[med-svn] [Git][med-team/pirs][master] 5 commits: routine-update: Fix watchfile to detect new versions on github
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue Aug 31 15:19:07 BST 2021
Andreas Tille pushed to branch master at Debian Med / pirs
Commits:
69fa5d01 by Andreas Tille at 2021-08-31T15:58:41+02:00
routine-update: Fix watchfile to detect new versions on github
- - - - -
e2ce3eed by Andreas Tille at 2021-08-31T15:59:06+02:00
routine-update: Standards-Version: 4.6.0
- - - - -
ec9ca2aa by Andreas Tille at 2021-08-31T15:59:12+02:00
Apply multi-arch hints.
+ pirs-examples, pirs-profiles: Add Multi-Arch: foreign.
Changes-By: apply-multiarch-hints
- - - - -
63c63cdb by Andreas Tille at 2021-08-31T16:15:00+02:00
Use default name run-unit-test for autopkgtest script
- - - - -
44f20b4c by Andreas Tille at 2021-08-31T16:17:07+02:00
Upload to unstable
- - - - -
8 changed files:
- + debian/README.test
- debian/changelog
- debian/control
- debian/pirs.docs
- debian/tests/control
- − debian/tests/gcContCvgBias-test
- debian/tests/pirs-test → debian/tests/run-unit-test
- debian/watch
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,9 @@
+Notes on how this package can be tested.
+────────────────────────────────────────
+
+This package can be tested by running the provided test:
+
+ sudo apt install pirs-examples
+ sh run-unit-test
+
+in order to confirm its integrity.
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+pirs (2.0.2+dfsg-10) unstable; urgency=medium
+
+ * Fix watchfile to detect new versions on github (routine-update)
+ * Standards-Version: 4.6.0 (routine-update)
+ * Apply multi-arch hints.
+ + pirs-examples, pirs-profiles: Add Multi-Arch: foreign.
+ * Use default name run-unit-test for autopkgtest script
+
+ -- Andreas Tille <tille at debian.org> Tue, 31 Aug 2021 16:15:12 +0200
+
pirs (2.0.2+dfsg-9) unstable; urgency=medium
* Standards-Version: 4.5.1 (routine-update)
=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 13),
libboost-dev,
zlib1g-dev,
libgzstream-dev
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
Vcs-Browser: https://salsa.debian.org/med-team/pirs
Vcs-Git: https://salsa.debian.org/med-team/pirs.git
Homepage: https://github.com/galaxy001/pirs
@@ -42,6 +42,7 @@ Description: Profile based Illumina pair-end Reads Simulator
Package: pirs-profiles
Architecture: all
Depends: ${misc:Depends}
+Multi-Arch: foreign
Description: profile basd Illumina pair-end Reads Simulator (profile data)
The program pIRS can be used for simulating Illumina PE reads, with a
series of characters generated by Illumina sequencing platform, such as
@@ -66,6 +67,7 @@ Description: profile basd Illumina pair-end Reads Simulator (profile data)
Package: pirs-examples
Architecture: all
Depends: ${misc:Depends}
+Multi-Arch: foreign
Description: profile basd Illumina pair-end Reads Simulator (example data)
The program pIRS can be used for simulating Illumina PE reads, with a
series of characters generated by Illumina sequencing platform, such as
=====================================
debian/pirs.docs
=====================================
@@ -1 +1,3 @@
README
+debian/tests/run-unit-test
+debian/README.test
=====================================
debian/tests/control
=====================================
@@ -1,2 +1,3 @@
-Tests: gcContCvgBias-test, pirs-test
+Tests: run-unit-test
Depends: @, pirs-examples
+Restrictions: allow-stderr
=====================================
debian/tests/gcContCvgBias-test deleted
=====================================
@@ -1,18 +0,0 @@
-#!/bin/sh -e
-
-pkg=pirs
-testbin=gcContCvgBias
-
-if [ "$AUTOPKGTEST_TMP" = "" ] ; then
- AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-${testbin}-test.XXXXXX)
- # trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
-fi
-
-cd $AUTOPKGTEST_TMP
-
-cp -a /usr/share/doc/${pkg}/examples/${testbin}/* .
-# find . -type f -name "*.gz" -exec gunzip \{\} \;
-gc_coverage_bias -r gcdeptestref.fa.gz -o test -w 100,200 --gcdump --depwindump gcdeptest.depth.gz
-gc_coverage_bias_plot test_100.dat
-gc_coverage_bias_plot test_200.dat
-ls -l test*
=====================================
debian/tests/pirs-test → debian/tests/run-unit-test
=====================================
@@ -1,16 +1,28 @@
#!/bin/sh -e
pkg=pirs
-testbin=pirs
if [ "$AUTOPKGTEST_TMP" = "" ] ; then
AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-${testbin}-test.XXXXXX)
- # trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+ trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cd $AUTOPKGTEST_TMP
-cp -a /usr/share/doc/${pkg}/examples/${testbin}/* .
+mkdir gcContCvgBias
+cd gcContCvgBias
+cp -a /usr/share/doc/${pkg}/examples/gcContCvgBias/* .
+# find . -type f -name "*.gz" -exec gunzip \{\} \;
+gc_coverage_bias -r gcdeptestref.fa.gz -o test -w 100,200 --gcdump --depwindump gcdeptest.depth.gz
+gc_coverage_bias_plot test_100.dat
+gc_coverage_bias_plot test_200.dat
+ls -l test*
+
+cd ..
+
+mkdir pirs
+cd pirs
+cp -a /usr/share/doc/${pkg}/examples/pirs/* .
find . -type f -name "*.gz" -exec gunzip \{\} \;
pirs diploid ref_seq.fa -s 0.001 -R 2 -d 0.0001 -v 0.000001 -c gzip -o ref22 >SimDiploid.out 2>SimDiploid.err
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
version=4
opts="uversionmangle=s/b/~b/;s/(\d)(\d+)/$1.$2/,repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \
- https://github.com/galaxy001/pirs/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
\ No newline at end of file
+ https://github.com/galaxy001/pirs/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz
\ No newline at end of file
View it on GitLab: https://salsa.debian.org/med-team/pirs/-/compare/f0503002be355f5cfde1faabd0de51393778246b...44f20b4c5c5036f7e0d0a71b01b1e9c8ab88397f
--
View it on GitLab: https://salsa.debian.org/med-team/pirs/-/compare/f0503002be355f5cfde1faabd0de51393778246b...44f20b4c5c5036f7e0d0a71b01b1e9c8ab88397f
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