[med-svn] [Git][med-team/swarm-cluster][master] Add autopkgtest

[Liubov Chuprikova]

Liubov Chuprikova pushed to branch master at Debian Med / swarm-cluster


Commits:
b4a8c15a by Liubov Chuprikova at 2018-06-16T19:14:47+02:00
Add autopkgtest

- - - - -


8 changed files:

- + debian/README.test
- debian/changelog
- debian/copyright
- debian/docs
- + debian/source/include-binaries
- + debian/tests/control
- + debian/tests/run-unit-test
- + debian/tests/test-data/input.fasta.gz


Changes:

=====================================
debian/README.test
=====================================
--- /dev/null
+++ b/debian/README.test
@@ -0,0 +1,8 @@
+Notes on how this package can be tested.
+_______________________________________
+
+This package can be tested by execution
+
+	sh run-unit-test
+
+in order to confirm its integrity.


=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+swarm-cluster (2.2.2+dfsg-2) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * Add autopkgtest
+
+ -- Liubov Chuprikova <chuprikovalv at gmail.com>  Sat, 16 Jun 2018 19:08:01 +0200
+
 swarm-cluster (2.2.2+dfsg-1) unstable; urgency=medium
 
   * New upstream version (no pdf versions of makefiles any more)


=====================================
debian/copyright
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -696,3 +696,21 @@ Copyright: 2014-2015 Tim Booth <tbooth at ceh.ac.uk>
 License: GPL-3+
  On Debian Systems you can find a copy of the GNU GENERAL PUBLIC LICENSE
  at /usr/share/common-licenses/GPL-3.
+
+Files: debian/tests/test-data/input.fasta.gz
+Copyright: 1996-2018 NCBI
+License: unrestricted
+ Databases of molecular data on the NCBI Web site include such examples as
+ nucleotide sequences (GenBank), protein sequences, macromolecular structures,
+ molecular variation, gene expression, and mapping data. They are designed to
+ provide and encourage access within the scientific community to sources of
+ current and comprehensive information. Therefore, NCBI itself places no
+ restrictions on the use or distribution of the data contained therein. Nor do
+ we accept data when the submitter has requested restrictions on reuse or
+ redistribution.
+Comment:
+ The test data file was prepared from a SRA data file with accession number
+ SRR7082946 according to the instructions described in README.html
+ .
+ To download the original file you can use fastq-dump tool from SRA Toolkit:
+    fastq-dump SRR7082946


=====================================
debian/docs
=====================================
--- a/debian/docs
+++ b/debian/docs
@@ -1 +1,4 @@
 README.html
+debian/tests/test-data
+debian/tests/run-unit-test
+debian/README.test


=====================================
debian/source/include-binaries
=====================================
--- /dev/null
+++ b/debian/source/include-binaries
@@ -0,0 +1 @@
+debian/tests/test-data/input.fasta.gz


=====================================
debian/tests/control
=====================================
--- /dev/null
+++ b/debian/tests/control
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @
+Restrictions: allow-stderr


=====================================
debian/tests/run-unit-test
=====================================
--- /dev/null
+++ b/debian/tests/run-unit-test
@@ -0,0 +1,18 @@
+#!/bin/sh -e
+
+pkg="swarm"
+
+if [ "$AUTOPKGTEST_TMP" = "" ]; then
+    AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+    trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
+fi
+
+cd $AUTOPKGTEST_TMP
+cp /usr/share/doc/${pkg}/test-data/* .
+gunzip *.gz
+
+echo "Testing swarm with parameters recommended...\n"
+swarm -f -w OTUs.fasta input.fasta > /dev/null
+[ -s OTUs.fasta ]
+
+echo "\nPASS"


=====================================
debian/tests/test-data/input.fasta.gz
=====================================
Binary files /dev/null and b/debian/tests/test-data/input.fasta.gz differ



View it on GitLab: https://salsa.debian.org/med-team/swarm-cluster/commit/b4a8c15ae667ea019db9c6be7e49b9b2512441de

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