Andreas Tille pushed to branch master at Debian Med / kmerresistance
Commits: aa8d498c by Andreas Tille at 2023-10-09T17:09:31+02:00 Add autopkgtest - - - - - 49d8b945 by Andreas Tille at 2023-10-09T17:09:44+02:00 routine-update: Standards-Version: 4.6.2 - - - - - 4 changed files: - debian/changelog - debian/control - + debian/tests/control - + debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,14 @@ +kmerresistance (2.2.0-5) UNRELEASED; urgency=medium + + [ Luma ] + * Add autopkgtest + Closes: #1009159 + + [ Andreas Tille ] + * Standards-Version: 4.6.2 (routine-update) + + -- Andreas Tille <[email protected]> Mon, 09 Oct 2023 17:09:07 +0200 + kmerresistance (2.2.0-4) unstable; urgency=medium * d/watch: switch to git mode following changes in bitbucket. ===================================== debian/control ===================================== @@ -6,7 +6,7 @@ Section: science Priority: optional Build-Depends: debhelper-compat (= 13), kma -Standards-Version: 4.6.1 +Standards-Version: 4.6.2 Vcs-Browser: https://salsa.debian.org/med-team/kmerresistance Vcs-Git: https://salsa.debian.org/med-team/kmerresistance.git Homepage: https://bitbucket.org/genomicepidemiology/kmerresistance ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @, build-essential +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,30 @@ +#!/bin/bash +set -e + +pkg=kmerresistance + +export LC_ALL=C.UTF-8 +if [ "$AUTOPKGTEST_TMP" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM +fi + +cp -a /usr/share/doc/${pkg}/* "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" + +gunzip -r * + +echo "Testing C binary" +kmerresistance -i reads_se.fq.gz -o output/name -t_db templates -s_db species +kmerresistance -ipe reads_1.fq.gz reads_2.fq.gz -o output/name -t_db templates -s_db species +echo "PASS" + +echo "Test Templates" +kma index -i ResFinder.fsa -o ResFinder +kma index -i bacteria.fsa -o bacteria -Sparse ATG +kmerresistance -i sample_1.fastq sample_2.fastq -o out -t_db ResFinder -s_db bacteria +echo "PASS" + + + View it on GitLab: https://salsa.debian.org/med-team/kmerresistance/-/compare/ff2ca609c9e2c7602eaf516d3397d063f6810ade...49d8b945aee1ccf460b7d28f7553e7f70402fab0 -- View it on GitLab: https://salsa.debian.org/med-team/kmerresistance/-/compare/ff2ca609c9e2c7602eaf516d3397d063f6810ade...49d8b945aee1ccf460b7d28f7553e7f70402fab0 You're receiving this email because of your account on salsa.debian.org.
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