--- python-biopython-1.52.orig/debian/python-biopython.files +++ python-biopython-1.52/debian/python-biopython.files @@ -0,0 +1 @@ +usr/lib/python*/*-packages/Bio --- python-biopython-1.52.orig/debian/copyright +++ python-biopython-1.52/debian/copyright @@ -0,0 +1,35 @@ +Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=424 +Upstream-Name: Biopython +Upstream-Source: http://biopython.org/DIST/biopython-1.49.tar.gz + +Files: * +Copyright: © 2002-2009 Biopython contributors +License: other + 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. + +Files: debian/* +Copyright: © 2009 Charles Plessy + 2004-2009 Philipp Benner +License: GPL-2+ + The Debian packaging information is under the GPL, version 2 or later. + +On Debian GNU/Linux systems, the complete text of the GNU General +Public License can be found in `/usr/share/common-licenses/GPL' and the +complete text of the GNU Lesser General Public License can be found in +`/usr/share/common-licenses/LGPL'. --- python-biopython-1.52.orig/debian/docs +++ python-biopython-1.52/debian/docs @@ -0,0 +1,3 @@ +CONTRIB +DEPRECATED +NEWS --- python-biopython-1.52.orig/debian/changelog +++ python-biopython-1.52/debian/changelog @@ -0,0 +1,211 @@ +python-biopython (1.52-1) unstable; urgency=low + + * New upstream release. + + -- Philipp Benner Wed, 30 Sep 2009 10:16:03 +0000 + +python-biopython (1.51final-2) unstable; urgency=low + + * Merged patch from ubuntu to make the package ready for + python2.6 (Closes: #543236). + + -- Philipp Benner Mon, 24 Aug 2009 09:29:27 +0000 + +python-biopython (1.51final-1) unstable; urgency=low + + * New upstream release + * debian/control: suggesting muscle, clustalw, mafft, emboss, and + blast2 for installation + + -- Philipp Benner Wed, 19 Aug 2009 10:41:19 +0000 + +python-biopython (1.51b-2) unstable; urgency=low + + * Dropped python-biopython-martel. + * Dropped dependency on python-egenix-mxtexttools. + * Removed DM-Upload-Allowed: yes. + + -- Philipp Benner Tue, 11 Aug 2009 19:47:52 +0000 + +python-biopython (1.51b-1) unstable; urgency=low + + * New upstream release + * debian/control: + - moved python-martel back to section python (python packages do not + use section oldlibs) + * debian/patches/02-fix-wise-test.patch + - removed (merged with upstream) + * debian/control: + - Changed the description of python-biopython-sql according to Peter Cock's + suggestions. + [Charles Plessy] + + -- Philipp Benner Sat, 27 Jun 2009 15:14:52 +0000 + +python-biopython (1.49-1) unstable; urgency=low + + * New upstream release. + - uses NumPy rather than its precursor Numeric (Closes: #478457) + - Martel, Bio.Mindy, Bio.MetaTool, Bio.EUtils, Bio.Saf, Bio.NBRF, and + Bio.IntelliGenetics are deprecated. + - Bio.PubMed and the online code in Bio.GenBank are now considered obsolete + and will be deprecated in a future release. + - Bio.Fasta is also considered to be obsolete and will eventually be + deprecated. + * debian/control: + - added myself as Uploader. + - 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. + - build-depend on python-mysqldb and wise for the tests after building. + * 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 tilde 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. + * debian/patches/02-fix-wise-test.patch: prevents tests failing with Debian's + version of Wise. + * debian/rules: perform tests after build. + + -- Charles Plessy Fri, 23 Jan 2009 22:19:50 +0900 + +python-biopython (1.47-1) unstable; urgency=low + + * New upstream release + * Standards version 3.8.0 + + -- Philipp Benner Sun, 03 Aug 2008 14:29:33 +0200 + +python-biopython (1.45-3) unstable; urgency=low + + * Removed dependency on python-numeric-ext since it is already in + the recommends field + + -- Philipp Benner Sun, 01 Jun 2008 10:34:48 +0200 + +python-biopython (1.45-2) unstable; urgency=low + + * Add dependency on python-numeric-ext (Bio.PDB uses MLab from this package) + + -- Morten Kjeldgaard Wed, 23 Apr 2008 00:01:16 +0200 + +python-biopython (1.45-1) unstable; urgency=low + + * New upstream release. + * Added doc-base. + + -- Philipp Benner Sat, 29 Mar 2008 12:20:41 +0100 + +python-biopython (1.44-3) unstable; urgency=low + + * New maintainer e-mail address. + * debian/control: Added DM-Upload-Allowed: yes. + + -- Philipp Benner Mon, 14 Jan 2008 18:35:18 +0100 + +python-biopython (1.44-2) unstable; urgency=low + + * Moved suggested package python-numeric-ext to recommends field + (Closes: #452379). + * Moved wise from recommends to suggests field. + * Removed package tags from debian/control. + * Added homepage field to debian/control. + * Changed maintainer to Debian-Med Packaging Team. + * Removed .DS_Store.gz file from doc package. + + -- Philipp Benner Thu, 22 Nov 2007 13:35:00 +0100 + +python-biopython (1.44-1) unstable; urgency=low + + * New upstream release. + * Machine interpretable copyright file. + + -- Philipp Benner Fri, 16 Nov 2007 16:49:11 +0100 + +python-biopython (1.43-2) unstable; urgency=low + + * Rebuild for python-2.5 support (Closes: #424025). + + -- Philipp Benner 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 Tue, 27 Mar 2007 17:45:58 +0200 + +python-biopython (1.42-2) unstable; urgency=low + + * uscan support + * package tags + + -- Philipp Benner Sat, 9 Sep 2006 14:39:18 +0200 + +python-biopython (1.42-1) unstable; urgency=low + + * New upstream release + + -- Philipp Benner 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 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 Mon, 20 Feb 2006 21:02:18 +0100 + +python-biopython (1.41-1) unstable; urgency=low + + * New upstream release + + -- Philipp Benner 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 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 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 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 Sun, 10 Oct 2004 19:48:04 +0200 + +python-biopython (1.30-1) unstable; urgency=low + + * Initial Release. (closes: #157402) + + -- Philipp Benner Tue, 21 Sep 2004 20:02:00 +0200 --- python-biopython-1.52.orig/debian/python-biopython-doc.doc-base +++ python-biopython-1.52/debian/python-biopython-doc.doc-base @@ -0,0 +1,13 @@ +Document: biopython-tutorial +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/Tutorial.html +Files: /usr/share/doc/python-biopython-doc/Doc/Tutorial.html + /usr/share/doc/python-biopython-doc/Doc/Tutorial.* --- python-biopython-1.52.orig/debian/control +++ python-biopython-1.52/debian/control @@ -0,0 +1,59 @@ +Source: python-biopython +Priority: optional +Section: python +Maintainer: Debian-Med Packaging Team +Uploaders: Philipp Benner , + Charles Plessy +Build-Depends: debhelper (>= 7), quilt, python-all-dev, flex, python-support, + python-reportlab, python-numpy, +# For the purpose of the tests + python-mysqldb, wise +XS-Python-Version: >= 2.3 +Standards-Version: 3.8.3 +Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/python-biopython/trunk/?rev=0&sc=0 +Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/python-biopython/trunk/ +Homepage: http://biopython.org + +Package: python-biopython +Architecture: any +Depends: ${python:Depends}, ${shlibs:Depends}, python-numpy, python-reportlab +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}) +Suggests: python-tk, wise, muscle, clustalw, mafft, emboss, blast2 +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. + +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. + +Package: python-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}, 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: Biopython support for the BioSQL database schema + 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. --- python-biopython-1.52.orig/debian/compat +++ python-biopython-1.52/debian/compat @@ -0,0 +1 @@ +7 --- python-biopython-1.52.orig/debian/pycompat +++ python-biopython-1.52/debian/pycompat @@ -0,0 +1 @@ +2 --- python-biopython-1.52.orig/debian/watch +++ python-biopython-1.52/debian/watch @@ -0,0 +1,6 @@ +# Compulsory line, this is a version 3 file +version=3 + +opts="uversionmangle=s/b/~b/" \ +http://biopython.org/DIST/biopython-(.\.\w+)\.tar\.gz \ + debian uupdate --- python-biopython-1.52.orig/debian/rules +++ python-biopython-1.52/debian/rules @@ -0,0 +1,90 @@ +#!/usr/bin/make -f + +include /usr/share/quilt/quilt.make + +PWD := $(shell pwd) +PYDEF := $(shell pyversions -d) +PYVERS := $(shell pyversions -r) + +build: patch 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 --install-layout=deb + + dh_movefiles -ppython-biopython \ + -ppython-biopython-sql \ + --sourcedir=debian/python$*-tmp + +clean: unpatch $(PYVERS:%=clean-%) + dh_testdir + dh_testroot + + dh_clean + + $(RM) build-stamp + +# fix bugs in setup.py + $(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 + +test: + python$* setup.py test + +binary: binary-indep binary-arch test + +.PHONY: clean build install binary binary-indep binary-arch --- python-biopython-1.52.orig/debian/README.source +++ python-biopython-1.52/debian/README.source @@ -0,0 +1,4 @@ +01-enable-mmCIF.patch: + Enable building mmCIF support + + -- Philipp Benner , Wed, 30 Sep 2009 11:50:43 +0000 --- python-biopython-1.52.orig/debian/README.Debian +++ python-biopython-1.52/debian/README.Debian @@ -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 , Tue, 11 Aug 2009 19:50:03 +0000 --- python-biopython-1.52.orig/debian/python-biopython-doc.docs +++ python-biopython-1.52/debian/python-biopython-doc.docs @@ -0,0 +1,2 @@ +Doc/ +Tests/ --- python-biopython-1.52.orig/debian/python-biopython-sql.files +++ python-biopython-1.52/debian/python-biopython-sql.files @@ -0,0 +1 @@ +usr/lib/python*/*-packages/BioSQL --- python-biopython-1.52.orig/debian/patches/01-enable-mmCIF.patch +++ python-biopython-1.52/debian/patches/01-enable-mmCIF.patch @@ -0,0 +1,26 @@ +Author: Charles Plessy +Description: enables mmCIF support. +Forwarded: no +License: same as Biopython itself. +--- 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'] + ), --- python-biopython-1.52.orig/debian/patches/series +++ python-biopython-1.52/debian/patches/series @@ -0,0 +1 @@ +01-enable-mmCIF.patch