[med-svn] [Git][med-team/python-pyvcf][master] 6 commits: Breaks+Replaces: python3-pyvcf

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / python-pyvcf


Commits:
4030f0fa by Andreas Tille at 2019-12-09T08:08:38Z
Breaks+Replaces: python3-pyvcf

- - - - -
587b437d by Andreas Tille at 2019-12-09T09:41:46Z
Run Build-Time test, add autopkgtest

- - - - -
f0bf1db1 by Andreas Tille at 2019-12-09T09:43:59Z
Depends: python3-pysam

- - - - -
d4e460cc by Andreas Tille at 2019-12-09T09:44:54Z
Fix dependency for pyvcf package

- - - - -
7714f2c8 by Andreas Tille at 2019-12-09T10:12:26Z
Do not unzip originally gzipped files, It turned out that re-gzipping after unzipping will break the test!

- - - - -
4d681337 by Andreas Tille at 2019-12-09T10:15:25Z
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/tests/control
- + debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,9 +1,13 @@
-python-pyvcf (0.6.8+git20170215.476169c-4) UNRELEASED; urgency=medium
+python-pyvcf (0.6.8+git20170215.476169c-5) unstable; urgency=medium
 
-  TODO: Reupload with source-only upload
-        Craft real test based on code snippets in README.rst
+  * Breaks+Replaces: python3-pyvcf
+    Closes: #946427
+  * Run Build-Time test
+  * Add autopkgtest
+  * Depends: python3-pysam
+  * Fix dependency for pyvcf package
 
- -- Andreas Tille <tille at debian.org>  Fri, 29 Nov 2019 13:02:31 +0100
+ -- Andreas Tille <tille at debian.org>  Mon, 09 Dec 2019 11:12:54 +0100
 
 python-pyvcf (0.6.8+git20170215.476169c-3) unstable; urgency=medium
 


=====================================
debian/control
=====================================
@@ -8,7 +8,9 @@ Build-Depends: debhelper-compat (= 12),
                dh-python,
                cython3,
                python3-all-dev,
-               python3-setuptools
+               python3-setuptools,
+               python3-pytest <!nocheck>,
+               python3-pysam <!nocheck>,
 Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/python-pyvcf
 Vcs-Git: https://salsa.debian.org/med-team/python-pyvcf.git
@@ -18,7 +20,11 @@ Package: python3-vcf
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         ${python3: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
@@ -40,7 +46,7 @@ Package: pyvcf
 Architecture: all
 Depends: ${misc:Depends},
          ${python3:Depends},
-         python3-pyvcf
+         python3-vcf
 Description: helper scripts for Variant Call Format (VCF) parser
  The Variant Call Format (VCF) specifies the format of a text file used
  in bioinformatics for storing gene sequence variations. The format has


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,28 @@
+#!/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



View it on GitLab: https://salsa.debian.org/med-team/python-pyvcf/compare/676807f1816f710e05dfc63d0f88bc34d8b58601...4d681337bab4672bc4d832d8a4359f8296100e57

-- 
View it on GitLab: https://salsa.debian.org/med-team/python-pyvcf/compare/676807f1816f710e05dfc63d0f88bc34d8b58601...4d681337bab4672bc4d832d8a4359f8296100e57
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