[med-svn] [Git][med-team/bowtie2][master] 4 commits: Merge all autopkgtest scripts into run-unit-test as usual in Debian Med packages
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Jan 17 16:41:35 GMT 2023
Andreas Tille pushed to branch master at Debian Med / bowtie2
Commits:
414d323e by Andreas Tille at 2023-01-17T16:13:18+01:00
Merge all autopkgtest scripts into run-unit-test as usual in Debian Med packages
- - - - -
b92025c9 by Andreas Tille at 2023-01-17T16:14:58+01:00
Prevent autopkgtest on s390x since the package is no built here
- - - - -
77d2101a by Andreas Tille at 2023-01-17T16:15:12+01:00
routine-update: Standards-Version: 4.6.2
- - - - -
43afb83b by Andreas Tille at 2023-01-17T16:48:39+01:00
Fix autopkgtest and upload to unstable
- - - - -
8 changed files:
- + debian/README.test
- debian/bowtie2.docs
- debian/changelog
- debian/control
- − debian/tests/binary-run
- debian/tests/control
- − debian/tests/indexing-ref-genome
- debian/tests/check-wo-arguments → debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,8 @@
+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/bowtie2.docs
=====================================
@@ -2,3 +2,5 @@ MANUAL
TUTORIAL
doc/manual.html
doc/style.css
+debian/tests/run-unit-test
+debian/README.test
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+bowtie2 (2.5.0-3) unstable; urgency=medium
+
+ * Merge all autopkgtest scripts into run-unit-test as usual in Debian Med
+ packages
+ * Prevent autopkgtest on s390x since the package is no built here
+ * Standards-Version: 4.6.2 (routine-update)
+
+ -- Andreas Tille <tille at debian.org> Tue, 17 Jan 2023 16:15:35 +0100
+
bowtie2 (2.5.0-2) unstable; urgency=medium
* Package does not build on s390x any more
=====================================
debian/control
=====================================
@@ -15,7 +15,7 @@ Build-Depends: debhelper-compat (= 13),
libfile-which-perl,
zlib1g-dev,
libsimde-dev
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/bowtie2
Vcs-Git: https://salsa.debian.org/med-team/bowtie2.git
Homepage: https://bowtie-bio.sourceforge.net/bowtie2
=====================================
debian/tests/binary-run deleted
=====================================
@@ -1,9 +0,0 @@
-#!/bin/sh
-
-set -e
-pkg=`dpkg-parsechangelog | sed -n 's/^Source: //p'`
-for file in build align inspect
-do
- ${pkg}-${file}-l -h >/dev/null 2>&1
- ${pkg}-${file}-s -h >/dev/null 2>&1
-done
=====================================
debian/tests/control
=====================================
@@ -1,5 +1,4 @@
-Tests: check-wo-arguments
-
-Tests: indexing-ref-genome
-
-Tests: binary-run
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
+Architecture: !s390x
=====================================
debian/tests/indexing-ref-genome deleted
=====================================
@@ -1,15 +0,0 @@
-#!/bin/sh
-
-set -e
-pkg=`dpkg-parsechangelog | sed -n 's/^Source: //p'`
-examplesdir=/usr/share/doc/$pkg/examples
-WORKDIR=$(mktemp -d)
-cd $WORKDIR
-for file in reference/lambda_virus.fa.gz reads/reads_1.fq.gz
-do
- extracted=`echo $file | awk -F/ '{print $NF}'`
- zcat $examplesdir/$file >${extracted%.gz}
-done
-
-bowtie2-build lambda_virus.fa lambda_virus >/dev/null 2>&1
-bowtie2 -x lambda_virus -U reads_1.fq -S eg1.sam >/dev/null 2>&1
=====================================
debian/tests/check-wo-arguments → debian/tests/run-unit-test
=====================================
@@ -1,13 +1,46 @@
-#/bin/sh -e
+#!/bin/bash
+set -e
+pkg=bowtie2
+
+export LC_ALL=C.UTF-8
+if [ "${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}"
+
+# check-wo-arguments
TMP="$(mktemp)"
# Run bowtie2 without any arguments and save stderr in a temporary file:
+set +e
STDOUT="$(bowtie2 2> ${TMP})"
# Exit status of the previous command should be 1
[ "$?" -eq 1 ]
+set -e
# Save help message into a variable:
HELP_MESSAGE="$(bowtie2 --help)"
# Check if stderr contains help message:
grep -q "${HELP_MESSAGE}" "${TMP}"
echo "SUCCESS: help message was detected!"
rm "${TMP}"
+
+# indexing-ref-genome
+examplesdir=/usr/share/doc/$pkg/examples
+for file in reference/lambda_virus.fa.gz reads/reads_1.fq.gz
+do
+ extracted=`echo $file | awk -F/ '{print $NF}'`
+ zcat $examplesdir/$file >${extracted%.gz}
+done
+bowtie2-build lambda_virus.fa lambda_virus >/dev/null 2>&1
+bowtie2 -x lambda_virus -U reads_1.fq -S eg1.sam >/dev/null 2>&1
+
+# binary-run
+for file in build align inspect
+do
+ ${pkg}-${file}-l -h >/dev/null 2>&1
+ ${pkg}-${file}-s -h >/dev/null 2>&1
+done
View it on GitLab: https://salsa.debian.org/med-team/bowtie2/-/compare/025759842516d95d143515254fa79f2e5d3aac96...43afb83bb0e52164200a9575333c357b33b75ead
--
View it on GitLab: https://salsa.debian.org/med-team/bowtie2/-/compare/025759842516d95d143515254fa79f2e5d3aac96...43afb83bb0e52164200a9575333c357b33b75ead
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