plessy at alioth.debian.org
Fri Jan 16 08:18:40 UTC 2009 

Author: plessy
Date: 2009-01-16 08:18:40 +0000 (Fri, 16 Jan 2009)
New Revision: 2996

Added:
   trunk/packages/python-biopython/trunk/debian/patches/
   trunk/packages/python-biopython/trunk/debian/patches/01-enable-mmCIF.patch
   trunk/packages/python-biopython/trunk/debian/patches/series
Modified:
   trunk/packages/python-biopython/trunk/debian/changelog
   trunk/packages/python-biopython/trunk/debian/compat
   trunk/packages/python-biopython/trunk/debian/control
   trunk/packages/python-biopython/trunk/debian/python-biopython-doc.doc-base
   trunk/packages/python-biopython/trunk/debian/rules
Log:
Added mmCIF support, use Debhelper 7 and quilt, fixed doc-base registration.



Modified: trunk/packages/python-biopython/trunk/debian/changelog
===================================================================
--- trunk/packages/python-biopython/trunk/debian/changelog	2009-01-15 14:18:52 UTC (rev 2995)
+++ trunk/packages/python-biopython/trunk/debian/changelog	2009-01-16 08:18:40 UTC (rev 2996)
@@ -13,10 +13,17 @@
     - depends on python-numpy instead of python-numeric-ext.
     - moved python-martel to oldlibs section, priority extra as it is
       deprecated, and indicate this in the description.
+  * Use Debhelper 7 (debian/co{ntrol,mpat}).
   * debian/copyright: added myself to the Hall of Fame and updated to latest
     draft of the machine-readable format.
   * debian/watch: makes beta versions lower by prepending a tiled between
     numbers and letters (1.49b -> 1.49~b).
+  * mmCIF support enabled:
+    - debian/patches/01-enable-mmCIF.patch: as the name indicates ;)
+    - debian/rules: patch and unpatch through /usr/share/quilt/quilt.make.
+    - debian/control: build-depends on quilt.
+  * debian/python-biopython-doc.doc-base: corrected index name that was changed
+    upstream.
 
  -- Charles Plessy <plessy at debian.org>  Thu, 15 Jan 2009 13:15:44 +0900
 

Modified: trunk/packages/python-biopython/trunk/debian/compat
===================================================================
--- trunk/packages/python-biopython/trunk/debian/compat	2009-01-15 14:18:52 UTC (rev 2995)
+++ trunk/packages/python-biopython/trunk/debian/compat	2009-01-16 08:18:40 UTC (rev 2996)
@@ -1 +1 @@
-4
+7

Modified: trunk/packages/python-biopython/trunk/debian/control
===================================================================
--- trunk/packages/python-biopython/trunk/debian/control	2009-01-15 14:18:52 UTC (rev 2995)
+++ trunk/packages/python-biopython/trunk/debian/control	2009-01-16 08:18:40 UTC (rev 2996)
@@ -5,7 +5,7 @@
 Uploaders: Philipp Benner <pbenner at uni-osnabrueck.de>,
            Charles Plessy <plessy at debian.org>
 DM-Upload-Allowed: yes
-Build-Depends: debhelper (>= 5.0.37.2), python-all-dev, flex, python-support,
+Build-Depends: debhelper (>= 7), quilt, python-all-dev, flex, python-support,
  python-reportlab, python-numpy,
 # Should be removed when the deprecated Martel and Bio.Mindy are removed from upstream source.:
  python-egenix-mxtexttools

Added: trunk/packages/python-biopython/trunk/debian/patches/01-enable-mmCIF.patch
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/01-enable-mmCIF.patch	                        (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/patches/01-enable-mmCIF.patch	2009-01-16 08:18:40 UTC (rev 2996)
@@ -0,0 +1,22 @@
+--- biopython-1.49.orig/setup.py
++++ biopython-1.49/setup.py
+@@ -340,13 +340,12 @@
+                'Bio/csupport.c'],
+               include_dirs=["Bio"]
+               ),
+-#Commented out due to the build dependency on flex, see Bug 2619
+-#   Extension('Bio.PDB.mmCIF.MMCIFlex',
+-#              ['Bio/PDB/mmCIF/lex.yy.c',
+-#               'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
+-#              include_dirs=["Bio"],
+-#              libraries=["fl"]
+-#              ),
++    Extension('Bio.PDB.mmCIF.MMCIFlex',
++              ['Bio/PDB/mmCIF/lex.yy.c',
++               'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
++              include_dirs=["Bio"],
++              libraries=["fl"]
++              ),
+     Extension('Bio.Nexus.cnexus',
+               ['Bio/Nexus/cnexus.c']
+               ),

Added: trunk/packages/python-biopython/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/patches/series	2009-01-16 08:18:40 UTC (rev 2996)
@@ -0,0 +1 @@
+01-enable-mmCIF.patch

Modified: trunk/packages/python-biopython/trunk/debian/python-biopython-doc.doc-base
===================================================================
--- trunk/packages/python-biopython/trunk/debian/python-biopython-doc.doc-base	2009-01-15 14:18:52 UTC (rev 2995)
+++ trunk/packages/python-biopython/trunk/debian/python-biopython-doc.doc-base	2009-01-16 08:18:40 UTC (rev 2996)
@@ -2,8 +2,12 @@
 Title: Biopython Tutorial and Cookbook
 Author: Jeff Chang, Brad Chapman, Iddo Friedberg, Thomas Hamelryck, Michiel de Hoon, Peter Cock
 Section: Science/Biology
+Abstract: The Biopython Tutorial and Cookbook
+ contains the main bulk of Biopython documentation. It provides information to
+ get you started with Biopython, in addition to specific documentation on a
+ number of modules.
 
 Format: HTML
-Index: /usr/share/doc/python-biopython-doc/Doc/index.html
-Files: /usr/share/doc/python-biopython-doc/Doc/index.html
+Index: /usr/share/doc/python-biopython-doc/Doc/Tutorial.html
+Files: /usr/share/doc/python-biopython-doc/Doc/Tutorial.html
  /usr/share/doc/python-biopython-doc/Doc/Tutorial.*

Modified: trunk/packages/python-biopython/trunk/debian/rules
===================================================================
--- trunk/packages/python-biopython/trunk/debian/rules	2009-01-15 14:18:52 UTC (rev 2995)
+++ trunk/packages/python-biopython/trunk/debian/rules	2009-01-16 08:18:40 UTC (rev 2996)
@@ -1,10 +1,12 @@
 #!/usr/bin/make -f
 
+include /usr/share/quilt/quilt.make
+
 PWD    := $(shell pwd)
 PYDEF  := $(shell pyversions -d)
 PYVERS := $(shell pyversions -r)
 
-build: build-stamp
+build: patch build-stamp
 build-stamp: $(PYVERS:%=build-%)
 	touch build-stamp
 build-python%:
@@ -34,7 +36,7 @@
 		     -ppython-biopython-martel	\
 		     --sourcedir=debian/python$*-tmp
 
-clean: $(PYVERS:%=clean-%)
+clean: unpatch $(PYVERS:%=clean-%)
 	dh_testdir
 	dh_testroot

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