[med-svn] [Git][med-team/pilercr][master] 4 commits: Add test data
Shruti Sridhar (@shruti_sridhar)
gitlab at salsa.debian.org
Tue Jun 15 14:57:10 BST 2021
Shruti Sridhar pushed to branch master at Debian Med / pilercr
Commits:
6c1f2502 by Shruti Sridhar at 2021-06-15T19:19:42+05:30
Add test data
- - - - -
8e55d018 by Shruti Sridhar at 2021-06-15T19:20:16+05:30
Add autopkgtests
- - - - -
59defa21 by Shruti Sridhar at 2021-06-15T19:21:30+05:30
Install docs
- - - - -
b1b4f378 by Shruti Sridhar at 2021-06-15T19:26:41+05:30
Update changelog
- - - - -
8 changed files:
- + debian/README.test
- debian/changelog
- debian/copyright
- + debian/docs
- + debian/examples
- + debian/tests/control
- + debian/tests/data/example.fasta
- + debian/tests/run-unit-test
Changes:
=====================================
debian/README.test
=====================================
@@ -0,0 +1,14 @@
+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.
+
+Notes on the files used for testing
+────────────────────────────────────────
+Files: debian/tests/data/*
+Source: https://crisprcas.i2bc.paris-saclay.fr/CrisprCasFinder/Index
+
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+pilercr (1.06+dfsg-5) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Add test data
+ * Add autopkgtests
+ * Install docs
+
+ -- Shruti Sridhar <shruti.sridhar99 at gmail.com> Tue, 15 Jun 2021 19:25:25 +0530
+
pilercr (1.06+dfsg-4) unstable; urgency=medium
* Team upload.
=====================================
debian/copyright
=====================================
@@ -35,3 +35,7 @@ License: GPL-2+
.
On Debian systems, the complete text of the GNU General
Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
+Files : debian/tests/data/*
+Copyright: 2017- CRISPR-Cas++ team (CNRS, Université Paris-Saclay, Institut Pasteur, Université de Lille)
+License: GPL-2+
\ No newline at end of file
=====================================
debian/docs
=====================================
@@ -0,0 +1,2 @@
+debian/README*
+debian/tests/run-unit-test
\ No newline at end of file
=====================================
debian/examples
=====================================
@@ -0,0 +1 @@
+debian/tests/data/*
\ No newline at end of file
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr
=====================================
debian/tests/data/example.fasta
=====================================
@@ -0,0 +1,120 @@
+>example_1
+CGAGAGCTCCTCCCCCCTGACGAGGGAGGCCGAGGTTACCCTGTACTCCAGGGCCCCGGGGCCCAAGCTC
+ACGCTGCCCTCGCAGGAGGCCAGCTGGGCCACCTGGGGCGCGGAGAGCGACGAGGCGACTGCCACCACGG
+CGCCCCTGAGCCTCTCGCCCTTCCTCACCACGATGGGCCTGTCGCCCTGGGAGTAGAGCCTCCTGCCGCT
+GCCGTCCGCGAGGGACCTGAAGGTCACCGCCTCCCTGTGGGCCAGGTAAAGCTCCCAGAGGGGGTGAAGG
+GTTTCAACACCATTCCTTGGTTTCCCATTGGTAAATGAGATTGTGGTTACGCATCCAGAGCATAAGTTTC
+AACACCATTCCTTGGTTTCGCCGTTGAAGTAGTCCTCGTCGTCGTGCACCACCTCCTCCAGTTTCAACAC
+CATTCCTTGGTTTCTGATTGTAACTGGGGCGCTGACAGGGTACATGTAGGTGGTTTCAACACCATTCCTT
+GGTTTCACGTGCCCTATGGAACGCTGAAGGTATACCTATCAAGGTCAAGTTTCAACGCCATTCCTTGGTT
+TCGCCAGAGTGTCAATTAACTCCCCCAACGTAAGCGGAGGGCGTTTCAACACCATTCCTTGGTTTCATCT
+CCTTCTTGTCCCTGCCCAGGTACGCAATTATGGTTTCAACACCATTCCTTGGTTTCTTATGTCATACTCC
+TTTGCTGCCTCGTGGAGCTGTCCTGCTAGTTTCAACACCATTCCTTGGTTTCTAGAGGACTTTCTTAACA
+ACGCCATTGATATCCTTGTAATCAGGTTTCAACACCATTCCTTGGTTTCTAGAGCATATAAAGGAGGAAG
+ATATCGAGAAGTTCCTGTTTCAACACCATTCCTTGGTTTCGCCAAGCACAAGCGACAACCCTAACCGCCC
+CCATGTGTTTCAACACCATTCCTTGGTTTCCAAGAGAAGTTTTATTTGACGCAGTAGACAACAAGGAAAG
+AGGTTTCAACACCATTCCTTGGTTTCGCGTAGACCTGGAAGCGGTACTCTGCGTAGACAAGGGTTTCAAC
+ACCATTCCTTGGTTTCACATTTTGTTTAGGCAGAGGACAGCAAATTTAACAGTGTTTCAACACCATTCCT
+TGGTTTCTAAATAACTCTCTCGTTCTCGTCTACCTCATAACGGTCGTTCCTAAGTTTCAACACCATTCCT
+TGGTTTCCAAGTTTGTTCAGAAAATTGCCTTGAAAGATTCAAGCTATTTCTGTTTCAACACCATTCCTTG
+GTTTCTCGGAAAGAGAGGAAAGAAGGGAAAGGGGTAACGTTGTTAAGTTTCAACACCATTCCTTGGTTTC
+CGAGCCCTGAGCTGTTATGCTTGTCCCTGTCCTCCGCGCGGCCTGGGGCCTGCCCTTCCCCCGCTCCTCT
+GTCCCACTGTTGTCCTCTGCTGGGAAATACTTAAGTTTACCGCCGGCCCCCGGGGGACTTCCCATGTGAA
+ACGTGGGAATTACCCGGCTAAGTAGTTTATAAGGTAAATTAACAAAATAATCAAAACTGCTGCCTAGTGG
+>example_2
+AAGGCAGCGTCTGGCCTCAGCCACGGCATGAGGAGGAGCCTCAGTCCCATGCGGGGCACACCCTCCTGAA
+CCAGCAGGAGCTGCACCTCTCAGACCTGTACGCCCTTGGGGGCTCCTCCGACTCAAGTACGTCCCTGACC
+CTGGCCACGAGCTCCTCCGCCTCCCTGAGGACGTGGCCGTCAACCTCAAGGGCGAGGAGGTCGCCCCCGT
+GGTACAGGTAGGCCTCCCTGACCCTGCCCAGGAGCCTGTTGGCCAGCAGGGCGTAGAACTTGAGCTGGTT
+CGCGAAGGGCCTCAGCCTCTCCCCGGCGGCCCTGAAGGCCTTGACCTCGAGGACCCGCAGCCTCCCGCTC
+CCGGAGACCAGGTCAACGACCCCGGCCGCCCCAAGCCCCCTGTCCCTCAGGGGCACCTCCTCAAGCCAGG
+GGTTTCAACACAATCTTATGGTTTCAGTGTCGAGGATATGTTATAAGCATAGATTTCCTCTTGTTACAAC
+ACCATCTCGTGGTTTCGCGGATGTATCACCTAAAGCCGAAGTTTGTGATAAGGGTTACAACACCATCTCG
+TGGTTTCTGGATTACTTGCGGCAAACATACTTAGTTTCTACTCTTTGTTACAACACCATCTCGTGGTTTC
+CCGAGTATGTTCACGTCCTCTGCCTCAGAAAGGCCGAGCCTTTGTTACAACACCATCTCGTGGTTTCGCA
+GGCTCTGGAAGGCCATACTGTCCCTACAGAACCCAGACGTTACAACACCATCTCGTGGTTTCTTTCTATC
+TGAGGCGTGAGAGCATGGGTGAGAGGGTTTCTCGTTACAACACCATCTCGTGGTTTCGAAGTTTAAGCTA
+TTCTTGCTAACACATATCAATCAACTCAAGTTACAACACCATCTCGTGGTTTCAGTTTTTATGAAAAAAT
+CCTTAAAGAACTTGGCCTTTCTTGTTACAACACCATCTCGTGGTTTCGCGTTTATTCACGCGACCTGGGG
+CAGCGCAACAGTGGAAGAGTTACAACACCATCTCGTGGTTTCGCGTCTTTCTTTATAATTGACCATTCAT
+GAATTTTGTTTTGTTACAACACCATCTCGTGGTTTCGTTGTATACGATAACTACGGGTTCTGGGTCCATC
+CAACCTTGTTACAACACCATCTCGTGGTTTCTACAAACACGTTTGCCTGTTTGAAGAAGCTGGGCCTTAT
+AGGTTACAACACCATCTCGTGGTTTCGTCTCAGAATGAAAGCTCGGAGGGGACTCCCCAGACTCGTTACA
+ACACCATCTCGTGGTTTCCGAGAGACGTGAGCGAGGTGAGGAATGTGGAGAGCGAGTTGGGTTACAACAC
+CATCTCGTGGTTTCACGGGGAAAGAAACCATCACCGGAACGGTAGTAGGGGGGAATGAGTTACAACACCA
+TCTCGTGGTTTCGGCTGTTCAGTGCCTGCAGGAGCACCCAGAGTACTTGGGTTACAACACCATCTCGTGG
+TTTCGAGGTGCTAAAGAACGGGTTCACATCTGTCGTGGGCCACCCGTTACAACACCATCTCGTGGTTTCA
+GGAAGTTCAGTTCGTTGAACTTCTACGACATAATCTTTTGTTACAACACCATCTCGTGGTTTCTAGCCGT
+TCGGGATTGACGTGGAACGGCTGCGCTCTTATGGGGTTACAACACCATCTCGTGGTTTCATTACATCTCA
+AGATCAGGGCTAACATGGAGCGGTTGGTTACAACACCATCTCGTGGTTTCTATTCATTATGGACAAAGCG
+GTTCAATGTTTACAACAACACCCGTTACAACACCATCTCGTGGTTTCTCGTATGGGTCTTTTTTGGGCTC
+TACGCATGTTTGGAAAGTTACAACACCATCTCGTGGTTTCTCAGCGCTACAAACATGTCCTTCCCAGCTG
+GCTACATAGGTTACAACACCATCTCGTGGTTTCTAGCTCTTTTTCTTCGCCTTGCCCCATGGCCCCATGG
+CCGTTACAACACCATCTCGTGGTTTCTATCAGGAGGTTGCCATCAGCATTTGTTCTGGCTGGGGCTAGGT
+TACAACACCATCTCGTGGTTTCCGAGCCATGGGACGCCGTGCCTCGGCCTTAGCCTTCACGTGGCCCGGG
+GCGGCCCTCCTGTCCCACCACTGTTTTCTGCAGGGGAATACTTAAGCCTACTGCCCGCCCTGCGGCCGCT
+TCCCATGTGAAACATGGGAAGTCGCCATAGGCCTTTAAATTTTCATAATGTTTAGTTAAGTAAAATTGAT
+GTTCCCACCGCTCCCACCGGGCAAGGCACTCCCATGTCTCACATGGGAAATACCCGGCTAAGTAGTTTAT
+AAGGTAAAATAACAAAATAACATGTTAATCATTATGAAAGGAGGATCCTGTGACTCTATGCTAGACACGG
+CTAGCAGGCTCGGGACAGCGACGACGGCCCTGTACCTCAGCTCGGGGGCCACGCCGAGGGTCAGGCACCG
+ACCACCGCTACAGCCCTACGATTTTGGATGGAACCACAGGCCGCAGGGCCTCTTGAGTGGTATTTGTTGA
+GGGCCTGCGCGTGGAGGAAGTCCCCAAGTCCTAGGACTCAGGAGGACGCCGTACATGGAGCTCGTGTGGA
+>Acidilobus_saccharovorans_CR3
+GAACCCCAGCGTCACCGGGACCGCCAGCGAGAGGGCCGAGGCGGCCCCTTGGACGGCCCTCACAGTCATT
+ACCTGGAGCTGGTTGGGGGCGTTAGTCACGTCTGAGACCACGTAAACAGCGTCATAGTCGGCGGCCCTGA
+GCTCCAGCAGCTTCCTTGAGATGTGATAGGCCGCCATGGCCTGGGAGTCATAGGGGCTGACGTCTATCCT
+CATGGAGCCGCCCCCGCTGAGCCTGAAGGTGCCCCTCAGCGGCACGGCCCTGAGCTCCAGGTTATCCTCC
+TTAAACTATTTTATAAACATTATAAACAGTGTTATGCTTTTGTTATTTTGTTAATTTACCTTATAAACTA
+CTTAGCCGGGTAATTCCCATGTGAGACATGGGAAGTCACTTGCCCGGTGGGAGCGGTGGGAACATCAATT
+TTACTTAACTAAACATTATGAAAATTTAAAGGCCTATGGGGGCTTCCCATGTTCCACGTGGGAAGCTGCC
+CTGGAGCCGGCGGTAAACTTAAGTATTCCCGTGCAGAGGACAACGGTGGGACAGAGGGGCAGAGGAAGGG
+GCAGGCCCCTGGCACGGTAAGCGAACATAACCTGTATGGTGTCCCAGAGCTCGGAAACCAAGGAATGGTG
+TTGAAACTCTCTAAATACAATCGGCTTCTGATCCTTGGTAAATGCGAAACCAAGGAATGGTGTTGAAACC
+CTCATGTTCATTGGGATATAAATTGACAACTATCCACGGGAAACCAAGGAATGGTGTTGAAACGCTTCAT
+GCCGATAAGGCCGGCTGACCTAAATTGGTTAAGAAGAAACCAAGGAATGGTGTTGAAACCATAGAAAGAT
+AGTTTCAGGGGTTTAAATTTCCATAGGTTCAGGAAACCAAGGAATGGTGTTGAAACTGACGTTAGCGTGA
+ACGGGGACAGGATAAGCATAACTATAAGAAACCAAGGAATGGTGTTGAAACACTAGAACTTTATCCATGT
+CCACAAACCATGTTATGGCCGAAACCAAGGAATGGTGTTGAAACCGAGAAACCAATTAACTTAGACGCAT
+ACAAAAAGATAATTAACGAGTCAAGAAACCAAGGAATGGTGTTGAAACTAAGTATCTTCAAAGCCCTTAT
+AAAACTTGCTACCCTCTTGAAGAAACCAAGGAATGGTGTTGAAACACGCAATCATAGCCTTTGATGTTAT
+CGCCACAGCTAACTAGAAACCAAGGAATGGTGTTGAAACCCTCCACTGGCCTGTAGGTATAGTTTGCGAA
+GTGGTATGCGAAACCAAGGAATGGTGTTGAAACCAAAAGTCCGTGTGGTCTTCCCCCTCAAAATCGAAAT
+ATTGCGAAACCAAGGAATGGTGTTGAAACTCTGCACAGTGCACACTGAACCTGTTGGCCTTTCCGCCAGA
+AACCAAGGAATGGTGTTGAAACTCTGAACAAACTTGCGGGTTTAACATTAACGAGAAATACGACAGTGAA
+TAATAATATGAAACCAAGGAATGGTGTTGAAACCTGCTATTATTTCGCTTGCATAATCTGTTGGCATACC
+CCTGTGGGAAACCAAGGAATGGTGTTGAAACATCAGCGTAAGCTGTTCATACTTCCTCTGTGCAATTACA
+GTCGAAACCAAGGAATGGTGTTGAAACACTTTCCACTCATATCTATTCTGAACGTCAACAATATACAGAA
+ACCAAGGAATGGTGTTGAAACAGGTTATACTGCCCCCAGCGGCTTCGGCCTCCCCAGCGAAACCAAGGAA
+TGGTGTTGAAACCCATAGGGGAAGCTCCACTTCTTTCACAAACTCTGCGGAAACCAAGGAATGGTGTTGA
+AACGCAGCTTTGCCAGTTCTCCCTCAATAGTGTATTCATATGAAACCAAGGAATGGTGTTGAAACTTTAT
+GATATTAACGGTAGGCGCCGTGAGGACTATAGAAACCAAGGAATGGTGTTGAAACCTTGCTATCACGTCC
+CTAACGTTCATGCCCCTGGTCTTGAAACCAAGGAATGGTGTTGAAACTGGGGCCATTCTCTGCTATCTCA
+TACACTTCTTTCATATGAAACCAAGGAATGGTGTTGAAACACTTGACCTCGTAATGATATTCGTGGTCGG
+CATAGTGGGCTAGAAACCAAGGAATGGTGTTGAAACGCCTTTTCGGCGCTCACTTCCTCTTCCACTGTTG
+>Acidilobus_saccharovorans_CR4
+GGCTCCGGCAGCAGCCTGTAGGCGTTTGGGACCCTCCTTGACAGACGCGAGGCCCAGGGCGGGGTCATGA
+CCTTGAGCGGTATCGCTGTCGGCGTGAGGAACAAGAGCCTCACGGCCCCTCCCCTCCCGCCCAGGCCCAC
+CGAGAGCTCCTCCCCCCTGACGAGGGAGGCCGAGGTTACCCTGTACTCCAGGGCCCCGGGGCCCAAGCTC
+TGCCGCTGTAAAGGAGTCGTTTACGTCATACACCTTTGCAGTCAGAACTTCCTCTTCCACTGTTGTGCCG
+CCGAAACCAAGGAATGGTGTTGAAACGTAGGGACCAGTAATGACCGTGCTTCAGGGAGGAATAGGAGGAA
+ACGAAACCAAGGAATGGTGTTGAAACAGTTCTTCAAACATCGCAAAAATAGCTGAGGAAAACGTGAAACC
+AAGGAATGGTGTTGAAACTTTATATAAAACCTGGTGAACTACATGGCTACTCGTAAGCTTCTGAAACCAA
+GGAATGGTGTTGAAACATCCTAATGACGTCCATTGGCACTCCAGGGACTTCCTCAAGAAACCAAGGAATG
+GTGTTGAAACTAGATATTTGGGCTCACGAAAATCTTTCTGTCATGAAGTAGAAACCAAGGAATGGTGTTG
+AAACTGCTGGATGCCGGTAGCGGGCCCCTTGGCACTTCTACGGTAGAACAGAAACCAAGGAATGGTGTTG
+AAACACTACGCCGTGGAGGCAATGTCCTTTGCTCTCGAGAGAAACCAAGGAATGGTGTTGAAACGTCCTC
+ACCAGGCCCACAAGTTCAATTGGTGTTTTAGCGAGAAACCAAGGAATGGTGTTGAAACACTTCCTGCGCG
+CTCACGCTCTCTCGCCTCGCTTTTCTGTGGAAACCAAGGAATGGTGTTGAAACTCTTATTTCTTCGCCGC
+CCCAGGCCGCTACTATTTCCGCGGAAACCAAGGAATGGTGTTGAAACCAGGTGAAACAAAATATAATATG
+TCAATTGCGTTGTTTAGGAAACTAAGGAATGGTGTTGAAACATGCACCACAAGGTAGTATCCTTCGTCGA
+GATACCTACTCGAAACCAAGGAATGGTGTTGAAACTCACTGTTTCCCTCGCACGGGTTGGGTAGATTCCA
+CGGAAACCAAGGAATGGTGTTGAAACTGTGGCAAGCTTTCTCCTTTGCTTTATCTCGCTTATTGTCTTTG
+CGAAACCAAGGAATGGTGTTGAAACATGGCGTTCTGCGCAAGAATGCCGTGCTGTGGTATGTCATAGGAA
+ACTAAGGAATGGTGTTGAAACACCTCCCTCTTCAATTCTTCTTCCAGACTCTCCCCCACCTGGAAACCAA
+GGAATGATGTTGAAACTGGAAAGCGGTTTGTCGAAGAATATGATAAGTATGGCGATGGAAGCCATAGAAT
+GATGTTGAAGTTGAAATTAACTACTACGCCCCTTGCCACGCTGGTGCTCTCAAGGACGCCACAGGGTTTC
+GTCGTGAAGCCGGTCTACGCGTACCAGAGGCTCCTGTGGGCGGTCAAGGCGTTCGCTGACATGCAGATCT
+TTAACTACCTGGAGAACATAATAGCTGCCCAGCGTGGCGGCGAGGGAGCTGGCTTAGTGCACGAGGCGCG
+GCCGAGCCCGTTGGCCCTGGGGGTCCTTGGGGTCATCCCCTGCCTGGCCATTCCTTGAAGCGCCCTTGCC
+GCGGCGTTTATAGCAGCCAGGTATCAGCCGTGGAGCCGCGCTAGGGGTAACAAAGAGCAGTCCAAGCAGC
+
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,25 @@
+#!/bin/bash
+set -e
+
+pkg=pilercr
+
+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}"
+
+pilercr -in example.fasta -out report
+if [ $(dpkg-architecture -qDEB_BUILD_ARCH) = "amd64" ]
+ then
+ echo "0f093c279323fd1c9fd1ba2f695f949b report" > checksums
+ md5sum --check checksums
+ echo "PASS"
+ else
+ [ -s "report" ] || exit 1
+ echo "PASS"
+ fi
View it on GitLab: https://salsa.debian.org/med-team/pilercr/-/compare/f3b8c315e0cdd09a99d16bcc5caa11e9c033f3d6...b1b4f378150ab0f8daeb0805d8c2b34469e9994f
--
View it on GitLab: https://salsa.debian.org/med-team/pilercr/-/compare/f3b8c315e0cdd09a99d16bcc5caa11e9c033f3d6...b1b4f378150ab0f8daeb0805d8c2b34469e9994f
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