python-pysam (0.22.1+ds-2) unstable; urgency=medium * htslib-1.20.patch: new: anticipate test failure. Upcoming upload of htslib 1.20 comes with improvements causing a test failure in pysam. This change anticipates the correction without introduction of regressions with existing releases of htslib. Thanks to John Marshall -- Étienne Mollier Wed, 29 May 2024 13:23:03 +0200 python-pysam (0.22.1+ds-1) unstable; urgency=medium * New upstream version 0.22.1+ds * d/copyright: update copyright year. * d/control: declare compliance to standards version 4.7.0. * d/python-pysam.links: delete: now irrelevant. This file set symbolic links up to help with Python 2.7, which is obsolete and should not be used anymore, so these links are not useful anymore. * d/control: remove dh-exec: it is not in use anymore. * skip_test_remote.patch: unfuzz. * skip-test-on-32-bit.patch: refresh. -- Étienne Mollier Sun, 12 May 2024 14:35:42 +0200 python-pysam (0.22.0+ds-1) unstable; urgency=medium * New upstream version Closes: #1055505 * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update) * Fix clean target Closes: #1047165 -- Andreas Tille Wed, 08 Nov 2023 10:23:13 +0100 python-pysam (0.21.0+ds-1) unstable; urgency=medium * New upstream version * Patches triage: - disable-tests-python3.11.patch removed: applied upstream - python3.11.patch removed: applied upstream - skip_test_remote.patch: forwarding not-needed - skip-test-on-32-bit.patch: provide dep3 header - clean_less patch: forwarding not-needed * d/copyright: bump copyright year. * d/rules: delete extra license files. * typos.patch: add; fix typos caught by lintian. -- Étienne Mollier Fri, 23 Jun 2023 20:10:54 +0200 python-pysam (0.20.0+ds-3) unstable; urgency=medium * Team Upload. * Add patch to fix proper "SO" extension. -- Nilesh Patra Sat, 31 Dec 2022 22:26:09 +0530 python-pysam (0.20.0+ds-2) unstable; urgency=medium * disable-tests-python3.11.patch: add; work around test failure. Thanks to John Marshall and Graham Inggs (Closes: #1024425) * d/control: restore dependency on python3-all-dev. * d/control: restore autodep8-python autopkgtest. * Standards-Version: 4.6.2 (routine-update) -- Étienne Mollier Tue, 27 Dec 2022 11:41:25 +0100 python-pysam (0.20.0+ds-1) unstable; urgency=medium * New upstream version * Update lintian override info format in d/python-pysam.lintian-overrides on line 4. * skip_test_remote.patch: refresh. * test-truncated-bam.patch: delete; applied upstream. * d/control: make build only depend on python3-dev. * d/control: disable autopkgtest-pkg-python due to missing python3.11 support; classical autopkgtest is still active though. -- Étienne Mollier Tue, 29 Nov 2022 21:55:48 +0100 python-pysam (0.19.1+ds-1) unstable; urgency=medium [ Andreas Tille ] * New upstream version * Standards-Version: 4.6.1 (routine-update) * Remove unused license definitions for LGPL-2.1+, BSD-3-clause. [ Étienne Mollier ] * test-truncated-bam.patch: added; fix test truncated BAM failure. Thanks to John Marshall * d/*.lintian-overrides: refresh mismatches. * d/control: add myself to uploaders. * d/*.lintian-overrides: remove unused overrides. -- Étienne Mollier Sun, 02 Oct 2022 11:41:36 +0200 python-pysam (0.18.0+ds-1~exp2) experimental; urgency=medium * Bump Build-Depends: libhts-dev (>= 1.14~) Closes: #1001284 -- Andreas Tille Wed, 08 Dec 2021 13:23:03 +0100 python-pysam (0.18.0+ds-1~exp1) experimental; urgency=medium * New upstream version * No tab in license text (routine-update) * Update renamed lintian tag names in lintian overrides. * Avoid explicitly specifying -Wl,--as-needed linker flag. * Remove constraints unnecessary since buster: + Build-Depends: Drop versioned constraint on bcftools, libhts-dev and samtools. * Drop outdated and unused tests -- Andreas Tille Tue, 07 Dec 2021 15:14:07 +0100 python-pysam (0.17.0+ds-2) unstable; urgency=medium * Team Upload. * Move from experimental to unstable * Skip failing test on 32-bit -- Nilesh Patra Fri, 15 Oct 2021 13:17:18 +0530 python-pysam (0.17.0+ds-1) experimental; urgency=medium * Team Upload. [ Andreas Tille ] * debhelper-compat 13 (routine-update) * Update copyright * Do not ignore test results via '|| true' * Exclude another test that is failing [ Nilesh Patra ] * New upstream version 0.17.0+ds * Standards version: 4.6.0 * Bump watch file version to 4 * Re-diff patches -- Nilesh Patra Fri, 15 Oct 2021 01:13:49 +0530 python-pysam (0.15.4+ds-3) unstable; urgency=medium * Remove Python2 package Closes: #938092 * Remove unneeded debian/gbp.conf * Standards-Version: 4.5.0 (routine-update) * Add salsa-ci file (routine-update) * Rules-Requires-Root: no (routine-update) * Set upstream metadata fields: Bug-Submit. -- Andreas Tille Fri, 08 May 2020 20:27:35 +0200 python-pysam (0.15.4+ds-2) unstable; urgency=medium * Dont run unittests for python2 binary, to reduce pytest rdeps -- Sandro Tosi Mon, 13 Apr 2020 23:49:01 -0400 python-pysam (0.15.4+ds-1) unstable; urgency=medium * Team upload. * New upstream version * python-pysam-tests: Multi-Arch: foreign * Try to keep example_no_seq_in_header_null_bytes.bam from being deleted -- Michael R. Crusoe Thu, 23 Jan 2020 15:00:17 +0100 python-pysam (0.15.3+ds-5) unstable; urgency=medium [ Chris Lamb ] * make the build reproducible Closes: #948280 [ Andreas Tille ] * Standards-Version: 4.4.1 * debian/copyright: use spaces rather than tabs to start continuation lines. * Set upstream metadata fields: Bug-Database, Repository, Repository- Browse. -- Andreas Tille Mon, 06 Jan 2020 17:44:23 +0100 python-pysam (0.15.3+ds-4) unstable; urgency=medium * Team upload. * Replace missing hts_seek and hts_tell equivalents -- Michael R. Crusoe Sun, 05 Jan 2020 21:23:11 +0100 python-pysam (0.15.3+ds-3) unstable; urgency=medium * Team upload. * -docs: oops, don't try to ship nonexistent debian/tests/run-nose{3,}-tests -- Michael R. Crusoe Sun, 05 Jan 2020 08:01:33 +0100 python-pysam (0.15.3+ds-2) unstable; urgency=medium * Team upload. * new patch: Update deprecated samtools import test commands to samtools view * new patch: Update samtools + bcftools to v1.10 * disable tests for now -- Michael R. Crusoe Sat, 04 Jan 2020 23:19:04 +0100 python-pysam (0.15.3+ds-1) unstable; urgency=medium * Team upload. * New upstream release. Not yet dropping py2 due to paleomix and pbsuite * debhelper-compat 12 * Standards-Version: 4.4.0 * Trim trailing whitespace. * Use secure URI in Homepage field. * Set upstream metadata fields: Repository. * New patch to remove symbols that were dropped in htslib 1.10: hts_utell, hts_useek (Closes: #947426) -- Michael R. Crusoe Fri, 03 Jan 2020 21:25:33 +0100 python-pysam (0.15.2+ds-2) unstable; urgency=medium * Team upload. * For the Tabix tests: test the index contents, not the compression scheme. Closes: #919928, #920250 -- Michael R. Crusoe Wed, 20 Feb 2019 02:45:47 -0800 python-pysam (0.15.2+ds-1) unstable; urgency=medium * Team upload. * New upstream version * Standards-Version: 4.3.0, no changes needed * added Py2 and Py3 versions of ${python:Provides} * Fix lintian found spelling typos. * debian/tests/control.autodep8 → debian/tests/control. * remove errant log.txt from the packages. -- Michael R. Crusoe Thu, 17 Jan 2019 01:25:11 -0800 python-pysam (0.15.1+ds-1) unstable; urgency=medium * Team upload. * New upstream version. - Removes autogenerated config.h - [many thanks!] https://github.com/pysam-developers/pysam/issues/714 - Explicit compatibility with Python 3.7 * Removed patch skipping test that complained on missing file -- Steffen Moeller Fri, 14 Sep 2018 10:44:51 +0200 python-pysam (0.15.0.1+ds-2) unstable; urgency=medium * Remove ancient fields X-Python*-Version * Adjust patches for build time test suite * Standards-Version: 4.2.1 -- Andreas Tille Wed, 12 Sep 2018 18:37:42 +0200 python-pysam (0.15.0.1+ds-1) experimental; urgency=medium * Team upload. [ Steffen Moeller ] * New upstream version. [ Afif Elghraoui ] * New upstream version 0.14.1+ds * Update patches [ Andreas Tille ] * Testsuite: autopkgtest-pkg-python * Rename d/tests/control to d/tests/control.autodep8 * Standards-Version: 4.1.4 -- Steffen Moeller Sun, 29 Jul 2018 00:51:38 +0200 python-pysam (0.14+ds-2) unstable; urgency=medium * Team upload * Add Python 2.7 compatibility symlink for libchtslib.so (Closes: #890748) * Update Vcs-* URIs for move to salsa.debian.org * Remove trailing whitespace from debian/changelog -- Graham Inggs Mon, 19 Feb 2018 10:11:17 +0000 python-pysam (0.14+ds-1) unstable; urgency=medium * New upstream version * d/rules: Exclude tests using http access * Bump versioned dependencies to samtools and related from 1.6 to 1.7 * cme fix dpkg-control * debhelper 11 * do not remove samtools/tmp_file.h in clean target * do not depend from non-existing data file in make test target * Update d/copyright * Update lintian overrides -- Andreas Tille Sat, 17 Feb 2018 21:45:07 +0100 python-pysam (0.13.0+ds-1) unstable; urgency=medium * New upstream version * Bump versioned Build-Depends on libhts-dev, samtools and bcftools to 1.6 * Exclude tests accessing remote http sites * Lintian-override for false positive * Remove unused paragraphs from d/copyright -- Andreas Tille Thu, 14 Dec 2017 16:36:43 +0100 python-pysam (0.12.0.1+ds-4) unstable; urgency=medium * Team upload. * Revert "Skip tests on ppc64el to avoid build-dep on bcftools currently uninstallable". It seems to be installable now, and anyway now that the python3 transition is done we should fix it properly anyway. * d/control: + Bump the libhts-dev buil-dep to 1.5-3, to make sure we gain appropriate versioned symbols and therefore an appropriate versioned dependency on libhts2. Closes: #879867 + Bump Standards-Version to 4.1.1. -- Mattia Rizzolo Fri, 10 Nov 2017 12:56:10 +0100 python-pysam (0.12.0.1+ds-3) unstable; urgency=medium * Team upload. * Support DEB_BUILD_OPTIONS=nocheck. * Skip tests on ppc64el to avoid build-dep on bcftools which is currently uninstallable. Hopefully this will help unstuck the current python3 transition. -- Mattia Rizzolo Tue, 24 Oct 2017 18:54:29 +0200 python-pysam (0.12.0.1+ds-2) unstable; urgency=low * Update autopkgtest for new test suite driver -- Afif Elghraoui Fri, 06 Oct 2017 23:38:45 -0400 python-pysam (0.12.0.1+ds-1) unstable; urgency=medium [ Andreas Tille ] * Drop patch applied upstream * Standards-Version: 4.1.0 (no changes needed) * Apply upstream patch to fix test suite * Use pytest instead of nosetest [ Afif Elghraoui ] * New upstream version Closes: #871083, #834856 * Bump htslib suite minimum versions * Use Build Profiles to mark build-dependencies needed only for tests * Temporarily skip a failing test (reported upstream) [ Steffen Moeller ] * created debian/upstream/metadata: references to registries -- Afif Elghraoui Sun, 01 Oct 2017 12:30:30 -0400 python-pysam (0.11.2.2+ds-3) unstable; urgency=medium * Team upload * Link with -Wl,--as-needed and avoid another Python 2.7 compatibility symlink for libchtslib.so -- Graham Inggs Tue, 01 Aug 2017 14:15:58 +0200 python-pysam (0.11.2.2+ds-2) unstable; urgency=medium * Team upload * Mark debian/python-pysam.links executable for dh-exec * Drop exclude_test_tyring_to_access_remote_ftpserver.patch, fixed upstream * Drop pysam_stdout_linkage.patch, not needed since compatibility symlinks were added -- Graham Inggs Mon, 31 Jul 2017 14:05:22 +0200 python-pysam (0.11.2.2+ds-1) unstable; urgency=medium [ Afif Elghraoui ] * Imported Upstream version 0.11.2.2+ds * Update patches [ Andreas Tille ] * Apply patches suggested by Steve Langasek (thanks for this Steve) Closes: #867017, LP: #1701268 * debhelper 10 * Standards-Version: 4.0.0 (no changes needed) * Add some symlinks to run autopkgtests correctly -- Andreas Tille Sat, 29 Jul 2017 09:03:05 +0200 python-pysam (0.10.0+ds-2) unstable; urgency=medium * d/rules: - Add some files that need to be removed after running tests - Remove other autogenerated files to build twice in a row * Exclude test tyring to access remote ftpserver Closes: #861496 -- Andreas Tille Thu, 04 May 2017 15:06:21 +0200 python-pysam (0.10.0+ds-1) unstable; urgency=medium [ Afif Elghraoui ] * New upstream release * Update patches [ Andreas Tille ] * d/rules: Remove redundant get-orig-source target * hardening=+all * Fix lintian overrides [ Afif Elghraoui ] * Do not use internal htslib -- Afif Elghraoui Thu, 26 Jan 2017 04:36:11 -0800 python-pysam (0.9.1.4+ds-1) unstable; urgency=medium * Imported Upstream version 0.9.1.4+ds * Drop patch applied upstream * Drop unused lintian overrides * Fix spelling issues -- Afif Elghraoui Sat, 23 Jul 2016 18:47:31 -0700 python-pysam (0.9.1+ds-1) unstable; urgency=medium * Imported Upstream version 0.9.1+ds * Force at least matching versions of the samtools suite * Bump Standards-Version to 3.9.8 * Globally use C.UTF-8 locale * Update patch for external htslib * Refresh patch * Drop obsolete patches * Fix handling of configuration headers generated at build time * Rely more on pybuild for build-time tests and respect exit code * Fix autopkgtests -- Afif Elghraoui Sun, 19 Jun 2016 18:43:53 -0700 python-pysam (0.9.0+ds-1) unstable; urgency=medium * Add filenamemangle to d/watch and space out content * Imported Upstream version 0.9.0+ds (Closes: #814765) * Bump htslib and samtools minimum versions * Update policy statndards-version to 3.9.7 * Use encrypted protocols for Vcs URLs in d/control * Use readthedocs page as pysam's homepage * Update packaging for external htslib link * Refresh patches * Delete obsolete patch -- Afif Elghraoui Wed, 09 Mar 2016 23:43:59 -0800 python-pysam (0.8.4+ds-1) unstable; urgency=medium * Add version constraints to build-dependencies. * Drop ds suffix versioning. * Imported Upstream version 0.8.4+ds * Remove patches applied upstream * Refresh existing patches * Refine d/rules * Set Vcs-Browser to point to cgit rather than gitweb * Reduce dependencies in autopktest dependencies * Replace patch for network-dependent tests * Add new lintian overrides -- Afif Elghraoui Fri, 13 Nov 2015 22:15:14 -0800 python-pysam (0.8.3+ds1-3) unstable; urgency=medium * Backport upstream commit 6efb22b to permit building with Cython 0.23.x (Closes: 800794) * Revise lintian overrides. -- Afif Elghraoui Tue, 06 Oct 2015 00:57:19 -0700 python-pysam (0.8.3+ds1-2) unstable; urgency=medium [ Afif Elghraoui ] * Improve python3 compatibility for upstream test sources * Refresh older patches * Fix autopkgtests * Fix error in sam_mpileup.patch * Remove unused lintian override [ Andreas Tille ] * Remove tests relying on online connection from test suite * For the moment do some dirty tricks in test run script * The automatic nosetest trigger does not work and this it is switched back to manual nosetests invocation -- Afif Elghraoui Fri, 24 Jul 2015 10:12:41 +0200 python-pysam (0.8.3+ds1-1) experimental; urgency=medium * Team upload. [ Jorge Soares ] * New upstream version * provide python3-pysam [ Charles Plessy ] * Requires Python 2.7 or higher. [ Andreas Tille ] * Link against htslib * d/watch: dversionmangle [ Afif Elghraoui ] * New upstream releases (Closes: #763218) * Remove unnecessary test-suite declaration in d/control * Remove nonexistent files from copyright explanations * Allow building of the package when non-ASCII characters are in the path * Add to package long description * Resolve lintian "duplicated-compressed-file" * Make package descriptions unique * Remove extra license definitions from d/copyright * Fix spelling errors in source distribution (forwarded upstream as well) * Add lintian overrides * Exclude bundled htslib convenience-copy * Provide get-orig-source rule * Support building with missing htslib directory * Add dependency on cython for autopkgtests to provide pyximport * Revamp debian/copyright -- Afif Elghraoui Thu, 25 Jun 2015 10:44:30 +0200 python-pysam (0.7.7-1) unstable; urgency=medium * New upstream releases. * Upstream source code moved to GitHub. * Watch the Python Package Index since there are no relevant tags on GitHub. * Added a git-buildpackage configuration file to mark its usage. * Build-depend samtools (>= 0.1.19); this is needed for the regression tests in Wheezy. * debian/patches/offline-tests.patch: correction from a later release. -- Charles Plessy Sat, 19 Apr 2014 14:17:42 +0900 python-pysam (0.7.5-5) unstable; urgency=medium * Add make to autopkgtest dependencies Closes: #741274 -- Andreas Tille Wed, 19 Mar 2014 13:30:15 +0100 python-pysam (0.7.5-4) unstable; urgency=medium * Fix autotest Closes: #741274 -- Andreas Tille Tue, 11 Mar 2014 20:08:15 +0100 python-pysam (0.7.5-3) unstable; urgency=medium * Do not install tests in world writable dir Closes: #739575 -- Andreas Tille Sat, 01 Mar 2014 23:40:21 +0100 python-pysam (0.7.5-2) unstable; urgency=medium * debian/rules: Set PYTHONPATH correctly using dh_python (thanks to Piotr Ożarowski for the patch) Closes: #739631 -- Andreas Tille Thu, 20 Feb 2014 19:01:46 +0100 python-pysam (0.7.5-1) unstable; urgency=low * Initial release (Closes: #738665) -- Andreas Tille Fri, 07 Feb 2014 18:29:40 +0100