python-pysam (0.23.0+ds-1) unstable; urgency=medium
* Migrate python-pysam 0.23.0 from experimental to unstable.
-- Étienne Mollier <emollier@debian.org> Thu, 06 Feb 2025 21:31:01 +0100
python-pysam (0.23.0+ds-0+exp1) experimental; urgency=medium
* New upstream version 0.23.0+ds
* d/copyright: account for uscan warning about missing files.
* d/copyright: update year and freshen authors list.
* htslib-1.20.patch: delete: applied upstream.
* d/patches/*: refresh patches.
* d/control: pysam 0.23 depends on htslib 1.21.
* d/patches/*: normalize Last-Update timestamp.
-- Étienne Mollier <emollier@debian.org> Wed, 05 Feb 2025 21:51:07 +0100
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 <emollier@debian.org> 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This file set symbolic links up to help with Python 2.7, which is
obsolete and should not be used anymore, so these links are not useful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 <emollier@debian.org> 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 <tille@debian.org> 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 <emollier@debian.org> 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 <nilesh@debian.org> 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 <emollier@debian.org> 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 <emollier@debian.org> 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 <emollier@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <nilesh@debian.org> 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 <nilesh@debian.org> 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 <tille@debian.org> 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 <morph@debian.org> 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 <michael.crusoe@gmail.com> 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 <tille@debian.org> 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 <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <michael.crusoe@gmail.com> 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 <moeller@debian.org> 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 <tille@debian.org> 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 <moeller@debian.org> 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 <ginggs@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <mattia@debian.org> 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 <mattia@debian.org> 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 <afif@debian.org> 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 <afif@debian.org> 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 <ginggs@debian.org> 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 <ginggs@debian.org> 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 <tille@debian.org> 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 <tille@debian.org> 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 <afif@debian.org> 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 <afif@debian.org> 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 <afif@debian.org> 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 <afif@debian.org> 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 <afif@ghraoui.name> 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 <afif@ghraoui.name> 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 <afif@ghraoui.name> 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 <afif@ghraoui.name> 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 <plessy@debian.org> 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 <tille@debian.org> Wed, 19 Mar 2014 13:30:15 +0100
python-pysam (0.7.5-4) unstable; urgency=medium
* Fix autotest
Closes: #741274
-- Andreas Tille <tille@debian.org> 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 <tille@debian.org> 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 <piotr@debian.org> for the patch)
Closes: #739631
-- Andreas Tille <tille@debian.org> Thu, 20 Feb 2014 19:01:46 +0100
python-pysam (0.7.5-1) unstable; urgency=low
* Initial release (Closes: #738665)
-- Andreas Tille <tille@debian.org> Fri, 07 Feb 2014 18:29:40 +0100