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

[Nilesh Patra]

Nilesh Patra pushed to branch master at Debian Med / abacas


Commits:
964a94ab by Nilesh Patra at 2020-05-28T19:20:55+05:30
Add autopkgtests

- - - - -
dc8f7cc8 by Nilesh Patra at 2020-05-28T19:21:12+05:30
Add relevant examples

- - - - -
137eb526 by Nilesh Patra at 2020-05-28T19:28:47+05:30
Fix Manpage

- - - - -
e468c6ae by Nilesh Patra at 2020-05-28T19:29:13+05:30
Bump compat version to 13

- - - - -
9e706a80 by Nilesh Patra at 2020-05-28T19:29:37+05:30
Add "Rules-Requires-Root:no"

- - - - -
27fef2c4 by Nilesh Patra at 2020-05-28T19:33:38+05:30
Add myself to uploaders

- - - - -


8 changed files:

- debian/abacas.1
- debian/control
- + debian/examples
- + debian/tests/README
- + debian/tests/control
- + debian/tests/data/454AllContigs.fna
- + debian/tests/data/SS_SC84.dna
- + debian/tests/run-unit-test


Changes:

=====================================
debian/abacas.1
=====================================
@@ -16,9 +16,7 @@ reference sequence in a single fasta file
 .TP
 \fIqs\fR
 contigs in multi\-fasta format
-.TP
-\fI\prog\fR
-MUMmer program to use: 'nucmer' or 'promer'
+MUMmer program to use 'nucmer' or 'promer'
 .TP
 \fIpsf\fR
 pseudomolecule/ordered sequence file in fasta format


=====================================
debian/control
=====================================
@@ -1,13 +1,15 @@
 Source: abacas
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+           Nilesh Patra <npatra974 at gmail.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (= 12)
+Build-Depends: debhelper-compat (= 13)
 Standards-Version: 4.5.0
 Vcs-Browser: https://salsa.debian.org/med-team/abacas
 Vcs-Git: https://salsa.debian.org/med-team/abacas.git
 Homepage: http://abacas.sourceforge.net/
+Rules-Requires-Root: no
 
 Package: abacas
 Architecture: all


=====================================
debian/examples
=====================================
@@ -0,0 +1 @@
+debian/tests/data/*


=====================================
debian/tests/README
=====================================
@@ -0,0 +1,5 @@
+Tests for abacas
+=================
+
+The data for tests has been referenced from:
+	https://www.sanger.ac.uk/resources/downloads/bacteria/streptococcus-suis.html


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


=====================================
debian/tests/data/454AllContigs.fna
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/tests/data/SS_SC84.dna
=====================================
The diff for this file was not included because it is too large.

=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,20 @@
+#!/bin/bash
+set -e
+
+pkg=abacas
+
+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 1'
+abacas -r SS_SC84.dna -q 454AllContigs.fna -p nucmer -f 150 -l 70 -V 3 -b
+
+echo 'Test 2'
+abacas -r SS_SC84.dna -q 454AllContigs.fna  -p nucmer -i 80 -v 30 -N  -m -c



View it on GitLab: https://salsa.debian.org/med-team/abacas/-/compare/6737dfd4060619ceaf4c84a58c6d09379a7e28c9...27fef2c4f4311c3cd91c4f0080ea9de3091a0da8

-- 
View it on GitLab: https://salsa.debian.org/med-team/abacas/-/compare/6737dfd4060619ceaf4c84a58c6d09379a7e28c9...27fef2c4f4311c3cd91c4f0080ea9de3091a0da8
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