[med-svn] [Git][med-team/segemehl][master] 4 commits: Add test data

[Shruti Sridhar (@shruti_sridhar)]

Shruti Sridhar pushed to branch master at Debian Med / segemehl


Commits:
fc89b603 by Shruti Sridhar at 2021-08-01T16:05:26+05:30
Add test data

- - - - -
28b8248a by Shruti Sridhar at 2021-08-01T16:05:49+05:30
Add autopkgtest

- - - - -
758a6136 by Shruti Sridhar at 2021-08-01T16:06:18+05:30
Install docs

- - - - -
6c607df4 by Shruti Sridhar at 2021-08-01T16:08:27+05:30
Update changelog

- - - - -


10 changed files:

- + debian/README.test
- debian/changelog
- debian/copyright
- + debian/docs
- + debian/examples
- + debian/tests/control
- + debian/tests/data/myseq.fa
- + debian/tests/data/seq1.fa
- + debian/tests/data/seq2.fa
- + debian/tests/run-unit-test


Changes:

=====================================
debian/README.test
=====================================
@@ -0,0 +1,15 @@
+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/*
+
+The files myseq.fa, seq1.fa and seq2.fa were written for testing this package.
+


=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+segemehl (0.3.4-4) UNRELEASED; urgency=medium
+
+  * Team Upload.
+  * Add test data
+  * Add autopkgtest
+  * Install docs
+
+ -- Shruti Sridhar <shruti.sridhar99 at gmail.com>  Sun, 01 Aug 2021 16:07:41 +0530
+
 segemehl (0.3.4-3) unstable; urgency=medium
 
   * Team Upload.


=====================================
debian/copyright
=====================================
@@ -11,6 +11,10 @@ Files: debian/*
 Copyright: 2016-2018 Andreas Tille <tille at debian.org>
 License: GPL-3+
 
+Files: debian/tests/data
+Copyright: Shruti Sridhar <shruti.sridhar99 at gmail.com>
+License: GPL-3+
+
 License: GPL-3+
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by


=====================================
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/myseq.fa
=====================================
@@ -0,0 +1,2 @@
+>myseq
+ATGCGACTCAGACGACGACGACGACGAGACTAAGCAGACATCAGCAGACGACGACGCATACGACGATA
\ No newline at end of file


=====================================
debian/tests/data/seq1.fa
=====================================
@@ -0,0 +1,2 @@
+>index1
+ATGCATGCATGCATTTAGAGACAGCAGACGATACGACTACACAGCATCAACGACATACGACATCAGACGAACAAAAAAAAAAAAAGATCATCAGAATGGCATGGCATGACTCGACATCGACATCAGACATCAGAAATCAGACTAAGCATAGCATAGAATCAATACGACGACATAGATAGATAGATAAGCAGACTAAGCATACAGCACATAGCATAGACGAATAGCATACGACATAGAATAGATATCAGCA
\ No newline at end of file


=====================================
debian/tests/data/seq2.fa
=====================================
@@ -0,0 +1,2 @@
+>index2
+ATGCTACGACGACGACGAGAAGAGAGAGAAAAAAAAAAATACGACATCAGACTACGACATACTACAGACTACAGCATCAGAATAG
\ No newline at end of file


=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,20 @@
+#!/bin/bash
+set -e
+
+pkg=segemehl
+
+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}"
+
+#do_stuff_to_test_package#
+segemehl -x index.idx -d seq1.fa
+segemehl -i index.idx -d seq1.fa -q myseq.fa > mymap.sam
+segemehl -S -i index.idx -d seq1.fa -q seq2.fa > my.sngl.bed
+[ -s "mymap.sam" ] && [ -s "index.idx" ] && [ -s "my.sngl.bed" ] || exit 1 && echo "PASS Test"
\ No newline at end of file



View it on GitLab: https://salsa.debian.org/med-team/segemehl/-/compare/2835fcd8e601071f5e3d3a4abac7af5fae357c29...6c607df4f452d425a634fae241f8a321c4f28a86

-- 
View it on GitLab: https://salsa.debian.org/med-team/segemehl/-/compare/2835fcd8e601071f5e3d3a4abac7af5fae357c29...6c607df4f452d425a634fae241f8a321c4f28a86
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