Nilesh Patra pushed to branch master at Debian Med / centrifuge
Commits: 36dbd8fd by Nilesh Patra at 2020-08-24T12:38:36+00:00 Add autopkgtests - - - - - a5fa16b2 by Nilesh Patra at 2020-08-24T18:18:12+05:30 Remove empty - - - - - 05a2f649 by Nilesh Patra at 2020-08-24T18:19:05+05:30 Update changelog - - - - - 4ec28ecb by Nilesh Patra at 2020-08-24T18:19:21+05:30 routine-update: Standards-Version: 4.5.0 - - - - - b422a810 by Nilesh Patra at 2020-08-24T18:19:22+05:30 routine-update: debhelper-compat 13 - - - - - 8ecfce23 by Nilesh Patra at 2020-08-24T18:19:39+05:30 routine-update: Remove trailing whitespace in debian/rules - - - - - ea205413 by Nilesh Patra at 2020-08-24T18:19:39+05:30 routine-update: Add salsa-ci file - - - - - d01c7f75 by Nilesh Patra at 2020-08-24T18:19:39+05:30 routine-update: Rules-Requires-Root: no - - - - - 6 changed files: - debian/changelog - debian/control - debian/rules - + debian/salsa-ci.yml - + debian/tests/control - + debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,19 @@ +centrifuge (1.0.3-4) UNRELEASED; urgency=medium + + [ Steffen Möller ] + * Added ref to conda + + [ Nilesh Patra ] + * Add autopkgtests + * Remove empty + * Standards-Version: 4.5.0 (routine-update) + * debhelper-compat 13 (routine-update) + * Remove trailing whitespace in debian/rules (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + + -- Nilesh Patra <[email protected]> Mon, 24 Aug 2020 18:18:47 +0530 + centrifuge (1.0.3-3) unstable; urgency=medium * Use 2to3 to port to Python3 ===================================== debian/control ===================================== @@ -3,15 +3,16 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper-compat (= 12), +Build-Depends: debhelper-compat (= 13), dh-python, dh-sequence-python3, hisat2, jellyfish -Standards-Version: 4.4.0 +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/centrifuge Vcs-Git: https://salsa.debian.org/med-team/centrifuge.git Homepage: https://ccb.jhu.edu/software/centrifuge/ +Rules-Requires-Root: no Package: centrifuge Architecture: any ===================================== debian/rules ===================================== @@ -29,3 +29,4 @@ override_dh_install: sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \ done rm -rf debian/*/usr/lib/centrifuge/share/centrifuge/doc + find debian -name manual.inc.html | xargs rm -rf ===================================== 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/tests/control ===================================== @@ -0,0 +1,4 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr + ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,29 @@ +#!/bin/bash +set -e + +pkg=centrifuge +CUR_DIR=`pwd` + +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +#cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}" +cp ${CUR_DIR}/example/* -a "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" +gunzip -r * + +echo 'Test 1' +centrifuge-build --conversion-table reference/gi_to_tid.dmp --taxonomy-tree reference/nodes.dmp --name-table reference/names.dmp reference/test.fa test +for f in *.cf +do + [ -s $f ] || exit 1 +done +echo "PASS" + +echo 'Test 2' +centrifuge -f -x test reads/input.fa +cat *.tsv +echo "PASS" View it on GitLab: https://salsa.debian.org/med-team/centrifuge/-/compare/7effbe1c1a999c51968dfad605b48aba552287cb...d01c7f75d38ccb22e915840f519c746ffe4ab3c9 -- View it on GitLab: https://salsa.debian.org/med-team/centrifuge/-/compare/7effbe1c1a999c51968dfad605b48aba552287cb...d01c7f75d38ccb22e915840f519c746ffe4ab3c9 You're receiving this email because of your account on salsa.debian.org.
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