[med-svn] [Git][med-team/python-pysam][master] 9 commits: Remove Python2 package
Andreas Tille
gitlab at salsa.debian.org
Fri May 8 19:40:39 BST 2020
Andreas Tille pushed to branch master at Debian Med / python-pysam
Commits:
d36deb6b by Andreas Tille at 2020-05-08T20:26:01+02:00
Remove Python2 package
- - - - -
1867e15f by Andreas Tille at 2020-05-08T20:27:04+02:00
Remove unneeded debian/gbp.conf
- - - - -
7462a0a9 by Andreas Tille at 2020-05-08T20:27:20+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
56002aaf by Andreas Tille at 2020-05-08T20:27:31+02:00
routine-update: Add salsa-ci file
- - - - -
d23008c7 by Andreas Tille at 2020-05-08T20:27:31+02:00
routine-update: Rules-Requires-Root: no
- - - - -
bfeebfcd by Andreas Tille at 2020-05-08T20:27:34+02:00
Set upstream metadata fields: Bug-Submit.
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
- - - - -
74e62e1e by Andreas Tille at 2020-05-08T20:30:55+02:00
Remove Python2 also from d/rules
- - - - -
e0281c98 by Andreas Tille at 2020-05-08T20:39:18+02:00
Upload to unstable
- - - - -
85ffaa3c by Andreas Tille at 2020-05-08T20:40:24+02:00
DEP3
- - - - -
7 changed files:
- debian/changelog
- debian/control
- − debian/gbp.conf
- debian/patches/clean_less
- debian/rules
- + debian/salsa-ci.yml
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+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 at 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
=====================================
debian/control
=====================================
@@ -10,9 +10,6 @@ Build-Depends: debhelper-compat (= 12),
dh-python,
libhts-dev (>= 1.9),
zlib1g-dev,
- python-all-dev,
- python-setuptools,
- cython (>= 0.23),
python3-all-dev,
python3-setuptools,
cython3 (>= 0.23),
@@ -20,23 +17,11 @@ Build-Depends: debhelper-compat (= 12),
samtools (>= 1.9) <!nocheck>,
bcftools (>= 1.9) <!nocheck>,
python3-pytest <!nocheck>
-Standards-Version: 4.4.1
+Standards-Version: 4.5.0
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
-
-Package: python-pysam
-Architecture: any
-Depends: ${shlibs:Depends},
- ${misc:Depends},
- ${python:Depends}
-Provides: ${python:Provides}
-Description: interface for the SAM/BAM sequence alignment and mapping format (Python 2)
- 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 2.
+Rules-Requires-Root: no
Package: python3-pysam
Architecture: any
@@ -54,7 +39,7 @@ Package: python-pysam-tests
Multi-Arch: foreign
Architecture: all
Depends: ${misc:Depends}
-Enhances: python-pysam
+Enhances: python3-pysam
Description: interface for the SAM/BAM sequence alignment and mapping format (test data)
Pysam is a Python module for reading and manipulating Samfiles. It's a
lightweight wrapper of the samtools C-API. Pysam also includes an interface
=====================================
debian/gbp.conf deleted
=====================================
@@ -1,5 +0,0 @@
-# This source package is managed with git-buildpackage and pristine-tar.
-
-[DEFAULT]
-# use pristine-tar:
-pristine-tar = True
=====================================
debian/patches/clean_less
=====================================
@@ -1,3 +1,7 @@
+Author: Michael R. Crusoe
+Last-Update: 2020-01-23 14:31:06 +0100
+Description: Do not clean *.bam files
+
--- python-pysam.orig/tests/pysam_data/Makefile
+++ python-pysam/tests/pysam_data/Makefile
@@ -87,7 +87,7 @@
=====================================
debian/rules
=====================================
@@ -16,13 +16,11 @@ export HTSLIB_LIBRARY_DIR=$(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_python2=-k-XTestRemoteFileHTTP -k-XTestRemoteFileHTTPWithHeader
#export PYBUILD_TEST_ARGS_python3=-k-XTestRemoteFileHTTP -k-XTestRemoteFileHTTPWithHeader
-export PYBUILD_DISABLE_python2=test
clean: clean-tests
%:
- dh $@ --with python2,python3 --buildsystem=pybuild
+ dh $@ --with python3 --buildsystem=pybuild
override_dh_install: clean-tests
dh_install -Xtest.gtf.gz
=====================================
debian/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
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,4 @@
+Bug-Submit: https://github.com/pysam-developers/pysam/issues/new
Registry:
- Name: OMICtools
Entry: OMICS_19073
View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/dbddf22211e3c9671b8e3cafcbe5a975fcf22b35...85ffaa3c0af4de86330d75b8c89d0120eddc59c8
--
View it on GitLab: https://salsa.debian.org/med-team/python-pysam/-/compare/dbddf22211e3c9671b8e3cafcbe5a975fcf22b35...85ffaa3c0af4de86330d75b8c89d0120eddc59c8
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