debian/0000755000000000000000000000000012263532375007176 5ustar debian/python-biopython-doc.doc-base0000644000000000000000000000112611134041340014651 0ustar 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.* debian/README.Debian0000644000000000000000000000042111240345660011225 0ustar 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 debian/rules0000755000000000000000000000041612215405207010245 0ustar #!/usr/bin/make -f # hardening flags DPKG_EXPORT_BUILDFLAGS = 1 include /usr/share/dpkg/buildflags.mk include /usr/share/cdbs/1/rules/debhelper.mk include /usr/share/cdbs/1/class/python-distutils.mk binary-post-install/python-biopython:: dh_numpy -ppython-biopython debian/upstream0000644000000000000000000000126611752240204010753 0ustar Reference: Author: Peter J. A. Cock and Tiago Antao and Jeffrey T. Chang and Brad A. Chapman and Cymon J. Cox and Andrew Dalke and Iddo Friedberg and Thomas Hamelryck and Frank Kauff and Bartek Wilczynski and Michiel J. L. de Hoon Title: "Biopython: freely available Python tools for computational molecular biology and bioinformatics" Journal: Bioinformatics Volume: 25 Number: 11 Pages: 1422-1423 Year: 2009 PMID: 19304878 DOI: 10.1093/bioinformatics/btp163 URL: http://bioinformatics.oxfordjournals.org/content/early/2009/03/20/bioinformatics.btp163.abstract eprint: http://bioinformatics.oxfordjournals.org/content/early/2009/03/20/bioinformatics.btp163.full.pdf+html debian/docs0000644000000000000000000000003010673424635010044 0ustar CONTRIB DEPRECATED NEWS debian/source/0000755000000000000000000000000012263532375010476 5ustar debian/source/format0000644000000000000000000000001412031642051011666 0ustar 3.0 (quilt) debian/python-biopython-doc.docs0000644000000000000000000000001410673424635014142 0ustar Doc/ Tests/ debian/python-biopython-sql.install0000644000000000000000000000004212215405207014677 0ustar usr/lib/python*/*-packages/BioSQL debian/copyright0000644000000000000000000000333711240345660011130 0ustar 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'. debian/control0000644000000000000000000000535012215405207010572 0ustar Source: python-biopython Priority: optional Section: python Maintainer: Debian Med Packaging Team Uploaders: Philipp Benner , Charles Plessy , Andreas Tille Build-Depends: debhelper (>= 9), dpkg-dev (>= 1.16.1~), cdbs (>= 0.4.90~), python-all (>= 2.6.6-3~), python-all-dev, flex, python-reportlab, python-numpy, # For the purpose of the tests python-mysqldb, wise X-Python-Version: >= 2.5 Standards-Version: 3.9.4 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/python-biopython/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/python-biopython/trunk/ Homepage: http://biopython.org Package: python-biopython Architecture: any Depends: ${python:Depends}, ${shlibs:Depends}, ${misc: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) Recommends: python-biopython-doc (= ${source:Version}) Suggests: python-tk, wise, muscle, clustalw, mafft, emboss, blast2, python-psycopg2, probcons 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 Depends: ${misc:Depends} 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}, ${misc: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) 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. debian/compat0000644000000000000000000000000212031642051010356 0ustar 9 debian/changelog0000644000000000000000000002166312263532142011050 0ustar python-biopython (1.63-1) unstable; urgency=low * New upstream release -- Philipp Benner Thu, 09 Jan 2014 15:38:19 +0100 python-biopython (1.62-1) unstable; urgency=low * New upstream release * Using CDBS to build the package -- Philipp Benner Sun, 15 Sep 2013 16:36:26 +0200 python-biopython (1.61-1) unstable; urgency=low [ Andreas Tille ] * debian/upstream: - Took over citation information from tasks file - Valid BibTeX authors field - Firstnames of authors * debian/control: Fixed Vcs fields [ Philipp Benner ] * New upstream release * Standards version 3.9.4 -- Philipp Benner Thu, 14 Feb 2013 22:08:04 +0100 python-biopython (1.60-1) unstable; urgency=low * New upstream release. * Removed quilt dependency. * Migrated to dh_python2. * patches/01-enable-mmCIF.patch: not required anymore. * debian/source/format: 3.0 (quilt) added. * debian/rules: added hardening flags. -- Philipp Benner Sat, 29 Sep 2012 16:43:59 +0200 python-biopython (1.59-1) unstable; urgency=low * New upstream release. * debian/control: Standards version 3.9.3. * debian/rules: added dh_numpy. -- Philipp Benner Fri, 09 Mar 2012 13:38:09 +0000 python-biopython (1.58-1) unstable; urgency=low * New upstream release. * debian/rules: added targets build-arch and build-indep. * debian/control: Standards version 3.9.2. -- Philipp Benner Wed, 02 Nov 2011 19:51:49 +0000 python-biopython (1.57-1) unstable; urgency=low * New upstream release (Closes: #585282). -- Philipp Benner Sun, 10 Apr 2011 17:58:01 +0000 python-biopython (1.56-1) unstable; urgency=low * New upstream release. -- Philipp Benner Thu, 02 Dec 2010 17:30:09 +0000 python-biopython (1.54-1) unstable; urgency=low * New upstream release. -- Philipp Benner Fri, 28 May 2010 00:06:43 +0200 python-biopython (1.53-1) unstable; urgency=low * New upstream release. -- Philipp Benner Mon, 21 Dec 2009 15:30:37 +0000 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 debian/python-biopython.install0000644000000000000000000000003712215405207014106 0ustar usr/lib/python*/*-packages/Bio debian/README.source0000644000000000000000000000020011260643254011340 0ustar 01-enable-mmCIF.patch: Enable building mmCIF support -- Philipp Benner , Wed, 30 Sep 2009 11:50:43 +0000 debian/watch0000644000000000000000000000023711133540214010213 0ustar # 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