Change log for python-biopython package in Debian
| 1 → 75 of 84 results | First • Previous • Next • Last |
| Published in sid-release |
python-biopython (1.84+dfsg-2) unstable; urgency=medium * d/t/run-unit-test: disable PDB_binary_cif for s390x in autopkgtest too. -- Étienne Mollier <email address hidden> Tue, 24 Sep 2024 19:44:19 +0200
| Published in sid-release |
python-biopython (1.84+dfsg-1) unstable; urgency=medium * Migrate Biopython 1.84 from experimental to unstable. * d/salsa-ci.yml: disable build path variation in reprotest. * d/rules: normalize HOME; this stabilizes build reproducibility. * d/rules: skip PDB_bcif on s390x architecture. -- Étienne Mollier <email address hidden> Mon, 23 Sep 2024 19:04:17 +0200
| Deleted in experimental-release (Reason: None provided.) |
python-biopython (1.84+dfsg-1~0exp1) experimental; urgency=medium * New upstream version 1.84+dfsg * d/watch: fix debian version mangling. * d/copyright: update copyright years. * fix-use-of-unversioned-python.patch: delete: hunk removed upstream. * reproduciblebuild.patch: delete: file disappeared upstream. * croak-on-muscle5.patch: refresh. * muscle3.patch: unfuzz. * seqxml-parser.patch: delete: issue fixed upstream. * skip-scipy-in-codonalign.patch: unfuzz. * d/rules: condensate dh_installdocs target to ease readability. * d/rules: cleanup irrelevant comments and more readable dh_auto_test. * d/t/run-unit-test: Tutorial.tex does not exist anymore. * d/t/run-unit-test: new PDB tests require compressed bcif files. * d/rules: replace distclean target by clean in Doc/. * d/control: documentation now depends on Sphinx and side modules. * d/rules: explicitly make html documentation. * d/copyright: do not advertise LGPL since it is not in use. * d/rules: cleanup documentation from embeding and privacy breaches. * d/control: documentation depends on libjs-sphinx and libjs-jquery. * d/python-biopython-doc.docs: install sphinx html artifacts. * d/python-biopython-doc.doc-base: update location of the Tutorial. * d/python-biopython-doc.examples: new: install examples. * d/python-biopython-doc.lintian-overrides: flag another empty test file. * fix-type-cast-i386.patch: new: fix PDB test failure on 32-bit. * d/TODO: build reproducibility needs fixing. -- Étienne Mollier <email address hidden> Mon, 16 Sep 2024 22:34:06 +0200
| Superseded in sid-release |
python-biopython (1.83+dfsg1-5) unstable; urgency=medium
* Team upload.
* Cherry-pick patch from upstream to fix FTBFS with Python 3.13.
Closes: #1081665
* Remove constraints unnecessary since bullseye (oldstable):
+ python3-biopython: Drop versioned constraint on ncbi-blast+ (>= 2.10.1-3)
in Recommends.
* d/control: adjust build-deps to be more cross-build friendly.
* Fix some of the DEP-3 patch metadata
-- Michael R. Crusoe <email address hidden> Sat, 14 Sep 2024 13:51:11 +0200
| Superseded in sid-release |
python-biopython (1.83+dfsg1-4) unstable; urgency=medium
* skip-scipy-in-codonalign.patch: new: skip scipy tests on riscv64.
This patch is introduced to give some breath to Risc-V CI runners while
the core of the problem is investigated. (Closes: #1079439)
* d/rules: skip ncbi tools tests due to #1079439.
* d/rules: update list of excluded tests due to missing packages.
-- Étienne Mollier <email address hidden> Wed, 04 Sep 2024 21:44:05 +0200
| Superseded in sid-release |
python-biopython (1.83+dfsg1-3) unstable; urgency=medium
* Replace skip-xmlio-tests.patch by seqxml-parser.patch.
Instead of skipping the test, upstream introduced a change that fixed
the XML parser for use with the newer version of expat. (Closes: #1064147)
* d/control: declare compliance to standards version 4.7.0.
* d/python3-biopython.lintian-overrides: update file name.
-- Étienne Mollier <email address hidden> Wed, 22 May 2024 15:14:56 +0200
Available diffs
- diff from 1.83+dfsg1-2 to 1.83+dfsg1-3 (2.4 KiB)
| Superseded in sid-release |
python-biopython (1.83+dfsg1-2) unstable; urgency=medium * Team upload. * Drop emboss from test dependencies on emboss due to #1069098. -- Andrius Merkys <email address hidden> Wed, 17 Apr 2024 07:32:28 -0400
Available diffs
- diff from 1.83+dfsg1-1 to 1.83+dfsg1-2 (516 bytes)
| Superseded in sid-release |
python-biopython (1.83+dfsg1-1) unstable; urgency=medium
* New upstream pseudo-version 1.83+dfsg1.
This is a minor version bump to include the new test artifact necessary
to allow the test suite to pass on big endian architectures. The nature
of the change makes it unsuitable to represent using the regular d/patches
series. See upstream issue 4658[1] for further information.
[1}: https://github.com/biopython/biopython/issues/4658
* d/rules: skip test Tutorial on non-amd64.
-- Étienne Mollier <email address hidden> Wed, 20 Mar 2024 21:10:02 +0100
Available diffs
| Superseded in sid-release |
python-biopython (1.83+dfsg-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version
* Exclude emboss from Build-Depends for 32bit architectures since
emboss will be removed for these architectures (see #1062371)
[ Étienne Mollier ]
* skip-xmlio-tests.patch: new: skip test failures.
This works around #1064147 so it is not a serious failure anymore.
The problem being still latent, said bug is not closed for now.
* d/t/run-unit-test: deploy newly needed test data.
* d/control: reduce availability of test dependencies.
Following the 64-bit time_t migration, and the removal of several
Debian Med packages from the 32-bit archives, these items are not
generally available anymore, and only checked on amd64 architecture.
-- Étienne Mollier <email address hidden> Sun, 10 Mar 2024 21:00:41 +0100
| Superseded in sid-release |
python-biopython (1.81+dfsg-3) unstable; urgency=medium * d/control: remove dependency on python3-unittest2. (Closes: #1058967) -- Étienne Mollier <email address hidden> Tue, 19 Dec 2023 15:06:46 +0100
Available diffs
- diff from 1.81+dfsg-2 to 1.81+dfsg-3 (468 bytes)
| Superseded in sid-release |
python-biopython (1.81+dfsg-2) unstable; urgency=medium
* python3.12.patch: new: fix ftbfs with python3.12.
Thanks to Antonio (Closes: #1055708)
* d/control: remove obsolete comment.
* d/control: move to dh-sequence-python3.
-- Étienne Mollier <email address hidden> Sat, 11 Nov 2023 11:16:46 +0100
Available diffs
| Superseded in sid-release |
python-biopython (1.81+dfsg-1) unstable; urgency=medium * Migrate biopython 1.81 to unstable. * Merges fixes from python-biopython 1.80+dfsg-6. -- Étienne Mollier <email address hidden> Mon, 10 Jul 2023 22:50:52 +0200
Available diffs
- diff from 1.80+dfsg-6 to 1.81+dfsg-1 (251.6 KiB)
| Superseded in sid-release |
python-biopython (1.80+dfsg-6) unstable; urgency=medium * d/control: depend on python3-reportlab (>= 4.0.4-1~). (Closes: #1040776) -- Étienne Mollier <email address hidden> Mon, 10 Jul 2023 22:27:12 +0200
Available diffs
| Superseded in sid-release |
python-biopython (1.80+dfsg-5) unstable; urgency=medium
[ Andreas Tille ]
* Drop nocheck profile from hevea since its also needed to create doc
(Closes: #1036174)
[ Lukas Märdian ]
* avoid the python3-renderpm dependency (Closes: #1039565)
[ Étienne Mollier ]
* d/rules: disable install-doc target with nodoc profile.
* d/control: enable numpy outside nocheck build profile.
* d/*.lintian-overrides: make the spelling override more generic.
-- Étienne Mollier <email address hidden> Sun, 09 Jul 2023 17:48:34 +0200
| Deleted in experimental-release (Reason: None provided.) |
python-biopython (1.81+dfsg-0+exp1) experimental; urgency=medium * New upstream version 1.81+dfsg * d/control: remove obsolete version constraint on dssp. * numpy-1.24.patch: remove: applied upstream. * muscle3.patch: fix typo in patch description. * remove-distutils-import.patch: add. -- Étienne Mollier <email address hidden> Sun, 09 Jul 2023 20:21:39 +0200
python-biopython (1.80+dfsg-4) unstable; urgency=medium
* Team Upload.
* Cherry-pick upstream patch to fix problems with
numpy 1.24 (Closes: #1027253)
-- Nilesh Patra <email address hidden> Thu, 29 Dec 2022 18:52:07 +0530
Available diffs
| Superseded in sid-release |
python-biopython (1.80+dfsg-3) unstable; urgency=medium
* muscle3.patch: ensure muscle3 is default even if unavailable.
This fixes the test_doctest failure which occurs because of a
mismatch between "muscle" and "muscle3" when none of them is
available.
* d/control: declare compliance to standards version 4.6.2.
-- Étienne Mollier <email address hidden> Fri, 23 Dec 2022 20:22:29 +0100
Available diffs
- diff from 1.80+dfsg-2 to 1.80+dfsg-3 (1013 bytes)
| Superseded in sid-release |
python-biopython (1.80+dfsg-2) unstable; urgency=medium
* d/NEWS: fix typo in news item.
* d/control: bring back t_coffee tests since upstream version revert.
Closes: #1022307
* d/control: restore muscle3 instead of plain muscle (version 5).
Closes: #1009118
* port_tutorial_to_muscle3.patch: add; fix doctest failures.
-- Étienne Mollier <email address hidden> Sun, 04 Dec 2022 19:15:42 +0100
Available diffs
- diff from 1.80+dfsg-1 to 1.80+dfsg-2 (1.7 KiB)
| Superseded in sid-release |
python-biopython (1.80+dfsg-1) unstable; urgency=medium
* Migrate biopython 1.80 from experimental to unstable.
Closes: #1024986, #1024858, #1024855, #1025014, #1025022
-- Étienne Mollier <email address hidden> Mon, 28 Nov 2022 22:19:25 +0100
Available diffs
| Deleted in experimental-release (Reason: None provided.) |
python-biopython (1.80+dfsg-1~0exp0) experimental; urgency=medium
* New upstream version
* Standards-Version: 4.6.1 (routine-update)
* Set upstream metadata fields: Security-Contact.
* privacy_breach_ie9.patch: refresh.
* adjust-test_GraphicsBitmaps.patch: delete; applied upstream.
* spelling.patch: delete; applied upstream.
* mkdssp4.patch: delete; fixed upstream.
* d/control: remove test dependency on problematic packages; muscle 5
wrapping is unsupported upstream, and t_coffee suffers from segmentation
faults documented in #1022570
* croak-on-muscle5.patch: add; raise RuntimeError with muscle 5.
* d/NEWS: describe incompatibility with muscle 5; also describe possible
workarounds.
* d/not-installed: add tree1 and other_trees.
* d/*.lintian-overrides: refresh override.
* debian/python3-biopython.lintian-overrides: override typo; the reported
spelling error does not seem to match anything meaningful on the side of
the source code.
* d/s/lintian-overrides: indicate location of Restriction.md, source of
Restriction.html.
* d/copyright: bump copyright years.
* muscle3.patch: add; default to use muscle3 command if available.
This is in preparation of the availability of a dedicated muscle3
package with the explicitly versioned command, since muscle 5 is a very
different program but can be installed in parallel.
-- Étienne Mollier <email address hidden> Thu, 24 Nov 2022 18:39:22 +0100
| Superseded in sid-release |
python-biopython (1.79+dfsg-3) unstable; urgency=medium
[ Peter Michael Green ]
* Restrict architecture list of muscle build-dependency to reflect
architectures where the current version of muscle is available.
(Closes: #1006667)
[ Étienne Mollier ]
* d/control,d/python3-biopython.links: move from w3-dtd-mathml to slightly
more recent w3c-sgml-lib.
Thanks to Peter Green and Vincent Lefevre.
* Remove d/python3-biopython.lintian-overrides; not in use anymore.
-- Étienne Mollier <email address hidden> Sat, 05 Mar 2022 15:36:12 +0100
Available diffs
| Superseded in sid-release |
python-biopython (1.79+dfsg-2) unstable; urgency=medium
* Move w3-dtd-mathml from Suggests to Depends to avoid dangling symlink
mathml2.dtd
-- Andreas Tille <email address hidden> Thu, 17 Feb 2022 20:15:09 +0100
Available diffs
- diff from 1.79+dfsg-1 to 1.79+dfsg-2 (858 bytes)
| Superseded in sid-release |
python-biopython (1.79+dfsg-1) unstable; urgency=medium
* Migrate from Experimental to Unstable.
* Mark spelling.patch as not needing forward.
It seems that the file being package might not exists in upcoming
Biopython versions anymore.
* adjust-test_GraphicsBitmaps.patch: forwarded upstream.
* d/control: breaks ncbi-acc-download (<< 0.2.7-2~)
-- Étienne Mollier <email address hidden> Fri, 22 Oct 2021 18:10:48 +0200
Available diffs
| Deleted in experimental-release (Reason: None provided.) |
python-biopython (1.79+dfsg-1~0exp0) experimental; urgency=medium
* New upstream version
* d/copyright: update years per LICENSE file.
* Refresh patches:
+ mkdssp4.patch:
- renamed from mkdssp4.path, fixing typo in the file extension,
- skip failing test_PDB_DSSP due to mkdssp 4 too recent,
- updated patch author's email address;
+ following renderpm upgrade, add adjust-test_GraphicsBitmaps.patch to
properly skip again the test failing due to missing font;
+ add spelling.patch to fix new spelling-error-in-binary caught by lintian.
-- Étienne Mollier <email address hidden> Sat, 16 Oct 2021 12:30:51 +0200
| Superseded in sid-release |
python-biopython (1.78+dfsg-6) unstable; urgency=medium
* d/control: bump python3-renderpm to python3-biopython dependency.
(Closes: #995689)
-- Étienne Mollier <email address hidden> Mon, 11 Oct 2021 22:25:02 +0200
| Superseded in sid-release |
python-biopython (1.78+dfsg-5) unstable; urgency=medium
* d/control: update uploader address
* d/watch: fix broken url to github
* d{,/tests}/control: add full_suite autopkgtest (Closes: #986410)
* Standards-Version: 4.6.0 (routine-update)
* Use secure URI in Homepage field.
-- Étienne Mollier <email address hidden> Sun, 22 Aug 2021 21:56:28 +0200
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 <email address hidden> Sat, 05 Dec 2020 23:32:40 +0100
Available diffs
| Superseded in sid-release |
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 <email address hidden> Sat, 17 Oct 2020 13:59:04 +0200
Available diffs
- diff from 1.77+dfsg-3 to 1.78+dfsg-3 (497.6 KiB)
| Superseded in sid-release |
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 <email address hidden> Fri, 02 Oct 2020 23:18:07 +0200
| Superseded in sid-release |
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 <email address hidden> Wed, 09 Sep 2020 22:53:13 +0200
| Superseded in sid-release |
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 <email address hidden> Mon, 22 Jun 2020 19:21:47 +0200
Available diffs
- diff from 1.77+dfsg-2 to 1.77+dfsg-3 (1.6 KiB)
| Superseded in sid-release |
python-biopython (1.77+dfsg-2) unstable; urgency=medium * Declared python3-biopython breaks: cnvkit (<< 0.9.7-1~) (Closes: #962944) -- Etienne Mollier <email address hidden> Tue, 16 Jun 2020 22:12:00 +0200
Available diffs
- diff from 1.77+dfsg-1 to 1.77+dfsg-2 (1.0 KiB)
| Superseded in sid-release |
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 <email address hidden> Thu, 11 Jun 2020 20:10:34 +0200
Available diffs
- diff from 1.76+dfsg-2 to 1.77+dfsg-1 (1.1 MiB)
| Superseded in sid-release |
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 <email address hidden> Fri, 15 May 2020 11:40:33 +0200
Available diffs
| Superseded in sid-release |
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 <email address hidden> Fri, 20 Dec 2019 11:00:46 -0800
Available diffs
- diff from 1.75+dfsg-4 to 1.76+dfsg-1 (346.8 KiB)
| Superseded in sid-release |
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 <email address hidden> Tue, 17 Dec 2019 11:35:41 +0100
Available diffs
- diff from 1.73+dfsg-1ubuntu4 (in Ubuntu) to 1.75+dfsg-4 (2.8 MiB)
- diff from 1.75+dfsg-3 to 1.75+dfsg-4 (727 bytes)
| Superseded in sid-release |
python-biopython (1.75+dfsg-3) unstable; urgency=medium * Team upload. * Restrict where we test phyml for now. -- Michael R. Crusoe <email address hidden> Mon, 16 Dec 2019 22:15:00 +0100
Available diffs
- diff from 1.75+dfsg-2 to 1.75+dfsg-3 (439 bytes)
| Superseded in sid-release |
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 <email address hidden> Sun, 15 Dec 2019 14:38:14 +0100
Available diffs
- diff from 1.75+dfsg-1 to 1.75+dfsg-2 (6.8 KiB)
| Superseded in sid-release |
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 <email address hidden> Wed, 04 Dec 2019 17:29:48 +0100
Available diffs
python-biopython (1.73+dfsg-1) unstable; urgency=medium * New upstream version * debhelper 12 * Standards-Version: 4.3.0 -- Andreas Tille <email address hidden> Fri, 11 Jan 2019 23:23:52 +0100
Available diffs
- diff from 1.72+dfsg-2 to 1.73+dfsg-1 (770.4 KiB)
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 <email address hidden> Wed, 05 Dec 2018 11:41:01 +0000
Available diffs
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 <email address hidden> 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 <email address hidden> Fri, 06 Apr 2018 09:03:06 +0200
Available diffs
- diff from 1.70+dfsg-4 to 1.71+dfsg-1 (692.5 KiB)
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 <email address hidden> Tue, 19 Dec 2017 11:07:47 +0100
Available diffs
- diff from 1.70+dfsg-3 to 1.70+dfsg-4 (950 bytes)
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 <email address hidden> Tue, 07 Nov 2017 13:24:21 +0100
Available diffs
python-biopython (1.70+dfsg-2) unstable; urgency=medium * Team upload * Fixed build dependencies (added python-setuptools) (Closes: #869597). -- Steffen Moeller <email address hidden> Mon, 31 Jul 2017 18:24:01 +0200
Available diffs
- diff from 1.68+dfsg-3build1 (in Ubuntu) to 1.70+dfsg-2 (2.1 MiB)
- diff from 1.70+dfsg-1 to 1.70+dfsg-2 (446 bytes)
| Superseded in sid-release |
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 <email address hidden> Sun, 23 Jul 2017 18:08:39 +0200
Available diffs
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 <email address hidden> Fri, 20 Jan 2017 16:52:04 +0100
Available diffs
- diff from 1.68+dfsg-1 to 1.68+dfsg-3 (2.2 KiB)
- diff from 1.68+dfsg-2 to 1.68+dfsg-3 (1.2 KiB)
| Superseded in sid-release |
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 <email address hidden> Sun, 15 Jan 2017 14:56:26 +0100
Available diffs
- diff from 1.68+dfsg-1 to 1.68+dfsg-2 (1.4 KiB)
python-biopython (1.68+dfsg-1) unstable; urgency=medium * New upstream version -- Andreas Tille <email address hidden> Mon, 29 Aug 2016 13:23:35 +0200
Available diffs
- diff from 1.67+dfsg-1 to 1.68+dfsg-1 (519.2 KiB)
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 <email address hidden> Thu, 09 Jun 2016 13:05:14 +0200
Available diffs
- diff from 1.66+dfsg-3 to 1.67+dfsg-1 (4.1 MiB)
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 <email address hidden> Thu, 19 May 2016 16:48:15 +0200
Available diffs
- diff from 1.66+dfsg-2 to 1.66+dfsg-3 (1.7 KiB)
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 <email address hidden> Wed, 09 Mar 2016 15:25:38 +0100
Available diffs
python-biopython (1.66+dfsg-1) unstable; urgency=medium * New upstream version (some patches applied upstream) -- Andreas Tille <email address hidden> Sun, 08 Nov 2015 19:28:26 +0100
Available diffs
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 <email address hidden> Tue, 06 Oct 2015 16:53:06 +0200
Available diffs
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 <email address hidden> 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 <email address hidden> Tue, 12 May 2015 11:08:43 +0200
Available diffs
- diff from 1.64+dfsg-5 to 1.65+dfsg-1 (1.6 MiB)
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 <email address hidden> Wed, 24 Sep 2014 10:08:12 +0200
Available diffs
- diff from 1.64+dfsg-4 to 1.64+dfsg-5 (2.0 KiB)
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
<email address hidden>)
Closes: #751277
* Install egg metadata
Closes: #743927
* Add samtools to Build-Depends + Recommends since it is checked in test
suite
-- Andreas Tille <email address hidden> Mon, 01 Sep 2014 15:59:30 +0200
Available diffs
- diff from 1.63-1 to 1.64+dfsg-4 (398.2 KiB)
- diff from 1.64+dfsg-2 to 1.64+dfsg-4 (2.8 KiB)
| Superseded in sid-release |
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 <email address hidden> Fri, 15 Aug 2014 11:41:23 +0200
| Superseded in sid-release |
python-biopython (1.64+dfsg-2) unstable; urgency=medium
* Use HOME in build_dir for testing (thanks to Jakub Wilk <email address hidden>
for the patch)
Closes: #751586
-- Andreas Tille <email address hidden> Sat, 14 Jun 2014 20:12:02 +0200
Available diffs
- diff from 1.64+dfsg-1 to 1.64+dfsg-2 (884 bytes)
| Superseded in sid-release |
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 <email address hidden> Sun, 08 Jun 2014 10:25:35 +0200
Available diffs
- diff from 1.63+dfsg-5 to 1.64+dfsg-1 (390.3 KiB)
| Superseded in sid-release |
python-biopython (1.63+dfsg-5) unstable; urgency=medium
* Apply upstream fix to fix cpairwise2 import issue under python3
Closes: #747494
-- Andreas Tille <email address hidden> Sat, 10 May 2014 07:52:48 +0200
Available diffs
- diff from 1.63+dfsg-4 to 1.63+dfsg-5 (871 bytes)
| Superseded in sid-release |
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 <email address hidden> Thu, 08 May 2014 11:33:47 +0200
Available diffs
| Superseded in sid-release |
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 <email address hidden> Sun, 04 May 2014 00:18:47 +0200
Available diffs
- diff from 1.63+dfsg-2 to 1.63+dfsg-3 (751 bytes)
| Superseded in sid-release |
python-biopython (1.63+dfsg-2) unstable; urgency=medium
* Force writable HOME to make sure t-coffee test will pass
Closes: #746624
-- Andreas Tille <email address hidden> Fri, 02 May 2014 23:14:50 +0200
Available diffs
- diff from 1.63+dfsg-1 to 1.63+dfsg-2 (590 bytes)
| Superseded in sid-release |
python-biopython (1.63+dfsg-1) unstable; urgency=medium
* Remove Bio\Entrez\DTDs\mathml2-qname-1.mod
Closes: #746484
-- Andreas Tille <email address hidden> Wed, 30 Apr 2014 14:47:53 +0200
python-biopython (1.63-1) unstable; urgency=low * New upstream release -- Philipp Benner <email address hidden> Thu, 09 Jan 2014 15:38:19 +0100
Available diffs
- diff from 1.62-1 to 1.63-1 (838.0 KiB)
python-biopython (1.62-1) unstable; urgency=low * New upstream release * Using CDBS to build the package -- Philipp Benner <email address hidden> Sun, 15 Sep 2013 16:36:26 +0200
Available diffs
- diff from 1.61-1 to 1.62-1 (3.0 MiB)
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 <email address hidden> Thu, 14 Feb 2013 22:08:04 +0100
Available diffs
- diff from 1.60-1 to 1.61-1 (4.4 MiB)
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 <email address hidden> Sat, 29 Sep 2012 16:43:59 +0200
Available diffs
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 <email address hidden> Fri, 09 Mar 2012 13:38:09 +0000
Available diffs
- diff from 1.58-1 (in Ubuntu) to 1.59-1 (1.3 MiB)
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 <email address hidden> Wed, 02 Nov 2011 19:51:49 +0000
python-biopython (1.57-1) unstable; urgency=low * New upstream release (Closes: #585282). -- Philipp Benner <email address hidden> Sun, 10 Apr 2011 17:58:01 +0000
python-biopython (1.56-1) unstable; urgency=low * New upstream release. -- Philipp Benner <email address hidden> Thu, 02 Dec 2010 17:30:09 +0000
| 1 → 75 of 84 results | First • Previous • Next • Last |
