debian/changelog

+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@debian.org>  Sat, 24 Aug 2019 15:48:00 +0200
+
 phyml (3:3.3.20190321-1) unstable; urgency=medium
 
   * New upstream version

debian/copyright

-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@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

-Contact: Stephane Guindon <guindon@stat.auckland.ac.nz>
-Name: PhyML
 Reference:
 - author: Stéphane Guindon
   title: Bayesian estimation of divergence times from large sequence alignments
@@ -13,7 +11,8 @@ Reference:
   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
+  title: A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum
+    Likelihood
   journal: Syst Biol
   volume: 52
   number: 5