[med-svn] [Git][med-team/python-pyvcf][master] 8 commits: routine-update: Packaging update
Lance Lin (@linqigang)
gitlab at salsa.debian.org
Mon Dec 4 16:40:20 GMT 2023
Lance Lin pushed to branch master at Debian Med / python-pyvcf
Commits:
96875012 by Lance Lin at 2023-12-04T21:04:46+07:00
routine-update: Packaging update
- - - - -
3ff8bd9f by Lance Lin at 2023-12-04T21:05:38+07:00
routine-update: Standards-Version: 4.6.2
- - - - -
7f8c2447 by Lance Lin at 2023-12-04T21:05:41+07:00
routine-update: Build-Depends: s/dh-python/dh-sequence-python3/
- - - - -
87a4d6ea by Lance Lin at 2023-12-04T21:36:18+07:00
Set upstream metadata fields: Repository-Browse.
Changes-By: lintian-brush
- - - - -
5a2cdcc2 by Lance Lin at 2023-12-04T21:41:42+07:00
d/clean: Remove autogenerated file, vcf/cparse.c (Closes: #1046140)
- - - - -
c25839b7 by Lance Lin at 2023-12-04T23:28:10+07:00
d/control: Replace autopkgtest-pkg-python with autopkgtest-pkg-pybuild
- - - - -
da638c89 by Lance Lin at 2023-12-04T23:29:01+07:00
d/rules: Copy tests to build directory
- - - - -
84c084d3 by Lance Lin at 2023-12-04T23:29:44+07:00
d/tests: Removed, run upstream tests with autopkgtest-pkg-pybuild
- - - - -
7 changed files:
- debian/changelog
- + debian/clean
- debian/control
- debian/rules
- − debian/tests/control
- − debian/tests/run-unit-test
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,17 @@
+python-pyvcf (0.6.8+git20170215.476169c-10) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Packaging update
+ * Standards-Version: 4.6.2 (routine-update)
+ * Build-Depends: s/dh-python/dh-sequence-python3/ (routine-update)
+ * Set upstream metadata fields: Repository-Browse.
+ * d/clean: Remove autogenerated file, vcf/cparse.c (Closes: #1046140)
+ * d/control: Replace autopkgtest-pkg-python with autopkgtest-pkg-pybuild
+ * d/rules: Copy tests to build directory
+ * d/tests: Removed, run upstream tests with autopkgtest-pkg-pybuild
+
+ -- Lance Lin <lq27267 at gmail.com> Mon, 04 Dec 2023 20:55:29 +0700
+
python-pyvcf (0.6.8+git20170215.476169c-9) unstable; urgency=medium
* Packaging update
=====================================
debian/clean
=====================================
@@ -0,0 +1 @@
+vcf/cparse.c
=====================================
debian/control
=====================================
@@ -2,16 +2,16 @@ Source: python-pyvcf
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
Section: python
-Testsuite: autopkgtest-pkg-python
+Testsuite: autopkgtest-pkg-pybuild
Priority: optional
Build-Depends: debhelper-compat (= 13),
- dh-python,
+ dh-sequence-python3,
cython3,
python3-all-dev,
python3-setuptools,
python3-pytest <!nocheck>,
- python3-pysam <!nocheck>,
-Standards-Version: 4.6.1
+ python3-pysam <!nocheck>
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/python-pyvcf
Vcs-Git: https://salsa.debian.org/med-team/python-pyvcf.git
Homepage: https://github.com/jamescasbon/PyVCF
@@ -23,9 +23,7 @@ Depends: ${shlibs:Depends},
${misc:Depends},
${python3:Depends},
python3-pysam
-Breaks: python3-pyvcf
Provides: python3-pyvcf
-Replaces: python3-pyvcf
Description: Variant Call Format (VCF) parser for Python 3
The Variant Call Format (VCF) specifies the format of a text file used
in bioinformatics for storing gene sequence variations. The format has
@@ -67,9 +65,8 @@ Description: helper scripts for Variant Call Format (VCF) parser
Package: python-pyvcf-examples
Architecture: all
-Depends: ${misc:Depends}
-Suggests: python3-pyvcf
Multi-Arch: foreign
+Depends: ${misc:Depends}
Description: Example data for Variant Call Format (VCF) parser for Python
The Variant Call Format (VCF) specifies the format of a text file used
in bioinformatics for storing gene sequence variations. The format has
=====================================
debian/rules
=====================================
@@ -10,8 +10,11 @@ export PYBUILD_NAME=vcf
examplesdir=debian/python-py$(PYBUILD_NAME)-examples/usr/share/doc/python3-$(PYBUILD_NAME)
helperdir=debian/py$(PYBUILD_NAME)/usr
+export PYBUILD_BEFORE_TEST = mkdir {build_dir}/vcf; \
+ cp -r {dir}/vcf/test {build_dir}/vcf/
+
%:
- dh $@ --with python3 --buildsystem=pybuild
+ dh $@ --buildsystem=pybuild
override_dh_install:
dh_install
=====================================
debian/tests/control deleted
=====================================
@@ -1,3 +0,0 @@
-Tests: run-unit-test
-Depends: @, python3-pytest
-Restrictions: allow-stderr
=====================================
debian/tests/run-unit-test deleted
=====================================
@@ -1,28 +0,0 @@
-#!/bin/bash
-set -e
-
-pkg=python3-vcf
-
-export LC_ALL=C.UTF-8
-if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
- AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
- trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
-fi
-
-set -x
-mkdir "${AUTOPKGTEST_TMP}"/vcf
-cp -a /usr/share/doc/${pkg}/test "${AUTOPKGTEST_TMP}"/vcf
-
-cd "${AUTOPKGTEST_TMP}"
-
-# Do not unzip originally gzipped files
-# It turned out that re-gzipping after unzipping will break the test!
-NO_UNZIP_DIR=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
-for gz in 1kg.vcf.gz issue-201.vcf.gz tb.vcf.gz ; do
- mv vcf/test/${gz} ${NO_UNZIP_DIR}
-done
-gunzip -r *
-mv ${NO_UNZIP_DIR}/* vcf/test
-rmdir ${NO_UNZIP_DIR}
-
-pytest-3
=====================================
debian/upstream/metadata
=====================================
@@ -9,3 +9,4 @@ Registry:
Entry: NA
Bug-Database: https://github.com/jamescasbon/PyVCF/issues
Bug-Submit: https://github.com/jamescasbon/PyVCF/issues/new
+Repository-Browse: https://github.com/jamescasbon/PyVCF
View it on GitLab: https://salsa.debian.org/med-team/python-pyvcf/-/compare/cce0d4a145999761b2f8f55dfa74ea2e1f77f6dd...84c084d37139c3aedf14c8beb5eb653b3bdbf7d1
--
View it on GitLab: https://salsa.debian.org/med-team/python-pyvcf/-/compare/cce0d4a145999761b2f8f55dfa74ea2e1f77f6dd...84c084d37139c3aedf14c8beb5eb653b3bdbf7d1
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