Import python-pysam_0.20.0+ds-3.debian.tar.xz

[dgit import tarball python-pysam 0.20.0+ds-3 python-pysam_0.20.0+ds-3.debian.tar.xz]

diff --git a/changelog b/changelog
new file mode 100644 (file)
index 0000000..15e9c05
--- /dev/null
+++ b/changelog
@@ -0,0 +1,529 @@
+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 --git a/clean b/clean
new file mode 100644 (file)
index 0000000..6987d15
--- /dev/null
+++ b/clean
@@ -0,0 +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 --git a/control b/control
new file mode 100644 (file)
index 0000000..e5e006f
--- /dev/null
+++ b/control
@@ -0,0 +1,50 @@
+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-exec,
+               dh-python,
+               libhts-dev (>= 1.14~),
+               zlib1g-dev,
+               python3-all-dev,
+               python3-setuptools,
+               cython3,
+               tabix <!nocheck>,
+               samtools <!nocheck>,
+               bcftools <!nocheck>,
+               python3-pytest <!nocheck>
+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 --git a/copyright b/copyright
new file mode 100644 (file)
index 0000000..d7d4d9c
--- /dev/null
+++ b/copyright
@@ -0,0 +1,76 @@
+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
+                .github
+                .gitignore
+
+Files: *
+Copyright: 2009-2018 Andreas Heger,
+                      Tildon Grant Belgrad,
+                      Martin Goodson,
+                      Kevin Jacobs <jacobs@bionformed.com>
+            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 <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 --git a/patches/clean_less b/patches/clean_less
new file mode 100644 (file)
index 0000000..b1ad6c7
--- /dev/null
+++ b/patches/clean_less
@@ -0,0 +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 --git a/patches/disable-tests-python3.11.patch b/patches/disable-tests-python3.11.patch
new file mode 100644 (file)
index 0000000..ecc9936
--- /dev/null
+++ b/patches/disable-tests-python3.11.patch
@@ -0,0 +1,28 @@
+Description: skip tests bound to fail past python3.11.
+ Thanks John Marshall and Graham Inggs for the independent suggestion.
+Author: Étienne Mollier <emollier@debian.org>
+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 --git a/patches/python3.11.patch b/patches/python3.11.patch
new file mode 100644 (file)
index 0000000..507b31c
--- /dev/null
+++ b/patches/python3.11.patch
@@ -0,0 +1,14 @@
+Description: Add patch to return proper sysconf so for current python
+Author: Nilesh Patra <nilesh@debian.org>
+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 --git a/patches/series b/patches/series
new file mode 100644 (file)
index 0000000..973b469
--- /dev/null
+++ b/patches/series
@@ -0,0 +1,5 @@
+skip_test_remote.patch
+clean_less
+skip-test-on-32-bit.patch
+disable-tests-python3.11.patch
+python3.11.patch

diff --git a/patches/skip-test-on-32-bit.patch b/patches/skip-test-on-32-bit.patch
new file mode 100644 (file)
index 0000000..3ce4e32
--- /dev/null
+++ b/patches/skip-test-on-32-bit.patch
@@ -0,0 +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 --git a/patches/skip_test_remote.patch b/patches/skip_test_remote.patch
new file mode 100644 (file)
index 0000000..4268e59
--- /dev/null
+++ b/patches/skip_test_remote.patch
@@ -0,0 +1,90 @@
+Author: Andreas Tille <tille@debian.org>
+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 --git a/python-pysam-tests.README.Debian b/python-pysam-tests.README.Debian
new file mode 100644 (file)
index 0000000..0c7ed43
--- /dev/null
+++ b/python-pysam-tests.README.Debian
@@ -0,0 +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 --git a/python-pysam-tests.install b/python-pysam-tests.install
new file mode 100644 (file)
index 0000000..a99a578
--- /dev/null
+++ b/python-pysam-tests.install
@@ -0,0 +1 @@
+tests  usr/share/doc/python-pysam

diff --git a/python-pysam-tests.lintian-overrides b/python-pysam-tests.lintian-overrides
new file mode 100644 (file)
index 0000000..1fa28b6
--- /dev/null
+++ b/python-pysam-tests.lintian-overrides
@@ -0,0 +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 --git a/python-pysam.links b/python-pysam.links
new file mode 100755 (executable)
index 0000000..8cc3b2c
--- /dev/null
+++ b/python-pysam.links
@@ -0,0 +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 --git a/python-pysam.lintian-overrides b/python-pysam.lintian-overrides
new file mode 100644 (file)
index 0000000..b9ca382
--- /dev/null
+++ b/python-pysam.lintian-overrides
@@ -0,0 +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 --git a/python3-pysam.lintian-overrides b/python3-pysam.lintian-overrides
new file mode 100644 (file)
index 0000000..0224eef
--- /dev/null
+++ b/python3-pysam.lintian-overrides
@@ -0,0 +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 --git a/rules b/rules
new file mode 100755 (executable)
index 0000000..3381a06
--- /dev/null
+++ b/rules
@@ -0,0 +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 --git a/salsa-ci.yml b/salsa-ci.yml
new file mode 100644 (file)
index 0000000..33c3a64
--- /dev/null
+++ b/salsa-ci.yml
@@ -0,0 +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 --git a/source/format b/source/format
new file mode 100644 (file)
index 0000000..163aaf8
--- /dev/null
+++ b/source/format
@@ -0,0 +1 @@
+3.0 (quilt)

diff --git a/tests/control b/tests/control
new file mode 100644 (file)
index 0000000..6dc4058
--- /dev/null
+++ b/tests/control
@@ -0,0 +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 --git a/upstream/metadata b/upstream/metadata
new file mode 100644 (file)
index 0000000..95241be
--- /dev/null
+++ b/upstream/metadata
@@ -0,0 +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 --git a/watch b/watch
new file mode 100644 (file)
index 0000000..c714a54
--- /dev/null
+++ b/watch
@@ -0,0 +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