[med-svn] r428 - in trunk/packages/python-biopython/trunk: . debian
pbenner-guest at alioth.debian.org
pbenner-guest at alioth.debian.org
Mon Sep 17 07:15:41 UTC 2007
Author: pbenner-guest
Date: 2007-09-17 07:15:41 +0000 (Mon, 17 Sep 2007)
New Revision: 428
Added:
trunk/packages/python-biopython/trunk/debian/
trunk/packages/python-biopython/trunk/debian/README.Debian
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/copyright
trunk/packages/python-biopython/trunk/debian/docs
trunk/packages/python-biopython/trunk/debian/pycompat
trunk/packages/python-biopython/trunk/debian/python-biopython-doc.docs
trunk/packages/python-biopython/trunk/debian/python-biopython-martel.files
trunk/packages/python-biopython/trunk/debian/python-biopython-sql.files
trunk/packages/python-biopython/trunk/debian/python-biopython.files
trunk/packages/python-biopython/trunk/debian/rules
trunk/packages/python-biopython/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications to trunk
Property changes on: trunk/packages/python-biopython/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/python-biopython/trunk/debian/README.Debian
===================================================================
--- trunk/packages/python-biopython/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/README.Debian 2007-09-17 07:15:41 UTC (rev 428)
@@ -0,0 +1,8 @@
+Biopython for Debian
+--------------------
+
+Users who want to use Biopython for development purpose
+should install `python-biopython-doc', which provides additional
+documentation and example scripts.
+
+ -- Philipp Benner <mail at philipp-benner.de> Tue, 21 Sep 2004 20:02:00 +0200
Added: trunk/packages/python-biopython/trunk/debian/changelog
===================================================================
--- trunk/packages/python-biopython/trunk/debian/changelog (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/changelog 2007-09-17 07:15:41 UTC (rev 428)
@@ -0,0 +1,81 @@
+python-biopython (1.43-2) unstable; urgency=low
+
+ * Rebuild for python-2.5 support (Closes: #424025).
+
+ -- Philipp Benner <mail at philipp-benner.de> Thu, 14 Jun 2007 21:40:18 +0200
+
+python-biopython (1.43-1) unstable; urgency=low
+
+ * New upstream release
+ * Adapted debian-med tags
+
+ -- Philipp Benner <mail at philipp-benner.de> Tue, 27 Mar 2007 17:45:58 +0200
+
+python-biopython (1.42-2) unstable; urgency=low
+
+ * uscan support
+ * package tags
+
+ -- Philipp Benner <mail at philipp-benner.de> Sat, 9 Sep 2006 14:39:18 +0200
+
+python-biopython (1.42-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Philipp Benner <mail at philipp-benner.de> Sat, 22 Jul 2006 01:30:51 +0200
+
+python-biopython (1.41-2.1) unstable; urgency=low
+
+ * Non-maintainer upload.
+ * Update package to the last python policy (Closes: #373515).
+
+ -- Pierre Habouzit <madcoder at debian.org> Fri, 30 Jun 2006 13:45:39 +0200
+
+python-biopython (1.41-2) unstable; urgency=low
+
+ * suggests python-numeric-ext
+ * now with KDTree
+
+ -- Philipp Benner <mail at philipp-benner.de> Mon, 20 Feb 2006 21:02:18 +0100
+
+python-biopython (1.41-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Philipp Benner <mail at philipp-benner.de> Sat, 5 Nov 2005 20:15:03 +0100
+
+python-biopython (1.40b-3) unstable; urgency=low
+
+ * now using compatibility level 4
+ * removed obsolete dependencies (closes: #328142)
+
+ -- Philipp Benner <mail at philipp-benner.de> Wed, 14 Sep 2005 12:06:06 +0200
+
+python-biopython (1.40b-2) unstable; urgency=low
+
+ * Function `mmcif_get_string' implicitly converted to pointer
+ (closes: #326403)
+ * now standards version 3.6.2
+
+ -- Philipp Benner <mail at philipp-benner.de> Wed, 7 Sep 2005 09:53:30 +0200
+
+python-biopython (1.40b-1) unstable; urgency=low
+
+ * new release
+ * dropped support for python2.2
+
+ -- Philipp Benner <mail at philipp-benner.de> Tue, 05 Apr 2005 20:55:59 +0200
+
+python-biopython (1.30-2) unstable; urgency=low
+
+ * Fixed bugs in debian/rules and debian/control which prevented
+ porting the package.
+ * Using -fPIC to build shared lib KDTree. (closes: #278959)
+
+ -- Philipp Benner <mail at philipp-benner.de> Sun, 10 Oct 2004 19:48:04 +0200
+
+python-biopython (1.30-1) unstable; urgency=low
+
+ * Initial Release. (closes: #157402)
+
+ -- Philipp Benner <mail at philipp-benner.de> Tue, 21 Sep 2004 20:02:00 +0200
Added: trunk/packages/python-biopython/trunk/debian/compat
===================================================================
--- trunk/packages/python-biopython/trunk/debian/compat (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/compat 2007-09-17 07:15:41 UTC (rev 428)
@@ -0,0 +1 @@
+4
Added: trunk/packages/python-biopython/trunk/debian/control
===================================================================
--- trunk/packages/python-biopython/trunk/debian/control (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/control 2007-09-17 07:15:41 UTC (rev 428)
@@ -0,0 +1,71 @@
+Source: python-biopython
+Priority: optional
+Section: python
+Maintainer: Philipp Benner <mail at philipp-benner.de>
+Build-Depends: debhelper (>= 5.0.37.2), python-all-dev (>= 2.3.5-11), flex,
+ python-support (>= 0.6.2), python-egenix-mxtexttools(>= 2.0.6-4),
+ python-reportlab (>=1.20debian-6), python-numeric (>= 24.2-7)
+XS-Python-Version: >= 2.3
+Standards-Version: 3.7.2.1
+
+Package: python-biopython
+Architecture: any
+Depends: ${python:Depends}, ${shlibs:Depends}, python-numeric,
+ python-biopython-martel (= ${source:Version}), python-reportlab,
+ python-egenix-mxtexttools
+Provides: ${python:Provides}
+Replaces: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1)
+Conflicts: python2.3-biopython (<< 1.42-1), python2.4-biopython (<< 1.42-1)
+XB-Python-Version: ${python:Versions}
+Recommends: python-biopython-doc (= ${source:Version}), wise
+Suggests: python-numeric-ext, python-tk
+Description: Python library for bioinformatics
+ 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. We work along with the Open Bioinformatics
+ Foundation, who generously provide web and CVS space for
+ the project.
+XB-Tag: field::biology:molecular, legacy::science, devel::library, langdevel::python, made-of::lang:python, role::shared-lib
+
+Package: python-biopython-doc
+Section: doc
+Architecture: all
+Recommends: python-biopython (= ${source:Version})
+Description: Documentation for the Biopython library
+ Documentation and examples about how to use the Biopython
+ library.
+XB-Tag: suite::debian-med:bio-devel, legacy::science, langdevel::python, role::documentation, devel::doc
+
+Package: python-biopython-sql
+Architecture: all
+Depends: ${python:Depends}, python-mysqldb, python-biopython
+Provides: ${python:Provides}
+Replaces: python2.3-biopython-sql (<< 1.42-1), python2.4-biopython-sql (<< 1.42-1)
+Conflicts: python2.3-biopython-sql (<< 1.42-1), python2.4-biopython-sql (<< 1.42-1)
+XB-Python-Version: ${python:Versions}
+Description: SQL support for the Biopython library
+ This is the python2.2 version of the Biopython-SQL
+ library which provides support for SQL.
+XB-Tag: field::biology:molecular, legacy::science, devel::library, langdevel::python, made-of::lang:python, role::shared-lib, devel::lang:sql
+
+Package: python-biopython-martel
+Architecture: all
+Depends: ${python:Depends}, python-biopython
+Provides: ${python:Provides}
+Replaces: python2.3-biopython-martel (<< 1.42-1), python2.4-biopython-martel (<< 1.42-1)
+Conflicts: python2.3-biopython-martel (<< 1.42-1), python2.4-biopython-martel (<< 1.42-1)
+XB-Python-Version: ${python:Versions}
+Description: Flat file parser for the Biopython library
+ Martel uses regular expression format definition to generate
+ a parser for flat- and semi-structured files.
+ The parse tree information is passed back to the caller using
+ XML SAX events. In other words, Martel lets you parse flat
+ files as if they are in XML.
+XB-Tag: field::biology:molecular, legacy::science, devel::library, langdevel::python, made-of::lang:python, role::shared-lib
Added: trunk/packages/python-biopython/trunk/debian/copyright
===================================================================
--- trunk/packages/python-biopython/trunk/debian/copyright (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/copyright 2007-09-17 07:15:41 UTC (rev 428)
@@ -0,0 +1,28 @@
+This package was debianized by Philipp Benner <mail at philipp-benner.de> on
+Tue, 21 Sep 2004 20:02:00 +0200.
+
+It was downloaded from http://biopython.org/files/
+
+Upstream Author: Sebastian Bassi <sbassi at genesdigitales.com>
+
+Copyright:
+
+ Biopython License Agreement
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.
Added: trunk/packages/python-biopython/trunk/debian/docs
===================================================================
--- trunk/packages/python-biopython/trunk/debian/docs (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/docs 2007-09-17 07:15:41 UTC (rev 428)
@@ -0,0 +1,3 @@
+CONTRIB
+DEPRECATED
+NEWS
Added: trunk/packages/python-biopython/trunk/debian/pycompat
===================================================================
--- trunk/packages/python-biopython/trunk/debian/pycompat (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/pycompat 2007-09-17 07:15:41 UTC (rev 428)
@@ -0,0 +1 @@
+2
Added: trunk/packages/python-biopython/trunk/debian/python-biopython-doc.docs
===================================================================
--- trunk/packages/python-biopython/trunk/debian/python-biopython-doc.docs (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/python-biopython-doc.docs 2007-09-17 07:15:41 UTC (rev 428)
@@ -0,0 +1,2 @@
+Doc/
+Tests/
Added: trunk/packages/python-biopython/trunk/debian/python-biopython-martel.files
===================================================================
--- trunk/packages/python-biopython/trunk/debian/python-biopython-martel.files (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/python-biopython-martel.files 2007-09-17 07:15:41 UTC (rev 428)
@@ -0,0 +1 @@
+usr/lib/python*/site-packages/Martel
Added: trunk/packages/python-biopython/trunk/debian/python-biopython-sql.files
===================================================================
--- trunk/packages/python-biopython/trunk/debian/python-biopython-sql.files (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/python-biopython-sql.files 2007-09-17 07:15:41 UTC (rev 428)
@@ -0,0 +1 @@
+usr/lib/python*/site-packages/BioSQL
Added: trunk/packages/python-biopython/trunk/debian/python-biopython.files
===================================================================
--- trunk/packages/python-biopython/trunk/debian/python-biopython.files (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/python-biopython.files 2007-09-17 07:15:41 UTC (rev 428)
@@ -0,0 +1 @@
+usr/lib/python*/site-packages/Bio
Added: trunk/packages/python-biopython/trunk/debian/rules
===================================================================
--- trunk/packages/python-biopython/trunk/debian/rules (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/rules 2007-09-17 07:15:41 UTC (rev 428)
@@ -0,0 +1,97 @@
+#!/usr/bin/make -f
+
+PWD := $(shell pwd)
+PYDEF := $(shell pyversions -d)
+PYVERS := $(shell pyversions -r)
+
+build: build-stamp
+build-stamp: $(PYVERS:%=build-%)
+ touch build-stamp
+build-python%:
+ echo $(DEB_HOST_ARCH)
+ yes | python$* setup.py build
+
+install: $(PYVERS:%=install-%)
+install-python%:
+ dh_testdir
+ dh_testroot
+
+ yes | python$* setup.py install --root $(CURDIR)/debian/python$*-tmp
+
+# <bugfix>
+ chmod 644 debian/python$*-tmp/usr/lib/python$*/site-packages/Bio/EUtils/DTDs/*dtd
+
+ for i in `find ./debian/python$*-tmp/usr/lib/python$*/site-packages -name "*.py"`; do \
+ sed -ir "s/^#\!\/usr\/bin\/env python\(2\.[234]\)\?$$//" $$i; \
+ sed -ir "s/^#\![ ]*\/usr\/bin\/python[ ]*\(-OO\)\?\(-i\)\?$$//" $$i; \
+ $(RM) $$i\r; \
+ done
+# </bugfix>
+
+ dh_movefiles -ppython-biopython \
+ -ppython-biopython-sql \
+ -ppython-biopython-martel \
+ --sourcedir=debian/python$*-tmp
+
+clean: $(PYVERS:%=clean-%)
+ dh_testdir
+ dh_testroot
+
+ dh_clean
+
+ $(RM) build-stamp
+
+# fix bugs in setup.py
+ $(RM) Martel/*.pyc
+ $(RM) Tests/*.pyc
+ $(RM) Tests/Graphics/*.eps
+ $(RM) Tests/Graphics/*.pdf
+ $(RM) Tests/dump
+ $(RM) Tests/NeuralNetwork/patternio.txt
+ $(RM) -r Tests/SCOP/scopseq-test/astral-scopdom-seqres-all-test.fa.idx
+
+ $(RM) -r build
+
+clean-python%:
+ dh_testdir
+ dh_testroot
+
+ python$* setup.py clean
+
+ $(RM) -r debian/python$*-tmp
+
+binary-indep: build install
+ dh_testdir
+ dh_testroot
+
+ dh_installdocs -i
+ dh_installchangelogs -i
+ dh_fixperms -i
+ dh_compress -i
+ dh_pysupport -i
+ dh_gencontrol -i
+ dh_md5sums -i
+ dh_installdeb -i
+ dh_builddeb -i
+
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+
+ dh_installdocs -a
+ dh_installchangelogs -a
+ dh_fixperms -a
+ dh_compress -a
+ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
+ dh_strip -a
+endif
+ dh_pysupport -a
+ dh_shlibdeps -a
+ dh_gencontrol -a
+ dh_md5sums -a
+ dh_installdeb -a
+ dh_builddeb -a
+
+binary: binary-indep binary-arch
+
+.PHONY: clean build install binary binary-indep binary-arch
Property changes on: trunk/packages/python-biopython/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/python-biopython/trunk/debian/watch
===================================================================
--- trunk/packages/python-biopython/trunk/debian/watch (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/watch 2007-09-17 07:15:41 UTC (rev 428)
@@ -0,0 +1,5 @@
+# Compulsory line, this is a version 3 file
+version=3
+
+http://biopython.org/DIST/biopython-(.\.\w+)\.tar\.gz \
+ debian uupdate
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