python-biopython (1.78+dfsg-4) unstable; urgency=medium * Add mkdssp4.patch. (Closes: #976542) * Standards-Version: 4.5.1 (routine-update) * Bump dependency on dssp version 4.0.0. -- Étienne Mollier Sat, 05 Dec 2020 23:32:40 +0100 python-biopython (1.78+dfsg-3) unstable; urgency=medium * Bumped ncbi-blast+ version requirement to 2.10.1-3 * Made sure run-unit-test did not attempt memory allocation override * debian/not-installed made more generic for various python versions (Closes: #972381) -- Étienne Mollier Sat, 17 Oct 2020 13:59:04 +0200 python-biopython (1.78+dfsg-2) unstable; urgency=medium * Bumped build requirement on ncbi-blast+ 2.10.1-2 and greater: - fixed building on mipsel; - removed patch working around makeblastdb bug in v5, now unnecessary. * Cleaned up patches: - added DEP3 description to blastdbv4-tests-filter-archs.patch; - reviewed and forwarded patches upstream when applicable. -- Étienne Mollier Fri, 02 Oct 2020 23:18:07 +0200 python-biopython (1.78+dfsg-1) unstable; urgency=medium * Bumped build requirement on ncbi-blast+ 2.10.0-3 and greater, * Reworked the patch working around makeblastd bug in v5 to fall back in v4 only on architectures on which corrections are yet to be implemented. * Removed patches applied upstream. * New upstream version * debhelper-compat 13 (routine-update) * Improved build reproducibility -- Étienne Mollier Wed, 09 Sep 2020 22:53:13 +0200 python-biopython (1.77+dfsg-3) unstable; urgency=medium [ Etienne Mollier ] * Forwarded implementation of makeblastdb's `-blastdb_version` flag to upstream. (minor change) [ Andreas Tille ] * Adapt to python3-scipy by taking over pull request https://github.com/biopython/biopython/pull/2998 as quilt patch. Closes: #966928 -- Etienne Mollier Mon, 22 Jun 2020 19:21:47 +0200 python-biopython (1.77+dfsg-2) unstable; urgency=medium * Declared python3-biopython breaks: cnvkit (<< 0.9.7-1~) (Closes: #962944) -- Etienne Mollier Tue, 16 Jun 2020 22:12:00 +0200 python-biopython (1.77+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version. * Test makeblastdb using format version 4, this is to work around issues on 32 bits CPU architectures. Closes: #960756. [ Steffen Moeller ] * Also clean .pygtex and .pygstyle files in Doc -- Etienne Mollier Thu, 11 Jun 2020 20:10:34 +0200 python-biopython (1.76+dfsg-2) unstable; urgency=medium * Team upload. [ Michael R. Crusoe ] * debian/control: mark the -doc package as Multi-Arch: foreign [ Dylan Aïssi ] * Add upstream patch to fix tests with new NCBI BLAST DB v5 (Closes: #959587) [ Andreas Tille ] * Standards-Version: 4.5.0 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository, Repository-Browse. * Refer to specific version of license GPL-2+. -- Dylan Aïssi Fri, 15 May 2020 11:40:33 +0200 python-biopython (1.76+dfsg-1) unstable; urgency=medium * Team upload. * New upstream version * Remove patches applied upstream: fix_doctests, ppc64el_precision, python_3.8_iteration_fix.patch * Remove patches missing from debian/patches/series. -- Michael R. Crusoe Fri, 20 Dec 2019 11:00:46 -0800 python-biopython (1.75+dfsg-4) unstable; urgency=medium * Team upload. * Patch added to reduce the required precision for one part of the test_phenotype_fit.TestPhenoMicro test -- Michael R. Crusoe Tue, 17 Dec 2019 11:35:41 +0100 python-biopython (1.75+dfsg-3) unstable; urgency=medium * Team upload. * Restrict where we test phyml for now. -- Michael R. Crusoe Mon, 16 Dec 2019 22:15:00 +0100 python-biopython (1.75+dfsg-2) unstable; urgency=medium [ Michael R. Crusoe ] * Team upload. * Skip PDB_ResidueDepth test, as http://mgltools.scripps.edu/packages/MSMS is not yet packaged for Debian * Skip test_mmtf{,_online} as https://github.com/rcsb/mmtf-python is not yet packaged for Debian * Added missing test dependencies: python-unittest2, python{,3}-networkx, samtools * i386: build-dep on raxml for testing purposes * debian/patches/arm64.patch from upstream to fix the PairwiseAligner * debian/patches/fix_doctest: from me to fix the Bio.Cluster._cluster doctests Now the tests are required to pass again. [ Andreas Tille ] * Drop Python2 package Closes: #937606 -- Michael R. Crusoe Sun, 15 Dec 2019 14:38:14 +0100 python-biopython (1.75+dfsg-1) unstable; urgency=medium * New upstream version Closes: #944242 * debhelper-compat 12 * Standards-Version: 4.4.1 * Remove trailing whitespace in debian/rules * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g * Set upstream metadata fields: Repository. * Build-Depends: python3-pygments * Python 3.8 iteration fix from upstream * Ignore remaining build time test errors since these are discussed with upstream and will be fixed soon. On the other hand latest version of biopython is needed to fix bugs in other Debian Med packages. * Seems explicit Depends: python is needed now for Python2 packages * Remove test test_Tutorial.py which is bound to fail from autopkgtest -- Andreas Tille Wed, 04 Dec 2019 17:29:48 +0100 python-biopython (1.73+dfsg-1) unstable; urgency=medium * New upstream version * debhelper 12 * Standards-Version: 4.3.0 -- Andreas Tille Fri, 11 Jan 2019 23:23:52 +0100 python-biopython (1.72+dfsg-2) unstable; urgency=medium [ Andreas Tille ] * Remove unneeded comment about samtools - which is not found by biopython anyway [ Graham Inggs ] * Team upload * Fix compatibility with ReportLab 3.5 (Closes: #913064) * Clean up some trailing whitespace in debian/* files -- Graham Inggs Wed, 05 Dec 2018 11:41:01 +0000 python-biopython (1.72+dfsg-1) unstable; urgency=medium * New upstream version Closes: #904317 * Standards-Version: 4.1.5 * debian/rules: Respect DEB_BUILD_OPTIONS in dh_auto_test * Drop ancient Python version fields * Deactivate exclusion of samtools_tool test and see if it works -- Andreas Tille Sat, 28 Jul 2018 04:45:32 +0200 python-biopython (1.71+dfsg-1) unstable; urgency=medium * New upstream version * Standards-Version: 4.1.3 * Point Vcs fields to salsa.debian.org * debhelper 11 * Add dh-python to Build-Depends since this will be dropped from python3's Depends soon * Fix Python version in Suggestes * Make sure Doc dir ends up in python-biopython-doc package -- Andreas Tille Fri, 06 Apr 2018 09:03:06 +0200 python-biopython (1.70+dfsg-4) unstable; urgency=medium * Symlink to mathml2.dtd of w3-dtd-mathml package Closes: #672407 * Standards-Version: 4.1.2 -- Andreas Tille Tue, 19 Dec 2017 11:07:47 +0100 python-biopython (1.70+dfsg-3) unstable; urgency=medium * Copy *.rst doc files. Closes: #872222 * Apply two upstream patches to deal with change in BWA output Closes: #880236 * Drop duplicated python*-numpy in Build-Depends * Standards-Version: 4.1.1 * Fix permission of dtd files -- Andreas Tille Tue, 07 Nov 2017 13:24:21 +0100 python-biopython (1.70+dfsg-2) unstable; urgency=medium * Team upload * Fixed build dependencies (added python-setuptools) (Closes: #869597). -- Steffen Moeller Mon, 31 Jul 2017 18:24:01 +0200 python-biopython (1.70+dfsg-1) unstable; urgency=medium * Team upload * New upstream release. * debian/upstream/metadata: Added references to OMICtools, bio.tools, RRID * debian/rules: Merged two redundant clean overrides -- Steffen Moeller Sun, 23 Jul 2017 18:08:39 +0200 python-biopython (1.68+dfsg-3) unstable; urgency=medium * (Build-)Depend: phyml only on those architectures where it is available * Relax test conditions in test_phenotype_fit to work around some rounding differences on arm64 (see https://github.com/biopython/biopython/issues/1038 ) -- Andreas Tille Fri, 20 Jan 2017 16:52:04 +0100 python-biopython (1.68+dfsg-2) unstable; urgency=medium * Add Tutorial.tex to *-doc package since its used in autopkgtest and its just an ignorable payload for this package * debhelper 10 * d/watch: version=4 * Add python-scipy since it is used in test suite -- Andreas Tille Sun, 15 Jan 2017 14:56:26 +0100 python-biopython (1.68+dfsg-1) unstable; urgency=medium * New upstream version -- Andreas Tille Mon, 29 Aug 2016 13:23:35 +0200 python-biopython (1.67+dfsg-1) unstable; urgency=medium * New upstream version * Point d/watch to github * xz compression in d/watch * Take over patch from upstream to fix detection of rpsblast * Skip test needing a network connection * Add +bindnow hardening option * Delete useless .cvsignore files from package * New Build-Depends for documentation: hevea, texlive-latex-base, texlive-latex-extra, texlive-fonts-recommended * Makefile for Doc needs to be separately called (clean and build) * Remove doc sources from binary doc package -- Andreas Tille Thu, 09 Jun 2016 13:05:14 +0200 python-biopython (1.66+dfsg-3) unstable; urgency=medium * Apply fix from upstream for test case dealing with new blastp output format Closes: #824048 * cme fix dpkg-control -- Andreas Tille Thu, 19 May 2016 16:48:15 +0200 python-biopython (1.66+dfsg-2) unstable; urgency=medium * Packaging moved from SVN to Git * Bumped Standards-Version * Exclude phyml test for the moment Closes: #813262 -- Andreas Tille Wed, 09 Mar 2016 15:25:38 +0100 python-biopython (1.66+dfsg-1) unstable; urgency=medium * New upstream version (some patches applied upstream) -- Andreas Tille Sun, 08 Nov 2015 19:28:26 +0100 python-biopython (1.65+dfsg-3) unstable; urgency=medium * Also run Tutorial test * Prefer Github as contact point * Build-Depends: python3-mysqldb Closes: #801112 -- Andreas Tille Tue, 06 Oct 2015 16:53:06 +0200 python-biopython (1.65+dfsg-2) unstable; urgency=medium * Build-Depends & Suggests: phylip + fixed test_phyml_tool Closes: #799820 * debian/clean: Remove test results occuring now since phylip can be used * Activate more tests formerly deactivated -- Andreas Tille Wed, 23 Sep 2015 15:18:58 +0200 python-biopython (1.65+dfsg-1) unstable; urgency=medium * New upstream version * Apply fix for broken test from Upstream Git * Versioned (Build-)Depends: python-rdflib (>= 4) * Prevent privacy-breach-logo -- Andreas Tille Tue, 12 May 2015 11:08:43 +0200 python-biopython (1.64+dfsg-5) unstable; urgency=medium * Exclude samtools test from unit testing for the moment since this package is in flux and it is not clear what architectures will be supported finally * Do not suggest python3 packages in python-biopython and no python package sin python3-biopython * cme fix dpkg-control -- Andreas Tille Wed, 24 Sep 2014 10:08:12 +0200 python-biopython (1.64+dfsg-4) unstable; urgency=medium * debian/patches/fix_test_problem_on_powerpc.patch: Patch provided by upstream to run test suite on PowerPC (thanks to Michiel de Hoon ) Closes: #751277 * Install egg metadata Closes: #743927 * Add samtools to Build-Depends + Recommends since it is checked in test suite -- Andreas Tille Mon, 01 Sep 2014 15:59:30 +0200 python-biopython (1.64+dfsg-3) unstable; urgency=medium * Skip test on mips architecture which is known to fail * Versioned (Build-)Depends wise (>= 2.4.1-16) to make sure tests will pass on each architecture (problems with previous wise on powerpc, s390x) -- Andreas Tille Fri, 15 Aug 2014 11:41:23 +0200 python-biopython (1.64+dfsg-2) unstable; urgency=medium * Use HOME in build_dir for testing (thanks to Jakub Wilk for the patch) Closes: #751586 -- Andreas Tille Sat, 14 Jun 2014 20:12:02 +0200 python-biopython (1.64+dfsg-1) unstable; urgency=medium * New upstream version * Build-Depends raxml only on those architectures where it is available Closes: #750845 -- Andreas Tille Sun, 08 Jun 2014 10:25:35 +0200 python-biopython (1.63+dfsg-5) unstable; urgency=medium * Apply upstream fix to fix cpairwise2 import issue under python3 Closes: #747494 -- Andreas Tille Sat, 10 May 2014 07:52:48 +0200 python-biopython (1.63+dfsg-4) unstable; urgency=medium [ Martin Pitt ] * Depend on our own packages in the autopkgtest and add missing "allow-stderr" restriction. Closes: #747391 [ Andreas Tille ] * Move ncbi-blast+ from Suggests to Recommends due to a hint from upstream -- Andreas Tille Thu, 08 May 2014 11:33:47 +0200 python-biopython (1.63+dfsg-3) unstable; urgency=medium * Set HOME=/tmp also in autopkgtest * Do not try to create doc in arch-only builds -- Andreas Tille Sun, 04 May 2014 00:18:47 +0200 python-biopython (1.63+dfsg-2) unstable; urgency=medium * Force writable HOME to make sure t-coffee test will pass Closes: #746624 -- Andreas Tille Fri, 02 May 2014 23:14:50 +0200 python-biopython (1.63+dfsg-1) unstable; urgency=medium * Remove Bio\Entrez\DTDs\mathml2-qname-1.mod Closes: #746484 -- Andreas Tille Wed, 30 Apr 2014 14:47:53 +0200 python-biopython (1.63-2) unstable; urgency=medium * Enable Python3 * debian/copyright: - Add Upstream-Contact - DEP5 * Run (nearly) full test suite * Add autopkgtest * Add packages from Build-Depends needed for tests to Depends -- Andreas Tille Thu, 06 Mar 2014 11:51:27 +0100 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