debian/README.test

+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+    sh run-unit-test
+
+in order to confirm its integrity.

debian/changelog

+clonalframe (1.2-10) unstable; urgency=medium
+
+  * Provide autopkgtest
+    Closes: #891730
+  * debhelper-compat 12
+
+ -- Andreas Tille <tille@debian.org>  Sun, 06 Oct 2019 09:00:01 +0200
+
 clonalframe (1.2-9) unstable; urgency=medium
 
   * More easy way to propagate Debian build flags (thanks to Jonas Smedegaard

debian/compat

-11

debian/control

@@ -3,10 +3,10 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 12),
                qt5-qmake,
                libgsl-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/clonalframe
 Vcs-Git: https://salsa.debian.org/med-team/clonalframe.git
 Homepage: http://www.xavierdidelot.xtreemhost.com/clonalframe.htm

debian/docs

+debian/README.test
+debian/tests/run-unit-test

debian/examples

+debian/tests/example.fasta

debian/tests/control

+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr

debian/tests/example.fasta

+# First gene: actA
+> ST12
+CGAGGAGTCCAGAAGCCTTAGCAA
+> ST25
+CGAGGAGTCCAGTAGCCTTAGCAA
+> ST53
+CGAGGAGTCCAGAAGCCTT-GCAA
+=
+# Second gene: recB
+> ST25
+CGCAGGAGTCCCAAAGAAGCCACTTAGAAACAA
+> ST12
+CGCAGGAGTCCCATAGAAGCCACTTAGAAACAA
+> ST53
+CGCAGGAGTCCC---GAAGCCACTTAGAAACAA
+=
+# Third gene fragment: mutX
+> ST53
+TGCATGCATGTGCATGCCCGAGAGCGCGATC
+> ST25
+-------------------------------
+> ST12
+TGCATGCATGTGAATGCCCGAGAGCGCGATC
+=

debian/tests/run-unit-test

+#!/bin/bash
+set -e
+
+pkg=clonalframe
+
+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}/examples/* "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+
+ClonalFrame example.fasta example.xmfa