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 <[email protected]> Fri, 29 Nov 2019 13:02:31 +0100 + -- Andreas Tille <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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