[med-svn] [Git][med-team/pal2nal][master] 6 commits: Add autopkgtests

[Nilesh Patra]

Nilesh Patra pushed to branch master at Debian Med / pal2nal


Commits:
2f3ccdb7 by Nilesh Patra at 2020-07-01T23:57:53+05:30
Add autopkgtests

- - - - -
40326fdc by Nilesh Patra at 2020-07-01T23:58:05+05:30
Add relevant examples

- - - - -
412bc28b by Nilesh Patra at 2020-07-01T23:58:45+05:30
Bump compat version to 13

- - - - -
3e9f13be by Nilesh Patra at 2020-07-01T23:59:27+05:30
Add "Rules-Requires-Root:no"

- - - - -
9b31152b by Nilesh Patra at 2020-07-02T00:03:49+05:30
Update metadata URLs

- - - - -
1be1df53 by Nilesh Patra at 2020-07-01T18:42:43+00:00
Bump standards version to 4.5.0

- - - - -


8 changed files:

- − debian/compat
- debian/control
- debian/examples
- + debian/tests/README
- + debian/tests/control
- + debian/tests/run-unit-test
- + debian/tests/test.expected
- debian/upstream/metadata


Changes:

=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11


=====================================
debian/control
=====================================
@@ -4,11 +4,12 @@ Uploaders: Pjotr Prins <pjotr.debian at thebird.nl>,
            Steffen Moeller <moeller at debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~)
-Standards-Version: 4.2.1
+Build-Depends: debhelper-compat (= 13)
+Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/pal2nal
 Vcs-Git: https://salsa.debian.org/med-team/pal2nal.git
 Homepage: http://www.bork.embl.de/pal2nal
+Rules-Requires-Root: no
 
 Package: pal2nal
 Architecture: all


=====================================
debian/examples
=====================================
@@ -1,2 +1,3 @@
 test.aln
 test.nuc
+debian/tests/test.expected


=====================================
debian/tests/README
=====================================
@@ -0,0 +1,5 @@
+Tests for pa2nal
+=================
+
+The expected output has been generated by running the command:
+	pal2nal.pl test.aln test.nuc -output paml -nogap > test.expected 2>/dev/null


=====================================
debian/tests/control
=====================================
@@ -0,0 +1,4 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
+


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,20 @@
+#!/bin/bash
+set -e
+
+pkg=pal2nal
+
+if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
+  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cp /usr/share/doc/${pkg}/examples/* -a "${AUTOPKGTEST_TMP}"
+
+cd "${AUTOPKGTEST_TMP}"
+gunzip -r *
+
+echo 'Test'
+pal2nal.pl test.aln test.nuc -output paml -nogap > res 2>/dev/null
+diff -u res test.expected
+echo 'PASS'
+


=====================================
debian/tests/test.expected
=====================================
@@ -0,0 +1,21 @@
+   2    531
+BC070280
+CTAAACTGCATCGTCGCTGTGTCCCAGAACATGGGCATCGGCAAGAACGGGGACCTGCCC
+CCACCGCTCAGGAATGAATTCTTCCAGAGAATGACCACAACCTCTTCAGTAGAAGGTAAA
+CAGAATCTGGTGATTATGGGTAAGAAGACCTGGTTCTCCATTCCTGAGAAGAATCGACCT
+TTAAAGGGTAGAATTAATTTAGTTCTCAGCAGAGAACTCAAGGAACCTCCACAAGGAGCT
+CATTTTCTTTCCAGTCTAGATGATGCCTTAAAACTTACTGAACAACCAGAATTAGCAAAT
+AAAGTAGACATGCTCTGGATAGTTGGTGGCAGTTCTGTTTATAAGGAAGCCATGAATGGC
+CATCTTAAACTATTTGTGACAAGGATCATGCAAGACTTTGAAAGTGACACGTTTTTTCCA
+GAAATTGATTTGGAGAAATATAAACTTCTGCCAGAATACCCAGGTGTTCTCTCTGATGTC
+CAGGAGGAGAAAGGCATTAAGTACAAATTTGAAGTATATGAGAAGAATGAT
+pseudogene
+CTAAACTGCATTGTCAATGATTCCCAGAAGATGGGCATCATCAGGAATGGGGACCTGCCC
+CCTCAGCTCAAAAATAAATTCTTCCAAAGAATGACCACACCCTCTTCAGCAGAGGGTAAA
+GAAAATTTAGTATTTTTAATTAGGAAGAACTGGTTCTCGATTACTGAGAAGAATCAACCT
+TTAAAGTATATAATTAATTTAGTTGTCAGTAGAGAATCCAAGGAACCACCGCAAAGACCT
+CCTTTTCTTGACAGTCTGGGTGATGCCTTAAAACGTATTGAGCAACTAAAATTAGCAAAT
+AAACAAGACGTGTTTTTTACAGTGGGAGGCAGTTCTGTTTATAAGGAATCCATGAATGAC
+CATTTTAAACTATTTGTGACATGGATCATGCAGGACTTTCAAAGTGACACGTTTTTTCCT
+GAAGGTGATTTAGAGAAATATAAACTTCTCCCAGAATACCCAGGTGTTGTCTCTGATGTG
+GAGGAGGAGAAAGGCATTAAGTACAAATTTGAAGTATATGAAAAGAATGAT


=====================================
debian/upstream/metadata
=====================================
@@ -9,9 +9,9 @@ Reference:
  Pages: W609-W612
  DOI: 10.1093/nar/gkl315
  PMID: 16845082
- URL: http://nar.oxfordjournals.org/content/34/suppl_2/W609
+ URL: https://academic.oup.com/nar/article/34/suppl_2/W609/2505720
  eprint: >
-  http://nar.oxfordjournals.org/content/34/suppl_2/W609.full.pdf+html
+  https://academic.oup.com/nar/article-pdf/34/suppl_2/W609/7623711/gkl315.pdf
 Registry:
  - Name: OMICtools
    Entry: OMICS_20386



View it on GitLab: https://salsa.debian.org/med-team/pal2nal/-/compare/13cafd11742542d50c8b11f7b52d6c2b26023161...1be1df53e3e7d71d2eb07a5c4826e628a5d8578b

-- 
View it on GitLab: https://salsa.debian.org/med-team/pal2nal/-/compare/13cafd11742542d50c8b11f7b52d6c2b26023161...1be1df53e3e7d71d2eb07a5c4826e628a5d8578b
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