[med-svn] [Git][med-team/phyml][master] 4 commits: Fix autopkgtest

[Andreas Tille]

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 <tille at debian.org>  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 <guindon at stat.auckland.ac.nz>
 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 <guindon at stat.auckland.ac.nz>
-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

-- 
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