python-cogent (2024.5.7a1+dfsg-3) unstable; urgency=medium
* Team upload.
* Update skip-parallel-tests-on-single-cpu-systems.patch
to skip "test_write_db_parallel" again. Closes: #1030885.
-- Santiago Vila <sanvila@debian.org> Fri, 05 Jul 2024 18:45:00 +0200
python-cogent (2024.5.7a1+dfsg-2) unstable; urgency=medium
* Fix binary-any build
Closes: #1074562
-- Andreas Tille <tille@debian.org> Tue, 02 Jul 2024 15:43:37 +0200
python-cogent (2024.5.7a1+dfsg-1) unstable; urgency=medium
[ Ananthu C V ]
* Team upload
* New upstream version 2024.5.7a1+dfsg
* Unfuzz patches
* Add python3-stevedore build dependency and apply wrap-and-sort
* Use execute_after syntax over override in d/rules where possible
[ Andreas Tille ]
* debian/control:
- Build-Depends: architecture-is-64-bit, architecture-is-little-endian
- Architecture: any
[ Emmanuel Arias ]
* d/control: Add ${sphinxdoc:Depends} as Depends in python-cogent-doc
package.
- d/rules: Add --with sphinxdoc.
* d/control: Add libjs-requirejs as build dependency. Also add as Depends in
the python-cogent-doc package.
- d/rules: add override_dh_sphinxdoc to replace external link to
require.min.js to use installed lib and avoid privacy leak.
- wrap-and-sort.
* d/control: Bump Standards-Version to 4.7.0 (from 4.6.2; no further changes
needed).
-- Emmanuel Arias <eamanu@debian.org> Wed, 26 Jun 2024 01:24:50 -0300
python-cogent (2023.12.15a1+dfsg-1) unstable; urgency=medium
* New upstream version
Closes: #1058370
* Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
* Build-Depends: python3-sphinxcontrib.bibtex, python3-sphinx-design,
python3-pydata-sphinx-theme
* Add build support for loongarch64
Closes: #1059557
* Fix patch to skip some tests which was lacking `import multiprocessing`
-- Andreas Tille <tille@debian.org> Fri, 26 Jan 2024 15:36:11 +0100
python-cogent (2023.2.12a1+dfsg-4) unstable; urgency=medium
* Team upload.
* Drop old patch fix-build-on-single-cpu-systems.patch,
as it disables parallel tests for everybody.
* Add new patch skip-parallel-tests-on-single-cpu-systems.patch
instead, which does what its name suggests. Closes: #1030885.
-- Santiago Vila <sanvila@debian.org> Sat, 28 Oct 2023 22:30:00 +0200
python-cogent (2023.2.12a1+dfsg-3) unstable; urgency=medium
* Team upload.
* Update fix-build-on-single-cpu-systems.patch to skip
"test_write_db_parallel" again. Closes: #1030885.
-- Santiago Vila <sanvila@debian.org> Fri, 20 Oct 2023 14:02:00 +0200
python-cogent (2023.2.12a1+dfsg-2) unstable; urgency=medium
* Restrict to 64 bit architectures
-- Andreas Tille <tille@debian.org> Fri, 24 Feb 2023 14:18:01 +0100
python-cogent (2023.2.12a1+dfsg-1) unstable; urgency=medium
* New upstream version
* Standards-Version: 4.6.2 (routine-update)
-- Andreas Tille <tille@debian.org> Wed, 22 Feb 2023 08:07:42 +0100
python-cogent (2022.10.31a1+dfsg-3) unstable; urgency=medium
* Team Upload.
* Drop jupyter-sphinx from build depends
-- Nilesh Patra <nilesh@debian.org> Sat, 11 Feb 2023 22:58:26 +0530
python-cogent (2022.10.31a1+dfsg-2) unstable; urgency=medium
* Skip build time tests also for armhf
-- Andreas Tille <tille@debian.org> Fri, 10 Feb 2023 07:55:13 +0100
python-cogent (2022.10.31a1+dfsg-1) unstable; urgency=medium
[ Andreas Tille ]
* New upstream version
Closes: #1030884
* Build-Depends: python3-typing-extensions
[ Étienne Mollier ]
* d/{control,rules}: migrate from flit to generic pyproject.
[ Santiago Vila ]
* Skip tests that are failing on single-cpu systems
Closes: 1030885
-- Andreas Tille <tille@debian.org> Thu, 09 Feb 2023 15:24:31 +0100
python-cogent (2022.8.24a1+dfsg-1) unstable; urgency=medium
* New upstream version
* Ignore some tests that try to access network
* Drop outdated debian/README.source and README.Debian
-- Andreas Tille <tille@debian.org> Thu, 29 Sep 2022 11:00:51 +0200
python-cogent (2022.5.25a1+dfsg-1) unstable; urgency=medium
* New upstream version
* Standards-Version: 4.6.1 (routine-update)
* Build-Depends: python3-plotly <!nocheck>
-- Andreas Tille <tille@debian.org> Fri, 29 Jul 2022 16:30:18 +0200
python-cogent (2021.10.12a1+dfsg-2) unstable; urgency=medium
* Team Upload.
* Remove refs to jupyter-sphinx
-- Nilesh Patra <nilesh@debian.org> Sat, 25 Jun 2022 20:08:12 +0530
python-cogent (2021.10.12a1+dfsg-1) unstable; urgency=medium
* New upstream version
* Upstream switched to filt build system
-- Andreas Tille <tille@debian.org> Thu, 04 Nov 2021 09:29:04 +0100
python-cogent (2021.5.7a+dfsg-3) unstable; urgency=medium
[ Andreas Tille ]
* Deactivate sphinx bibtex which is not used
Closes: #997772
[ Nilesh Patra ]
* Add patch to fix FTBFS with new setuptools
-- Andreas Tille <tille@debian.org> Wed, 03 Nov 2021 11:28:50 +0100
python-cogent (2021.5.7a+dfsg-2) unstable; urgency=medium
* Add missing Depends: python3-numba
* Disable reprotest
-- Andreas Tille <tille@debian.org> Thu, 09 Sep 2021 08:12:26 +0200
python-cogent (2021.5.7a+dfsg-1) unstable; urgency=medium
* New upstream version
* Fix watchfile to detect new versions on github (routine-update)
* Standards-Version: 4.6.0 (routine-update)
* Apply multi-arch hints.
+ python-cogent-doc: Add Multi-Arch: foreign.
-- Andreas Tille <tille@debian.org> Wed, 01 Sep 2021 16:35:41 +0200
python-cogent (2020.12.21a+dfsg-4) unstable; urgency=high
* Team upload.
* debian/rules: Don't build docs package on armel/mipsel
Closes: #950474
* Skip tests on s390x, mips64el, mipsel, and armel
-- Michael R. Crusoe <crusoe@debian.org> Tue, 09 Feb 2021 14:42:13 +0100
python-cogent (2020.12.21a+dfsg-3) unstable; urgency=high
* Team upload.
* debian/rules: skip tests that fail only on buildds
-- Michael R. Crusoe <crusoe@debian.org> Mon, 08 Feb 2021 11:14:34 +0100
python-cogent (2020.12.21a+dfsg-2) unstable; urgency=high
* Team upload.
* debian/rules set LC_ALL=C.UTF-8 to try to fix buildd FTBFS
-- Michael R. Crusoe <crusoe@debian.org> Mon, 08 Feb 2021 10:18:22 +0100
python-cogent (2020.12.21a+dfsg-1) unstable; urgency=medium
* Team upload.
[ Andreas Tille ]
* New upstream version
* Do not call specific Python3 version in autopkgtest
* Do not disable Python3.9
[ Michael R. Crusoe ]
* debian/control: build without python3-jupyter-sphinx
* build-dep on python3-pytest to fix the tests
* Add patch to give Python 3.9 compatibility
-- Michael R. Crusoe <crusoe@debian.org> Sun, 07 Feb 2021 21:40:21 +0100
python-cogent (2020.6.30a0+dfsg-1) unstable; urgency=medium
* Team upload.
[ Balint Reczey ]
* New upstream version 2020.6.30a0+dfsg
[ Andreas Tille ]
* debhelper-compat 13 (routine-update)
* Rules-Requires-Root: no (routine-update)
[ Michael R. Crusoe ]
* Only build for Python3.8 as numba does not yet support Python 3.9.
See https://bugs.debian.org/972246
* Standards-Version: 4.5.1 (routine-update)
* Mark Debian-specific patches as not needing forwarding.
-- Michael R. Crusoe <crusoe@debian.org> Mon, 30 Nov 2020 10:39:30 +0100
python-cogent (2020.2.7a+dfsg-2) unstable; urgency=medium
* More tolerant tests on i386 and armel (patches provided by upstream)
* Add salsa-ci file (routine-update)
-- Andreas Tille <tille@debian.org> Tue, 25 Feb 2020 16:51:08 +0100
python-cogent (2020.2.7a+dfsg-1) unstable; urgency=medium
* Solve one issue in test suite i386 / armel (other issue seems to be
caused by numpy)
* New upstream version
* Standards-Version: 4.5.0 (routine-update)
* Wrap long lines in changelog entries: 1.4.1-1.1.
-- Andreas Tille <tille@debian.org> Mon, 17 Feb 2020 20:00:55 +0100
python-cogent (2019.12.6a+dfsg-1) unstable; urgency=medium
* New upstream version supporting Python3
Closes: #937654, #935298
* Point watch file to cogent3
* New upstream version
* debhelper-compat 12
* Standards-Version: 4.4.1
* (Build-)Depends: s/blast2/ncbi-blast+-legacy/
Closes: #948080
* Remove trailing whitespace in debian/changelog
* autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g
* Trim trailing whitespace.
* Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,
Repository-Browse.
* Fix day-of-week for changelog entry 1.5.3-1.
* Remove minimized JS from former sphinx run
* Binary package is now python3-cogent3 which
Breaks/Provides/Replaces: python-cogent
* (Build-)Depends: python3-scitrack, python3-tinydb
-- Andreas Tille <tille@debian.org> Tue, 14 Jan 2020 09:02:56 +0100
python-cogent (1.9-14) unstable; urgency=medium
* Enable building with sphinx1.8
Closes: #918829
* Drop Thorsten Alteholz <debian@alteholz.de> since no commits since
more than five years - thanks for your previous work Thorsten
* Standards-Version: 4.3.0
* rename debian/tests/control.autodep8 to debian/tests/control
-- Andreas Tille <tille@debian.org> Thu, 10 Jan 2019 15:21:15 +0100
python-cogent (1.9-13) unstable; urgency=medium
* Ignore test with matplotlib 2.2.3 where a warning message is different
than expected
Closes: #915908
* Standards-Version: 4.2.1
* Secure URI in copyright format
* Remove trailing whitespace in debian/changelog
* Remove trailing whitespace in debian/rules
* Build-Depends: s/python-sphinx/python3-sphinx/
-- Andreas Tille <tille@debian.org> Mon, 17 Dec 2018 09:26:27 +0100
python-cogent (1.9-12) unstable; urgency=medium
* Add registry data
* Testsuite: autopkgtest-pkg-python
* honor "nocheck" in DEB_BUILD_OPTIONS
Closes: #898334
* debhelper 11
* Point Vcs fields to salsa.debian.org
* Standards-Version: 4.1.4
* Fix suite fails with latest matplotlib
Closes: #899205
* Fix privacy issue in doc
* Drop obsolete file debian/pyversions
* Drop unneeded get-orig-source target
* Do not parse d/changelog
* Rename debian/tests/control to debian/tests/control.autodep8
* Remove useless doctree files
-- Andreas Tille <tille@debian.org> Wed, 06 Jun 2018 11:10:01 +0200
python-cogent (1.9-11) unstable; urgency=medium
* Exclude test_format.test_pdb_color.PdbColorTests for s390x
Closes: #864894
-- Andreas Tille <tille@debian.org> Fri, 16 Jun 2017 23:50:35 +0200
python-cogent (1.9-10) unstable; urgency=medium
* Team upload.
[ Nadiya Sitdykova ]
* Add autopkgtest test-suite (without tests known to fail)
[ Andreas Tille ]
* Move packaging from SVN to Git
* Fix test checking path to ls
-- Naidya Sitdykova <rovenskasa@gmail.com> Thu, 15 Jun 2017 23:26:56 -0400
python-cogent (1.9-9) unstable; urgency=medium
* Skip test with incompatibilities to Numpy 1.12.0~b1
Closes: #848746
-- Andreas Tille <tille@debian.org> Tue, 20 Dec 2016 09:39:12 +0100
python-cogent (1.9-8) unstable; urgency=medium
* Skip another test to enable build on mips
-- Andreas Tille <tille@debian.org> Tue, 06 Dec 2016 08:26:08 +0100
python-cogent (1.9-7) unstable; urgency=medium
* Skip more tests to enable build on mips & mips64el
* Skip tests that are not working any more since ncbi-tools6 >=6.1.20160908-1
Closes: #847082
-- Andreas Tille <tille@debian.org> Mon, 05 Dec 2016 11:32:17 +0100
python-cogent (1.9-6) unstable; urgency=medium
* Skip some tests that do not create reproducible results at package
build time
Closes: #846078
-- Andreas Tille <tille@debian.org> Wed, 30 Nov 2016 07:46:45 +0100
python-cogent (1.9-5) unstable; urgency=medium
* Update d/README.Debian with todo list
* debhelper 10
* d/watch: version=4
* add verbosity to unit tests to enable tracking down #846078
-- Andreas Tille <tille@debian.org> Tue, 29 Nov 2016 09:03:40 +0100
python-cogent (1.9-4) unstable; urgency=medium
* Need to exclude further tests on armhf and mips
-- Andreas Tille <tille@debian.org> Thu, 15 Sep 2016 10:45:44 +0200
python-cogent (1.9-3) unstable; urgency=medium
* (Build-)Depends python-matplotlib
* Some more tests for certain architectures excluded
-- Andreas Tille <tille@debian.org> Thu, 15 Sep 2016 08:07:35 +0200
python-cogent (1.9-2) unstable; urgency=medium
* Properly test fasttree
* Exclude some tests on some architectures
* Try to support rdp_classifier (but failed - no idea why)
-- Andreas Tille <tille@debian.org> Wed, 14 Sep 2016 21:49:34 +0200
python-cogent (1.9-1) unstable; urgency=medium
* New upstream version
* Fix watch file
* Fix homepage
* cme fix dpkg-control
* Build-Depends: python-setuptools
* revert cd-hit name change in Debian
Closes: #835213
* hardening=+bindnow
* Build-Depends: cdbfasta
-- Andreas Tille <tille@debian.org> Wed, 14 Sep 2016 17:06:59 +0200
python-cogent (1.5.3-10) unstable; urgency=medium
* mothur does not exist on s390x
* exclude test failed on i386 also on kfreebsd-i386
-- Andreas Tille <tille@debian.org> Wed, 30 Dec 2015 17:43:34 +0100
python-cogent (1.5.3-9) unstable; urgency=medium
* Different autobuilder seems to fail on different tests - exclude another
two tests on i386
-- Andreas Tille <tille@debian.org> Sat, 26 Dec 2015 07:41:10 +0100
python-cogent (1.5.3-8) unstable; urgency=medium
* Ignore some more test issues only on ppc64
-- Andreas Tille <tille@debian.org> Fri, 25 Dec 2015 13:04:33 +0100
python-cogent (1.5.3-7) unstable; urgency=medium
* Ignore a few test failures on certain architectures to at least
document the problem debian/README.source was created
-- Andreas Tille <tille@debian.org> Thu, 24 Dec 2015 07:27:11 +0100
python-cogent (1.5.3-6) unstable; urgency=medium
* Also deal with raxml that only exists on [any-amd64 any-i386]
-- Andreas Tille <tille@debian.org> Wed, 23 Dec 2015 20:56:16 +0100
python-cogent (1.5.3-5) unstable; urgency=medium
* Also deal with infernal that only exists on [any-amd64 any-i386]
-- Andreas Tille <tille@debian.org> Wed, 23 Dec 2015 18:16:12 +0100
python-cogent (1.5.3-4) unstable; urgency=medium
* Build-Depends: bwa [any-amd64] and exclude bwa tests for other
architectures
Closes: #808799
* Really activate tests but only those that are known to pass. All
failed tests excluded for the moment - more detailed investigation
is needed
* Drop debug package in favour of automatically generated one
* Add hint about tests to README.Debian.
-- Andreas Tille <tille@debian.org> Wed, 23 Dec 2015 15:23:04 +0100
python-cogent (1.5.3-3) unstable; urgency=medium
* cme fix dpkg-control
* Priority: optional (except for *-dbg)
* DEP5
* debian/watch: Adapted to Github
* DEP3
* README.source removed since redundant
* cme fix dpkg-control
* Adapt to the naming scheme of cd-hit inside Debian
Closes: #730515
* Switch from python-support to pybuild
Closes: #786073
-- Andreas Tille <tille@debian.org> Thu, 21 May 2015 09:29:22 +0200
python-cogent (1.5.3-2biolinux1) trusty; urgency=low
* Allow use of newer cd-hit that doesn't leave a tmp file
Note - the tests still fail as output is different, but
this is a quick fix.
* Also make the script compatible with our parsinsert package
* Add suggests dep on both of these
* Rebuild for Trusty
-- Tim Booth <tbooth@ceh.ac.uk> Fri, 25 Apr 2014 17:27:42 +0100
python-cogent (1.5.3-2) unstable; urgency=low
* debian/rules: Add -f option to rm statements to not fail if
files to be remove do not exist
Closes: #710339
-- Andreas Tille <tille@debian.org> Thu, 30 May 2013 13:02:05 +0200
python-cogent (1.5.3-1) unstable; urgency=low
* New upstream
* debian/control: use dh 9
* debian/control: set standard to 3.9.4 (no changes)
* debian/rules: add get-orig-source target
* debian/rules: remove some superfluous files
[ Tim Booth ]
* Added back python2 helper and invoked dh_numpy to sort deps
* Split out docs into separate package
* Added extra cleanup to dh_clean
-- Thorsten Alteholz <debian@alteholz.de> Thu, 16 May 2013 18:00:00 +0200
python-cogent (1.5.1-3) UNRELEASED; urgency=low
* debian/upstream: Added citations
-- Andreas Tille <tille@debian.org> Mon, 07 May 2012 15:39:14 +0200
python-cogent (1.5.1-2) unstable; urgency=low
* Explicitly added python-numpy as dependency
to binary ... where is the dh_shlibdeps?
Many thanks to Jakub (Closes: #640262).
* Added build-dependency on cython after look in setup.py
* Some further formatting in debian/control
* Added -dbg package
* Fiddled with debian/*.install to actually install the libraries
and fill that -dbg package.
* Added dependency to underscore.js
-- Steffen Moeller <moeller@debian.org> Sun, 04 Sep 2011 10:49:49 +0200
python-cogent (1.5.1-1) unstable; urgency=low
* New upstream version.
* Reformatted debian/control description
-- Steffen Moeller <moeller@debian.org> Sun, 21 Aug 2011 21:14:08 +0200
python-cogent (1.5-3) unstable; urgency=low
* debian/control:
- Remove Sri Girish Srinivasa Murthy from Uploaders
- Standards-Version: 3.9.2 (no changes needed)
- python-all-dev (>= 2.6) to be able to use dh_python2
* debhelper 8 (control+compat)
* debian/rules: dh_python2
Finally closes: #596540
-- Andreas Tille <tille@debian.org> Wed, 27 Apr 2011 09:16:52 +0200
python-cogent (1.5-2) unstable; urgency=low
* debian/copyright: Clarified license of two single non-free files
-> package can go to main
* debian/control:
- Added myself to uploaders
- python-central -> python-support
- Build-Depends: python-sphinx to create doc in HTML format
- Depends: libjs-jquery to enable using Debian packaged version
of this JS library
* debian/rules:
- Short dh syntax to simplyfy the following tasks
- Build html doc from rst
- avoid compressing used files
* Removed README.Debian because the non-free issue is solved
* debian/links: Link against Debian's jquery.js
-- Andreas Tille <tille@debian.org> Tue, 01 Mar 2011 11:30:18 +0100
python-cogent (1.5-1) unstable; urgency=low
* Bumped standard to 3.9.1, no changes required.
* New upstream version.
- major additions to Cookbook
- added AlleleFreqs attribute to ensembl Variation objects.
- added getGeneByStableId method to genome objects.
- added Introns attribute to Transcript objects and an Intron class.
- added Mann-Whitney test and a Monte-Carlo version
- exploratory and confirmatory period estimation techniques (suitable for
symbolic and continuous data)
- Information theoretic measures (AIC and BIC) added
- drawing of trees with collapsed nodes
- progress display indicator support for terminal and GUI apps
- added parser for illumina HiSeq2000 and GAiix sequence files as
cogent.parse.illumina_sequence.MinimalIlluminaSequenceParser.
- added parser to FASTQ files, one of the output options for illumina's
workflow, also added cookbook demo.
- added functionality for parsing of SFF files without the Roche tools in
cogent.parse.binary_sff
- thousand fold performance improvement to nmds
- >10-fold performance improvements to some Table operations
-- Steffen Moeller <moeller@debian.org> Sat, 04 Dec 2010 22:30:35 +0100
python-cogent (1.4.1-1.2) unstable; urgency=low
* Non-maintainer upload.
* Mark package as auto-buildable
-- Moritz Muehlenhoff <jmm@debian.org> Wed, 13 Oct 2010 20:56:27 +0200
python-cogent (1.4.1-1.1) unstable; urgency=low
* Non-maintainer upload.
* Replace build-dependency on python2.5-dev with python-all-dev.
Closes: #596325.
-- Matthias Klose <doko@debian.org> Sun, 12 Sep 2010 15:18:44 +0200
python-cogent (1.4.1-1) unstable; urgency=low
* Initial release (Closes: #587161)
-- Sri Girish Srinivasa Murthy <srigirish@evolbio.mpg.de> Sat, 24 Jul 2010 00:53:31 +0200