[med-svn] [Git][med-team/clustalo][master] 6 commits: Run example test from BioPython that seems to fail on mipsel

[Andreas Tille]

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 <tille at debian.org>  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: clustalw at ucd.ie
 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
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