python-cogent (2020.12.21a+dfsg-4+deb11u1) bullseye; urgency=medium * Team upload. * Skip parallel tests on single-CPU systems. Closes: #1030885. -- Santiago Vila Wed, 13 Dec 2023 12:30:00 +0100 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Thu, 16 May 2013 18:00:00 +0200 python-cogent (1.5.1-3) UNRELEASED; urgency=low * debian/upstream: Added citations -- Andreas Tille 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 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 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 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 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 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 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 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 Sat, 24 Jul 2010 00:53:31 +0200