From: Nilesh Patra Date: Sat, 31 Dec 2022 16:56:09 +0000 (+0000) Subject: python-pysam (0.20.0+ds-3) unstable; urgency=medium X-Git-Tag: archive/raspbian/0.22.0+ds-1+rpi1~1^2~6 X-Git-Url: https://dgit.raspbian.org/?a=commitdiff_plain;h=7caaf3987bbf089d98fb922723a1b236c39d6cf3;p=python-pysam.git python-pysam (0.20.0+ds-3) unstable; urgency=medium * Team Upload. * Add patch to fix proper "SO" extension. [dgit import unpatched python-pysam 0.20.0+ds-3] --- 7caaf3987bbf089d98fb922723a1b236c39d6cf3 diff --cc debian/changelog index 0000000,0000000..15e9c05 new file mode 100644 --- /dev/null +++ b/debian/changelog @@@ -1,0 -1,0 +1,529 @@@ ++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 diff --cc debian/clean index 0000000,0000000..6987d15 new file mode 100644 --- /dev/null +++ b/debian/clean @@@ -1,0 -1,0 +1,4 @@@ ++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 diff --cc debian/control index 0000000,0000000..e5e006f new file mode 100644 --- /dev/null +++ b/debian/control @@@ -1,0 -1,0 +1,50 @@@ ++Source: python-pysam ++Maintainer: Debian Med Packaging Team ++Uploaders: Charles Plessy , ++ Andreas Tille , ++ Étienne Mollier ++Section: python ++Testsuite: autopkgtest-pkg-python ++Priority: optional ++Build-Depends: debhelper-compat (= 13), ++ dh-exec, ++ dh-python, ++ libhts-dev (>= 1.14~), ++ zlib1g-dev, ++ python3-all-dev, ++ python3-setuptools, ++ cython3, ++ tabix , ++ samtools , ++ bcftools , ++ python3-pytest ++Standards-Version: 4.6.2 ++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 0000000,0000000..d7d4d9c new file mode 100644 --- /dev/null +++ b/debian/copyright @@@ -1,0 -1,0 +1,76 @@@ ++Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ ++Upstream-Name: pysam ++Upstream-Contact: Andreas Heger ++Source: https://github.com/pysam-developers/pysam ++Files-Excluded: htslib/* ++ win32 ++ .github ++ .gitignore ++ ++Files: * ++Copyright: 2009-2018 Andreas Heger, ++ Tildon Grant Belgrad, ++ Martin Goodson, ++ Kevin Jacobs ++ 2008-2010 Genome Research Ltd. ++License: MIT ++ ++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 ++ 2015 Jorge Soares ++ 2014-2015 Charles Plessy ++ 2014-2018 Andreas Tille ++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 0000000,0000000..b1ad6c7 new file mode 100644 --- /dev/null +++ b/debian/patches/clean_less @@@ -1,0 -1,0 +1,15 @@@ ++Author: Michael R. Crusoe ++Last-Update: 2020-01-23 14:31:06 +0100 ++Description: Do not clean *.bam files ++ ++--- a/tests/pysam_data/Makefile +++++ b/tests/pysam_data/Makefile ++@@ -100,7 +100,7 @@ ++ cp ex1.cram $@ ++ ++ clean: ++- rm -fr [a-z]*.bam *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ +++ rm -fr *.bai *.csi *.fai *.gzi *.pileup* [a-z]*.cram *.crai \ ++ all.stamp *~ calDepth *.dSYM pysam_*.sam \ ++ ex2.sam ex2.sam.gz ex1.sam ex1.fa.gz \ ++ with_md.sam.gz \ diff --cc debian/patches/disable-tests-python3.11.patch index 0000000,0000000..ecc9936 new file mode 100644 --- /dev/null +++ b/debian/patches/disable-tests-python3.11.patch @@@ -1,0 -1,0 +1,28 @@@ ++Description: skip tests bound to fail past python3.11. ++ Thanks John Marshall and Graham Inggs for the independent suggestion. ++Author: Étienne Mollier ++Bug: https://github.com/pysam-developers/pysam/issues/1151 ++Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024425 ++Last-Update: 2022-12-27 ++--- ++This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ ++--- python-pysam.orig/tests/AlignmentFilePileup_test.py +++++ python-pysam/tests/AlignmentFilePileup_test.py ++@@ -1,5 +1,6 @@ ++ """Benchmarking module for AlignmentFile functionality""" ++ import os +++import sys ++ import pysam ++ import unittest ++ from TestUtils import make_data_files, BAM_DATADIR, IS_PYTHON3, force_str, flatten_nested_list ++@@ -206,6 +207,10 @@ ++ def tearDown(self): ++ self.samfile.close() ++ +++ @unittest.skipIf((sys.version_info.major == 3 +++ and sys.version_info.minor >= 11) +++ or sys.version_info.major >= 4, +++ "Test known to fail past python3.11.") ++ def testIteratorOutOfScope(self): ++ '''test if exception is raised if pileup col is accessed after ++ iterator is exhausted.''' diff --cc debian/patches/python3.11.patch index 0000000,0000000..507b31c new file mode 100644 --- /dev/null +++ b/debian/patches/python3.11.patch @@@ -1,0 -1,0 +1,14 @@@ ++Description: Add patch to return proper sysconf so for current python ++Author: Nilesh Patra ++Last-Update: 2022-12-30 ++--- a/pysam/__init__.py +++++ b/pysam/__init__.py ++@@ -96,5 +96,7 @@ ++ if pysam.config.HTSLIB == "builtin": ++ pysam_libs.append('libchtslib') ++ ++- so = sysconfig.get_config_var('SO') +++ so = sysconfig.get_config_var('EXT_SUFFIX') +++ if not so: +++ so = sysconfig.get_config_var('SO') ++ return [os.path.join(dirname, x + so) for x in pysam_libs] diff --cc debian/patches/series index 0000000,0000000..973b469 new file mode 100644 --- /dev/null +++ b/debian/patches/series @@@ -1,0 -1,0 +1,5 @@@ ++skip_test_remote.patch ++clean_less ++skip-test-on-32-bit.patch ++disable-tests-python3.11.patch ++python3.11.patch diff --cc debian/patches/skip-test-on-32-bit.patch index 0000000,0000000..3ce4e32 new file mode 100644 --- /dev/null +++ b/debian/patches/skip-test-on-32-bit.patch @@@ -1,0 -1,0 +1,29 @@@ ++--- a/tests/samtools_test.py +++++ b/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 ++ ++ IS_PYTHON3 = sys.version_info[0] >= 3 ++ ++@@ -92,7 +93,7 @@ ++ "flagstat ex1.bam > %(out)s_ex1.flagstat", ++ # Fails python 3.3 on linux, passes on OsX and when ++ # run locally ++- "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 ++@@ -118,6 +119,9 @@ ++ # ("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 0000000,0000000..4268e59 new file mode 100644 --- /dev/null +++ b/debian/patches/skip_test_remote.patch @@@ -1,0 -1,0 +1,90 @@@ ++Author: Andreas Tille ++Last-Update: Tue, 11 Sep 2018 14:12:55 +0200 ++Description: Skip tests trying to access remote site ++ ++--- python-pysam.orig/tests/AlignmentFile_test.py +++++ python-pysam/tests/AlignmentFile_test.py ++@@ -504,17 +504,6 @@ ++ "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", ++@@ -1640,6 +1629,7 @@ ++ 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 ++@@ -1017,6 +1017,7 @@ ++ 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" ++@@ -1056,25 +1057,28 @@ ++ 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 0000000,0000000..0c7ed43 new file mode 100644 --- /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 Fri, 28 Nov 2014 14:29:40 +0100 diff --cc debian/python-pysam-tests.install index 0000000,0000000..a99a578 new file mode 100644 --- /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 0000000,0000000..1fa28b6 new file mode 100644 --- /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.links index 0000000,0000000..8cc3b2c new file mode 100755 --- /dev/null +++ b/debian/python-pysam.links @@@ -1,0 -1,0 +1,4 @@@ ++#!/usr/bin/dh-exec ++/usr/lib/python2.7/dist-packages/pysam/libcsamtools.${DEB_HOST_GNU_TYPE}.so /usr/lib/python2.7/dist-packages/pysam/libcsamtools.so ++/usr/lib/python2.7/dist-packages/pysam/libcbcftools.${DEB_HOST_GNU_TYPE}.so /usr/lib/python2.7/dist-packages/pysam/libcbcftools.so ++/usr/lib/python2.7/dist-packages/pysam/libchtslib.${DEB_HOST_GNU_TYPE}.so /usr/lib/python2.7/dist-packages/pysam/libchtslib.so diff --cc debian/python-pysam.lintian-overrides index 0000000,0000000..b9ca382 new file mode 100644 --- /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 0000000,0000000..0224eef new file mode 100644 --- /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 0000000,0000000..3381a06 new file mode 100755 --- /dev/null +++ b/debian/rules @@@ -1,0 -1,0 +1,72 @@@ ++#!/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 $@ --with python3 --buildsystem=pybuild ++ ++override_dh_install: clean-tests ++ dh_install -Xtest.gtf.gz ++ find debian -name log.txt -delete ++ ++ifeq (,$(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) $* ++ ++.PHONY: clean-tests ++clean-tests: pysam_data.clean cbcf_data.clean ++ find . -name "*.pyc" -delete ++ find . -name "*.pyxbldc" -delete ++ find . -name "tmp_*.bam" -delete ++ find . -name "*.bai*" -delete ++ find . -name "*.cram*" -delete ++ find . -name "pysam_uncompressed.bam" -delete ++ rm -rf tests/pysam_test_work \ ++ tests/example_htslib.gtf.gz.tbi \ ++ tests/log.txt \ ++ tests/test.bam \ ++ tests/_compile_test.c \ ++ tests/pysam_ex2.sam \ ++ tests/__pycache__ \ ++ pysam/calignmentfile.c \ ++ pysam/cbcf.c \ ++ tests/GRCh38_full_analysis_set_plus_decoy_hla.fa.fai \ ++ tests/pysam_data/ex1.fa.gz \ ++ tests/pysam_data/ex1.fa.gz.gzi \ ++ tests/pysam_data/ex1_csi.bam.csi ++ rm -rf .pytest_cache/ diff --cc debian/salsa-ci.yml index 0000000,0000000..33c3a64 new file mode 100644 --- /dev/null +++ b/debian/salsa-ci.yml @@@ -1,0 -1,0 +1,4 @@@ ++--- ++include: ++ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml ++ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml diff --cc debian/source/format index 0000000,0000000..163aaf8 new file mode 100644 --- /dev/null +++ b/debian/source/format @@@ -1,0 -1,0 +1,1 @@@ ++3.0 (quilt) diff --cc debian/tests/control index 0000000,0000000..6dc4058 new file mode 100644 --- /dev/null +++ b/debian/tests/control @@@ -1,0 -1,0 +1,3 @@@ ++Test-Command: export HOME=$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 0000000,0000000..95241be new file mode 100644 --- /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 0000000,0000000..c714a54 new file mode 100644 --- /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