Andreas Tille pushed to branch master at Debian Med / clustalo
Commits: d2c696a0 by Andreas Tille at 2020-04-14T11:13:44+02:00 Run example test from BioPython that seems to fail on mipsel - - - - - 232a7c88 by Andreas Tille at 2020-04-14T11:19:24+02:00 routine-update: Standards-Version: 4.5.0 - - - - - e5a256fa by Andreas Tille at 2020-04-14T11:19:32+02:00 routine-update: Add salsa-ci file - - - - - a8791524 by Andreas Tille at 2020-04-14T11:19:32+02:00 routine-update: Rules-Requires-Root: no - - - - - 45a800e1 by Andreas Tille at 2020-04-14T11:19:43+02:00 Remove obsolete field Contact from debian/upstream/metadata (already present in machine-readable debian/copyright). - - - - - 842db433 by Andreas Tille at 2020-04-14T11:23:25+02:00 routine-update: Ready to upload to unstable - - - - - 9 changed files: - debian/changelog - debian/clustalo.examples - debian/control - debian/rules - + debian/salsa-ci.yml - + debian/tests/biopython_testdata/README - + debian/tests/biopython_testdata/f002 - debian/tests/run-unit-test - debian/upstream/metadata Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,15 @@ +clustalo (1.2.4-5) unstable; urgency=medium + + * Run example test from BioPython that seems to fail on mipsel + (see bug #956324) + * Standards-Version: 4.5.0 (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + * Remove obsolete field Contact from debian/upstream/metadata (already + present in machine-readable debian/copyright). + + -- Andreas Tille <[email protected]> Tue, 14 Apr 2020 11:19:44 +0200 + clustalo (1.2.4-4) unstable; urgency=medium [ Jelmer Vernooij ] ===================================== debian/clustalo.examples ===================================== @@ -1 +1,2 @@ debian/example.fa +debian/tests/biopython_testdata/f002 ===================================== debian/control ===================================== @@ -9,10 +9,11 @@ Build-Depends: debhelper-compat (= 12), doxygen, graphviz, sphinx-common -Standards-Version: 4.4.1 +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/clustalo Vcs-Git: https://salsa.debian.org/med-team/clustalo.git Homepage: http://www.clustal.org/omega/ +Rules-Requires-Root: no Package: clustalo Architecture: any ===================================== debian/rules ===================================== @@ -17,6 +17,15 @@ ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) echo "Do not run build time test" endif +override_dh_auto_test-arch: +ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS))) + dh_auto_test -a + # Run additional test from python-biopython package to verify that + # this will work as well + src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force + rm temp_test.aln temp_test.dnd +endif + override_dh_auto_install-arch: dh_auto_install -a rm -rf debian/tmp/usr/lib/pkgconfig ===================================== debian/salsa-ci.yml ===================================== @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml ===================================== debian/tests/biopython_testdata/README ===================================== @@ -0,0 +1,4 @@ +The file f002 was obtained from the source of python-biopython. It +can be found in Tests/Fasta/f002. This file is used to track down +bug #956324 which is probably caused by clustalo. + ===================================== debian/tests/biopython_testdata/f002 ===================================== @@ -0,0 +1,26 @@ +>gi|1348912|gb|G26680|G26680 human STS STS_D11729.^Agi|1396336|gb|G27617|G27617 human STS SHGC-32648. +CGGACCAGACGGACACAGGGAGAAGCTAGTTTCTTTCATGTGATTGANATNATGACTCTACTCCTAAAAG +GGAAAAANCAATATCCTTGTTTACAGAAGAGAAACAAACAAGCCCCACTCAGCTCAGTCACAGGAGAGAN +CACAGAAAGTCTTAGGATCATGANCTCTGAAAAAAAGAGAAACCTTATCTTTNCTTTGTGGTTCCTTTAA +ACACACTCACACACACTTGGTCAGAGATGCTGTGCTTCTTGGAAGCAAGGNCTCAAAGGCAAGGTGCACG +CAGAGGGACGTTTGAGTCTGGGATGAAGCATGTNCGTATTATTTATATGATGGAATTTCACGTTTTTATG +TNAAGCNTGACAACACCAGGCAGGTATGAGAGGAAAGCAAGGCCCGTCCATNGCTGTCCGTACNCTTACG +GNTTGCTTGTNGGAGNCATTTNGGTATTGTTTGTTGTAANANCCAAAANGGGCTTTGGNNTGGNAAAAGG +GCAGANNGGGGGGGTTGGTGTNGTTTTTTGGGGGGANNNTTTNGATTTGGTNCCGGGNTTTNGTTTNCCN +CGGNACCGGNTTTTGGTTGGGGNCCATTTNTGNGGGGCNTTGGNGTTNCNTTNCCCNNNTNNGANTGGTT +TNA +>gi|1348917|gb|G26685|G26685 human STS STS_D11734. +CGGAGCCAGCGAGCATATGCTGCATGAGGACCTTTCTATCTTACATTATGGCTGGGAATCTTACTCTTTC +ATCTGATACCTTGTTCAGATTTCAAAATAGTTGTAGCCTTATCCTGGTTTTACAGATGTGAAACTTTCAA +GAGATTTACTGACTTTCCTAGAATAGTTTCTCTACTGGAAACCTGATGCTTTTATAAGCCATTGTGATTA +GGATGACTGTTACAGGCTTAGCTTTGTGTGAAANCCAGTCACCTTTCTCCTAGGTAATGAGTAGTGCTGT +TCATATTACTNTAAGTTCTATAGCATACTTGCNATCCTTTANCCATGCTTATCATANGTACCATTTGAGG +AATTGNTTTGCCCTTTTGGGTTTNTTNTTGGTAAANNNTTCCCGGGTGGGGGNGGTNNNGAAA +>gi|1592936|gb|G29385|G29385 human STS SHGC-32652 +GATCAAATCTGCACTGTGTCTACATATAGGAAAGGTCCTGGTGTGTGCTAATGTTCCCAATGCAGGACTT +GAGGAAGAGCTCTGTTATATGTTTCCATTTCTCTTTATCAAAGATAACCAAACCTTATGGCCCTTATAAC +AATGGAGGCACTGGCTGCCTCTTAATTTTCAATCATGGACCTAAAGAAGTACTCTGAAGGGTCTCAACAA +TGCCAGGTGGGGACAGATATACTCAGAGATTATCCAGGTCTGCCTCCCAGCGAGCCTGGAGTACACCAGA +CCCTCCTAGAGAAATCTGTTATAATTTACCACCCACTTATCCACCTTTAAACTTGGGGAAGGNNGCNTTT +CAAATTAAATTTAATCNTNGGGGGNTTTTAAACTTTAACCCTTTTNCCNTTNTNGGGGTNGGNANTTGNC +CCCNTTAAAGGGGGNNCCCCTNCNNGGGGGAATAAAACAANTTNNTTTTTT \ No newline at end of file ===================================== debian/tests/run-unit-test ===================================== @@ -22,4 +22,7 @@ cd $AUTOPKGTEST_TMP /usr/bin/clustalo -i example.fa --iter=5 --max-guidetree-iterations=1 /usr/bin/clustalo -i example.fa -o example.a2m -v +# Run example test from biopython +/usr/bin/clustalo -i f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force + echo "PASS" ===================================== debian/upstream/metadata ===================================== @@ -1,5 +1,4 @@ Bug-Database: http://bioinf.ucd.ie/bugzilla/buglist.cgi?quicksearch=clustal -Contact: [email protected] Reference: - Author: > Fabian Sievers and Andreas Wilm and David Dineen and Toby J Gibson and View it on GitLab: https://salsa.debian.org/med-team/clustalo/-/compare/ca5f073406bb00275e6ae12f93e4685b24d5b392...842db43313cd0d4574d6f80c628c32cb36ff7756 -- View it on GitLab: https://salsa.debian.org/med-team/clustalo/-/compare/ca5f073406bb00275e6ae12f93e4685b24d5b392...842db43313cd0d4574d6f80c628c32cb36ff7756 You're receiving this email because of your account on salsa.debian.org.
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