Andreas Tille pushed to branch master at Debian Med / phyml
Commits: b12e6b02 by Andreas Tille at 2019-08-24T13:48:14Z Fix autopkgtest - - - - - 999add84 by Andreas Tille at 2019-08-24T13:48:34Z Secure URI in copyright format - - - - - a265eb4c by Andreas Tille at 2019-08-24T13:48:34Z Remove trailing whitespace in debian/changelog - - - - - bd5434fa by Andreas Tille at 2019-08-24T13:48:36Z Remove obsolete fields Name, Contact from debian/upstream/metadata. - - - - - 4 changed files: - debian/changelog - debian/copyright - debian/tests/run-unit-test - debian/upstream/metadata Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,12 @@ +phyml (3:3.3.20190321-2) UNRELEASED; urgency=medium + + * Fix autopkgtest + * Secure URI in copyright format + * Remove trailing whitespace in debian/changelog + * Remove obsolete fields Name, Contact from debian/upstream/metadata. + + -- Andreas Tille <[email protected]> Sat, 24 Aug 2019 15:48:00 +0200 + phyml (3:3.3.20190321-1) unstable; urgency=medium * New upstream version @@ -104,8 +113,8 @@ phyml (3:3.2.0+dfsg-3) unstable; urgency=medium [ Canberk Koç ] * autopkgtest added - * fix autopkgtest - + * fix autopkgtest + [ Andreas Tille ] * Add missing Depends: openmpi-bin * use wrapper to select MPI version if applicable ===================================== debian/copyright ===================================== @@ -1,4 +1,4 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: PhyML Upstream-Contact: Stephane Guindon <[email protected]> Source: https://github.com/stephaneguindon/phyml-downloads/releases ===================================== debian/tests/run-unit-test ===================================== @@ -3,15 +3,19 @@ set -e pkg="phyml" -if [ "$AUTOPKGTEST_TMP" = "" ] ; then - AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + # Double quote below to expand the temporary directory variable now versus + # later is on purpose. + # shellcheck disable=SC2064 + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM fi -cp -a /usr/share/doc/${pkg}/examples/* $AUTOPKGTEST_TMP +cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" -cd $AUTOPKGTEST_TMP +cd "${AUTOPKGTEST_TMP}" -gunzip *.gz +gunzip -r * export OMPI_MCA_plm_rsh_agent=/bin/false export OMPI_MCA_rmaps_base_oversubscribe=1 ===================================== debian/upstream/metadata ===================================== @@ -1,33 +1,32 @@ -Contact: Stephane Guindon <[email protected]> -Name: PhyML Reference: - - author: Stéphane Guindon - title: Bayesian estimation of divergence times from large sequence alignments - journal: Molecular Biology and Evolution - year: 2010 - volume: 27 - number: 8 - pages: 1768-81 - doi: 10.1093/molbev/msq060 - PMID: 20194424 - URL: http://mbe.oxfordjournals.org/content/early/2010/03/01/molbev.msq060.abstract - eprint: http://mbe.oxfordjournals.org/content/early/2010/03/01/molbev.msq060.full.pdf+html - - author: Guindon, Stephane and Gascuel, Olivier - title: A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood - journal: Syst Biol - volume: 52 - number: 5 - pages: 696-704 - doi: 10.1080/10635150390235520 - year: 2003 - URL: http://sysbio.oxfordjournals.org/cgi/content/abstract/52/5/696 - eprint: http://sysbio.oxfordjournals.org/cgi/reprint/52/5/696.pdf - PMID: 14530136 +- author: Stéphane Guindon + title: Bayesian estimation of divergence times from large sequence alignments + journal: Molecular Biology and Evolution + year: 2010 + volume: 27 + number: 8 + pages: 1768-81 + doi: 10.1093/molbev/msq060 + PMID: 20194424 + URL: http://mbe.oxfordjournals.org/content/early/2010/03/01/molbev.msq060.abstract + eprint: http://mbe.oxfordjournals.org/content/early/2010/03/01/molbev.msq060.full.pdf+html +- author: Guindon, Stephane and Gascuel, Olivier + title: A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum + Likelihood + journal: Syst Biol + volume: 52 + number: 5 + pages: 696-704 + doi: 10.1080/10635150390235520 + year: 2003 + URL: http://sysbio.oxfordjournals.org/cgi/content/abstract/52/5/696 + eprint: http://sysbio.oxfordjournals.org/cgi/reprint/52/5/696.pdf + PMID: 14530136 Webservice: http://www.atgc-montpellier.fr/phyml Registry: - - Name: SciCrunch - Entry: SRC_014629 - - Name: OMICtools - Entry: OMICS_04241 - - Name: bio.tools - Entry: PhyML +- Name: SciCrunch + Entry: SRC_014629 +- Name: OMICtools + Entry: OMICS_04241 +- Name: bio.tools + Entry: PhyML View it on GitLab: https://salsa.debian.org/med-team/phyml/compare/e50e707e93d487a6ee1bb63c7e4685faa8aec317...bd5434fa7fdf6da44db85b1a7bcfa4ac900d18d3 -- View it on GitLab: https://salsa.debian.org/med-team/phyml/compare/e50e707e93d487a6ee1bb63c7e4685faa8aec317...bd5434fa7fdf6da44db85b1a7bcfa4ac900d18d3 You're receiving this email because of your account on salsa.debian.org.
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