[med-svn] [Git][med-team/python-pysam][master] 5 commits: d/copyright: review, Add d/lrc.config
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Sep 16 15:16:34 BST 2026
Andreas Tille pushed to branch master at Debian Med / python-pysam
Commits:
c70cc0c0 by Andreas Tille at 2026-09-16T16:15:05+02:00
d/copyright: review, Add d/lrc.config
- - - - -
5680e5ef by Andreas Tille at 2026-09-16T15:15:17+01:00
Remove redundant Priority: optional from source stanza.
Changes-By: lintian-brush
Fixes: lintian: source: redundant-priority-optional-field
See-also: https://lintian.debian.org/tags/redundant-priority-optional-field.html
- - - - -
d56a5d58 by Andreas Tille at 2026-09-16T15:15:17+01:00
Update standards version to 4.7.4, no changes needed.
Upgrade checklist verified:
4.7.3 → 4.7.4:
* Package is not in non-free-firmware
Changes-By: lintian-brush
Fixes: lintian: source: out-of-date-standards-version 4.7.2 (released 2025-02-27) (current is 4.7.4.1)
See-also: https://lintian.debian.org/tags/out-of-date-standards-version.html
- - - - -
75ef3bda by Andreas Tille at 2026-09-16T15:15:20+01:00
Set upstream metadata fields: Documentation.
Changes-By: lintian-brush
- - - - -
041c1676 by Andreas Tille at 2026-09-16T16:16:26+02:00
Remove redundant Priority: optional from source stanza.
* Remove redundant Priority: optional from source stanza.
* Update standards version to 4.7.4, no changes needed.
* Set upstream metadata fields: Documentation.
* cme fix dpkg-control
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/lrc.config
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,5 +1,6 @@
python-pysam (0.23.3+ds-3) UNRELEASED; urgency=medium
+ [ Étienne Mollier ]
* preserve-stdout-from-gc.patch: new.
This patch originates from upstream and fixes an old issue spotted on
i386 architecture some time ago.
@@ -7,7 +8,15 @@ python-pysam (0.23.3+ds-3) UNRELEASED; urgency=medium
The original skip hunk of the patch is now fixed by the patch
preserve-stdout-from-gc.patch.
- -- Étienne Mollier <emollier at debian.org> Mon, 17 Nov 2025 19:37:54 +0100
+ [ Andreas Tille ]
+ * d/copyright: review
+ * Add d/lrc.config
+ * Remove redundant Priority: optional from source stanza.
+ * Update standards version to 4.7.4, no changes needed.
+ * Set upstream metadata fields: Documentation.
+ * cme fix dpkg-control
+
+ -- Andreas Tille <tille at debian.org> Wed, 16 Sep 2026 16:15:32 +0200
python-pysam (0.23.3+ds-2) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -1,32 +1,34 @@
Source: python-pysam
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Charles Plessy <plessy at debian.org>,
- Andreas Tille <tille at debian.org>,
- Étienne Mollier <emollier at debian.org>
+Uploaders:
+ Charles Plessy <plessy at debian.org>,
+ Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at 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: 4.7.2
+Build-Depends:
+ debhelper-compat (= 14),
+ dh-sequence-python3,
+ libhts-dev (>= 1.21~),
+ zlib1g-dev,
+ python3-all-dev,
+ python3-setuptools,
+ cython3,
+ tabix <!nocheck>,
+ samtools <!nocheck>,
+ bcftools <!nocheck>,
+ python3-pytest <!nocheck>,
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
Package: python3-pysam
Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- ${python3:Depends}
+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
@@ -37,8 +39,10 @@ Description: interface for the SAM/BAM sequence alignment and mapping format (Py
Package: python-pysam-tests
Architecture: all
Multi-Arch: foreign
-Depends: ${misc:Depends}
-Enhances: python3-pysam
+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
=====================================
debian/copyright
=====================================
@@ -56,6 +56,53 @@ Copyright: 2011-2012 Broad Institute
2012-2013 Peter Cock, The James Hutton Institute
License: MIT
+Files: samtools/lz4/*
+Copyright: 2011-2017, Yann Collet.
+License: BSD-2-Clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are
+ met:
+ .
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ * Redistributions in binary form must reproduce the above
+ copyright notice, this list of conditions and the following disclaimer
+ in the documentation and/or other materials provided with the
+ distribution.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Files: bcftools/utlist.h
+Copyright: 2007-2014, Troy D. Hanson
+License: BSD-1-clause
+ Redistribution and use in source and binary forms, with or without
+ modification, are permitted provided that the following conditions are met:
+ .
+ * Redistributions of source code must retain the above copyright
+ notice, this list of conditions and the following disclaimer.
+ .
+ THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS
+ IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED
+ TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+ PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER
+ OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+ EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+ PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
+ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
+ LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
+ NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
Files: debian/*
Copyright:
2015-2016 Afif Elghraoui <afif at debian.org>
=====================================
debian/lrc.config
=====================================
@@ -0,0 +1 @@
+bcftools/LICENSE
=====================================
debian/upstream/metadata
=====================================
@@ -1,4 +1,5 @@
Bug-Submit: https://github.com/pysam-developers/pysam/issues/new
+Documentation: https://pysam.readthedocs.io/
Registry:
- Name: OMICtools
Entry: OMICS_19073
View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/19ee09cfbbb0d6917bad3986c7d453ca196f7c10...041c167667472ad438bf9b96d5b9c91d1b912403
--
View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/19ee09cfbbb0d6917bad3986c7d453ca196f7c10...041c167667472ad438bf9b96d5b9c91d1b912403
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