python-pysam (0.23.0+ds-1) unstable; urgency=medium

  * Migrate python-pysam 0.23.0 from experimental to unstable.

[dgit import unpatched python-pysam 0.23.0+ds-1]

diff --cc debian/changelog
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..4384f3ee211445605e0cd5255775a772baf4e1c0
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/changelog
@@@ -1,0 -1,0 +1,597 @@@
++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

diff --cc debian/clean
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..d4b6fd3b4a0a1fd5de81708d84f439e6d8eee0e5
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/clean
@@@ -1,0 -1,0 +1,6 @@@
++tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai
++tests/pysam_data/ex1.fa.gz
++tests/pysam_data/ex1.fa.gz.gzi
++tests/pysam_data/ex1_csi.bam.csi
++tests/pysam_data/[A-Za-z]*.bam
++samtools/samtools_config_vars.h

diff --cc debian/control
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..c816f3cdf35ad2531f45a9e826bf5f4553cc6643
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/control
@@@ -1,0 -1,0 +1,49 @@@
++Source: python-pysam
++Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
++Uploaders: Charles Plessy <plessy@debian.org>,
++           Andreas Tille <tille@debian.org>,
++           Étienne Mollier <emollier@debian.org>
++Section: python
++Testsuite: autopkgtest-pkg-python
++Priority: optional
++Build-Depends: debhelper-compat (= 13),
++               dh-sequence-python3,
++               libhts-dev (>= 1.21~),
++               zlib1g-dev,
++               python3-all-dev,
++               python3-setuptools,
++               cython3,
++               tabix <!nocheck>,
++               samtools <!nocheck>,
++               bcftools <!nocheck>,
++               python3-pytest <!nocheck>
++Standards-Version: 4.7.0
++Vcs-Browser: https://salsa.debian.org/med-team/python-pysam
++Vcs-Git: https://salsa.debian.org/med-team/python-pysam.git
++Homepage: https://pysam.readthedocs.org/en/latest
++Rules-Requires-Root: no
++
++Package: python3-pysam
++Architecture: any
++Depends: ${shlibs:Depends},
++         ${misc:Depends},
++         ${python3:Depends}
++Description: interface for the SAM/BAM sequence alignment and mapping format (Python 3)
++ Pysam is a Python module for reading and manipulating Samfiles. It's a
++ lightweight wrapper of the samtools C-API. Pysam also includes an interface
++ for tabix.
++ .
++ This package installs the module for Python 3.
++
++Package: python-pysam-tests
++Architecture: all
++Multi-Arch: foreign
++Depends: ${misc:Depends}
++Enhances: python3-pysam
++Description: interface for the SAM/BAM sequence alignment and mapping format (test data)
++ Pysam is a Python module for reading and manipulating Samfiles. It's a
++ lightweight wrapper of the samtools C-API. Pysam also includes an interface
++ for tabix.
++ .
++ This package contains the data provided by upstream to run the pysam
++ test suite.

diff --cc debian/copyright
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..ef8e2681f91bb59a1ce6ee2028bfef5f2bc6c818
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/copyright
@@@ -1,0 -1,0 +1,84 @@@
++Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
++Upstream-Name: pysam
++Upstream-Contact: Andreas Heger <andreas.heger@gmail.com>
++Source: https://github.com/pysam-developers/pysam
++Files-Excluded: htslib/*
++                win32
++
++Files: *
++Copyright: 2009-2025 Andreas Heger,
++                      Tildon Grant Belgrad,
++                      Martin Goodson,
++                      Florian Finkernagel,
++                      Leo Goodstadt,
++                      John Marshall,
++                      Kevin Jacobs <jacobs@bionformed.com>,
++                      Gerton Lunter,
++                      Marcel Martin,
++                      Heng Li,
++                      Bob Handsaker
++           2008-2024 Genome Research Ltd.
++License: MIT
++Comment:
++ Authors list originates from the AUTHORS file, authors copyright years
++ originate from doc/conf.py.
++
++Files: bcftools/*
++Copyright:
++         2013-2018 Genome Research Ltd.
++         2010-2011 Broad Institute
++License: MIT
++
++Files: samtools/*
++Copyright: 2009-2012 Broad Institute
++           2008-2014 Genome Research Ltd.
++License: MIT
++
++Files: samtools/bam_cat.*
++Copyright: 2008-2009, 2011-2013 Genome Research Ltd.
++           2010 Illumina, Inc.
++License: MIT
++
++Files: samtools/bam_color.*
++Copyright: 2009, 2012 University of California - Los Angeles
++License: MIT
++
++Files: samtools/bam_index.*
++       samtools/bam_mate.*
++Copyright: 2008-2014 Genome Research Ltd.
++           2010-2011 Broad Institute
++           2012-2013 Peter Cock, The James Hutton Institute
++License: MIT
++
++Files: samtools/padding.*
++Copyright: 2011-2012 Broad Institute
++           2014 Genome Research Ltd.
++           2012-2013 Peter Cock, The James Hutton Institute
++License: MIT
++
++Files: debian/*
++Copyright:
++         2015-2016 Afif Elghraoui <afif@debian.org>
++         2015 Jorge Soares <j.s.soares@gmail.com>
++         2014-2015 Charles Plessy <plessy@debian.org>
++         2014-2018 Andreas Tille <tille@debian.org>
++License: MIT
++
++License: MIT
++ Permission is hereby granted, free of charge, to any person obtaining a copy
++ of this software and associated documentation files (the "Software"), to deal
++ in the Software without restriction, including without limitation the rights
++ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
++ copies of the Software, and to permit persons to whom the Software is
++ furnished to do so, subject to the following conditions:
++ .
++ The above copyright notice and this permission notice shall be included in
++ all copies or substantial portions of the Software.
++ .
++ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
++ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
++ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
++ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
++ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
++ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
++ THE SOFTWARE.

diff --cc debian/patches/clean_less
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..8d57bcab773483552d75a6108963cc17f08830d7
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/patches/clean_less
@@@ -1,0 -1,0 +1,16 @@@
++Author: Michael R. Crusoe
++Last-Update: 2020-01-23
++Description: Do not clean *.bam files
++Forwarded: not-needed
++
++--- python-pysam.orig/tests/pysam_data/Makefile
+++++ python-pysam/tests/pysam_data/Makefile
++@@ -100,7 +100,7 @@
++      cp ex1.cram $@
++ 
++ clean:
++-     rm -fr [A-Za-z]*.bam *.bai *.csi *.fai *.gzi *.pileup* [A-Za-z]*.cram *.crai \
+++     rm -fr *.bai *.csi *.fai *.gzi *.pileup* [A-Za-z]*.cram *.crai \
++      all.lock all.stamp *~ calDepth *.dSYM pysam_*.sam \
++      ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \
++      with_md.sam.gz \

diff --cc debian/patches/series
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..43ee38595c16e3f1c81ef0d1514da8ca9eb787f0
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/patches/series
@@@ -1,0 -1,0 +1,3 @@@
++skip_test_remote.patch
++clean_less
++skip-test-on-32-bit.patch

diff --cc debian/patches/skip-test-on-32-bit.patch
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..ed375886c63a1960b6db3e3cb6f5e2f1ecbd90a0
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/patches/skip-test-on-32-bit.patch
@@@ -1,0 -1,0 +1,34 @@@
++Description: Attempt skipping failing test on 32-bit
++Author: Nilesh Patra <nilesh@debian.org>
++Forwarded: not-needed
++Last-Update: 2021-10-15
++---
++--- python-pysam.orig/tests/samtools_test.py
+++++ python-pysam/tests/samtools_test.py
++@@ -20,6 +20,7 @@
++     check_samtools_view_equal, get_temp_filename, force_bytes, WORKDIR, \
++     make_data_files, BAM_DATADIR
++ 
+++import platform
++ 
++ def setUpModule():
++     make_data_files(BAM_DATADIR)
++@@ -86,7 +87,7 @@
++         # TODO: fixmate behaviour changed in 1.21
++         #"fixmate ex1.bam %(out)s_ex1.fixmate.bam",
++         "flagstat ex1.bam > %(out)s_ex1.flagstat",
++-        "calmd ex1.bam ex1.fa > %(out)s_ex1.calmd.bam",
+++        #"calmd ex1.bam ex1.fa > %(out)s_ex1.calmd.bam",
++         # use -s option, otherwise the following error in samtools 1.2:
++         # Samtools-htslib-API: bam_get_library() not yet implemented
++         # causes downstream problems
++@@ -112,6 +113,9 @@
++         # ("addreplacerg -r 'RG\tID:ga\tSM:hs' ex1.bam > %(out)s_ex1.addreplacerg",
++     ]
++ 
+++    if platform.architecture()[0] == '64bit':
+++        statements.append("calmd ex1.bam ex1.fa > %(out)s_ex1.calmd.bam")
+++
++     map_command = {
++     }
++ 

diff --cc debian/patches/skip_test_remote.patch
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..a54c65b42139ccfb025cc3a5a46db7da3f3b9b04
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/patches/skip_test_remote.patch
@@@ -1,0 -1,0 +1,91 @@@
++Author: Andreas Tille <tille@debian.org>
++Last-Update: 2018-09-11
++Description: Skip tests trying to access remote site
++Forwarded: not-needed
++
++--- python-pysam.orig/tests/AlignmentFile_test.py
+++++ python-pysam/tests/AlignmentFile_test.py
++@@ -497,17 +497,6 @@
++                        "tmp_ex2.sam",
++                        "rb", "wh")
++ 
++-    def testBAM2CRAM(self):
++-        # ignore header (md5 sum)
++-        self.checkEcho("ex2.bam",
++-                       "ex2.cram",
++-                       "tmp_ex2.cram",
++-                       "rb", "wc",
++-                       sequence_filename=os.path.join(BAM_DATADIR, "ex1.fa"),
++-                       checkf=partial(
++-                           check_samtools_view_equal,
++-                           without_header=True))
++-
++     def testCRAM2BAM(self):
++         # ignore header (md5 sum)
++         self.checkEcho("ex2.cram",
++@@ -1633,6 +1622,7 @@
++     reference_filename = os.path.join(BAM_DATADIR, 'ex1.fa')
++ 
++ 
+++@unittest.skip
++ class TestRemoteFileFTP(unittest.TestCase):
++ 
++     '''test remote access.
++--- python-pysam.orig/tests/tabix_test.py
+++++ python-pysam/tests/tabix_test.py
++@@ -1013,6 +1013,7 @@
++     globals()[n] = type(n, (TestVCFFromVariantFile,), dict(filename=vcf_file,))
++ 
++ 
+++@unittest.skip
++ class TestRemoteFileHTTP(unittest.TestCase):
++ 
++     url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example.gtf.gz"
++@@ -1052,25 +1053,28 @@
++         self.assertEqual(list(self.local_file.header), [])
++ 
++ 
++-class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):
++-
++-    url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz"
++-    region = "chr1:1-1000"
++-    local = os.path.join(TABIX_DATADIR, "example_comments.gtf.gz")
++-
++-    def setUp(self):
++-        if not getattr(pysam.config, "HAVE_LIBCURL", 0) or not check_url(self.url):
++-            self.remote_file = None
++-        else:
++-            self.remote_file = pysam.TabixFile(self.url, "r")
++-        self.local_file = pysam.TabixFile(self.local, "r")
++-
++-    def testHeader(self):
++-        if self.remote_file is None:
++-            return
++-
++-        self.assertEqual(list(self.local_file.header), ["# comment at start"])
++-        self.assertEqual(list(self.local_file.header), self.remote_file.header)
+++#@unittest.skip  #  this leads to
+++                 #  E   TypeError: Error when calling the metaclass bases
+++                 #  E       function() argument 1 must be code, not str
+++#class TestRemoteFileHTTPWithHeader(TestRemoteFileHTTP):
+++#
+++#    url = "http://genserv.anat.ox.ac.uk/downloads/pysam/test/example_comments.gtf.gz"
+++#    region = "chr1:1-1000"
+++#    local = os.path.join(TABIX_DATADIR, "example_comments.gtf.gz")
+++#
+++#    def setUp(self):
+++#        if not getattr(pysam.config, "HAVE_LIBCURL", 0) or not check_url(self.url):
+++#            self.remote_file = None
+++#        else:
+++#            self.remote_file = pysam.TabixFile(self.url, "r")
+++#        self.local_file = pysam.TabixFile(self.local, "r")
+++#
+++#    def testHeader(self):
+++#        if self.remote_file is None:
+++#            return
+++#
+++#        self.assertEqual(list(self.local_file.header), ["# comment at start"])
+++#        self.assertEqual(list(self.local_file.header), self.remote_file.header)
++ 
++ 
++ class TestIndexArgument(unittest.TestCase):

diff --cc debian/python-pysam-tests.README.Debian
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..0c7ed430f33913f86a7bfd9baac90c20451563a5
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/python-pysam-tests.README.Debian
@@@ -1,0 -1,0 +1,8 @@@
++Pysam for Debian
++================
++
++To verify whether your python-pysam and python3-pysam modules are working
++correctly you can run the test suite manually by running the scripts
++run-nose-tests and run-nose3-tests in this directory.
++
++ -- Jorge Soares <j.s.soares@gmail.com>  Fri, 28 Nov 2014 14:29:40 +0100

diff --cc debian/python-pysam-tests.install
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..a99a5780036fc700aafe73a43b49e7ce09f496ac
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/python-pysam-tests.install
@@@ -1,0 -1,0 +1,1 @@@
++tests usr/share/doc/python-pysam

diff --cc debian/python-pysam-tests.lintian-overrides
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..1fa28b6285fe7846ed4616e012b12eef2f5606d7
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/python-pysam-tests.lintian-overrides
@@@ -1,0 -1,0 +1,3 @@@
++# These files are intentionally empty to be used for testing
++zero-byte-file-in-doc-directory [usr/share/doc/python-pysam/tests/cbcf_data/example_empty.vcf]
++zero-byte-file-in-doc-directory [usr/share/doc/python-pysam/tests/tabix_data/empty.bed.gz]

diff --cc debian/python-pysam.lintian-overrides
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..b9ca38222580bbf35bbca0f353bebf6f525add4a
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/python-pysam.lintian-overrides
@@@ -1,0 -1,0 +1,4 @@@
++# These are apparently false-positives
++# Inspection of the build logs shows that these are indeed compiled with
++# -D_FORTIFY_SOURCE=2
++hardening-no-fortify-functions [usr/lib/python2.7/dist-packages/pysam/lib*.so]

diff --cc debian/python3-pysam.lintian-overrides
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..0224eef1f6d0965993b1c3a46188d6f2ac3c86d6
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/python3-pysam.lintian-overrides
@@@ -1,0 -1,0 +1,4 @@@
++# These are apparently false-positives
++# Inspection of the build logs shows that these are indeed compiled with
++# -D_FORTIFY_SOURCE=2
++hardening-no-fortify-functions [usr/lib/python3/dist-packages/pysam/lib*.so]

diff --cc debian/rules
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..4ab44a1fffa8071278d66873246c461a26da1e0f
new file mode 100755 (executable)
--- /dev/null
--- /dev/null
+++ b/debian/rules
@@@ -1,0 -1,0 +1,73 @@@
++#!/usr/bin/make -f
++
++include /usr/share/dpkg/default.mk
++
++export PYBUILD_NAME=pysam
++export LC_ALL = C.UTF-8
++
++export DEB_BUILD_MAINT_OPTIONS = hardening=+all
++
++TESTPKG    := $(DEB_SOURCE)-tests
++
++export HTSLIB_MODE=external
++HTSLIBDIR  := /usr/lib/$(DEB_HOST_MULTIARCH)
++export HTSLIB_LIBRARY_DIR=$(HTSLIBDIR)
++export HTSLIB_INCLUDE_DIR=/usr/include
++
++# unfortunately this does not work - any hint to fix this would be really welcome
++#export PYBUILD_TEST_ARGS_python3=-k-XTestRemoteFileHTTP -k-XTestRemoteFileHTTPWithHeader
++
++clean: clean-tests
++%:
++      dh $@ --buildsystem=pybuild
++
++override_dh_install: clean-tests
++      dh_install -Xtest.gtf.gz
++      find debian -name log.txt -delete
++      find debian -name LICENSE -delete
++
++ifeq (,$(findstring nocheck, $(DEB_BUILD_OPTIONS)))
++override_dh_auto_test: pysam_data.all cbcf_data.all
++      dh_auto_test
++else
++override_dh_auto_test:
++endif
++
++override_dh_auto_clean:
++      dh_auto_clean
++      $(RM) \
++              pysam/config.py \
++              pysam/config.h \
++              pysam/lib*.c \
++              samtools/config.h \
++              bcftools/config.h
++      rm -rf pysam.egg-info
++
++.PHONY: pysam_data.% cbcf_data.%
++cbcf_data.%:
++      cd tests/$(basename $@) && $(MAKE) $*
++pysam_data.%:
++      cd tests/$(basename $@) && $(MAKE) $*
++
++.PHONY: clean-tests
++clean-tests: pysam_data.clean cbcf_data.clean
++      find . -name "*.pyc" -delete
++      find . -name "*.pyxbldc" -delete
++      find . -name "tmp_*.bam" -delete
++      find . -name "*.bai*" -delete
++      find . -name "*.cram*" -delete
++      find . -name "pysam_uncompressed.bam" -delete
++      rm -rf  tests/pysam_test_work \
++              tests/example_htslib.gtf.gz.tbi \
++              tests/log.txt \
++              tests/test.bam \
++              tests/_compile_test.c \
++              tests/pysam_ex2.sam \
++              tests/__pycache__ \
++              pysam/calignmentfile.c \
++              pysam/cbcf.c \
++              tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \
++              tests/pysam_data/ex1.fa.gz \
++              tests/pysam_data/ex1.fa.gz.gzi \
++              tests/pysam_data/ex1_csi.bam.csi
++      rm -rf .pytest_cache/

diff --cc debian/salsa-ci.yml
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..33c3a640d2a84306b6a8b5640692ac3481739e65
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/salsa-ci.yml
@@@ -1,0 -1,0 +1,4 @@@
++---
++include:
++  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
++  - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml

diff --cc debian/source/format
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..163aaf8d82b6c54f23c45f32895dbdfdcc27b047
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/source/format
@@@ -1,0 -1,0 +1,1 @@@
++3.0 (quilt)

diff --cc debian/tests/control
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..6dc40585b2ae1e2c1ddd255973ea6e1a77eced5b
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/tests/control
@@@ -1,0 -1,0 +1,3 @@@
++Test-Command: export HOME=$PWD && make -C tests/pysam_data && make -C tests/cbcf_data && pytest-3
++Depends: @builddeps@, python3-pysam,
++Restrictions: allow-stderr, rw-build-tree

diff --cc debian/upstream/metadata
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..95241be6aaf2624cfe41719769cb33c2753d3d44
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/upstream/metadata
@@@ -1,0 -1,0 +1,13 @@@
++Bug-Submit: https://github.com/pysam-developers/pysam/issues/new
++Registry:
++- Name: OMICtools
++  Entry: OMICS_19073
++- Name: SciCrunch
++  Entry: NA
++- Name: bio.tools
++  Entry: pysam
++- Name: conda:bioconda
++  Entry: pysam
++Repository: https://github.com/pysam-developers/pysam.git
++Bug-Database: https://github.com/pysam-developers/pysam/issues
++Repository-Browse: https://github.com/pysam-developers/pysam

diff --cc debian/watch
index 0000000000000000000000000000000000000000,0000000000000000000000000000000000000000..c714a54ff0fa598e7c64b0114719c4a02c068237
new file mode 100644 (file)
--- /dev/null
--- /dev/null
+++ b/debian/watch
@@@ -1,0 -1,0 +1,5 @@@
++version=4
++
++opts="repacksuffix=+ds,dversionmangle=s/\+ds//g,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%python-pysam-$1.tar.gz%" \
++      https://github.com/pysam-developers/pysam/tags \
++      (?:.*/)?v?(\d[\d\.]*)\.tar\.gz