[med-svn] r17379 - in trunk/packages/velvet/trunk/debian: . tests

[Andreas Tille]

Author: tille
Date: 2014-06-30 19:25:09 +0000 (Mon, 30 Jun 2014)
New Revision: 17379

Added:
   trunk/packages/velvet/trunk/debian/tests/
   trunk/packages/velvet/trunk/debian/tests/control
   trunk/packages/velvet/trunk/debian/tests/run-unit-test
   trunk/packages/velvet/trunk/debian/velvet-tests.install
Modified:
   trunk/packages/velvet/trunk/debian/changelog
   trunk/packages/velvet/trunk/debian/control
   trunk/packages/velvet/trunk/debian/rules
   trunk/packages/velvet/trunk/debian/velvet-example.install
Log:
Add autopkgtest


Modified: trunk/packages/velvet/trunk/debian/changelog
===================================================================
--- trunk/packages/velvet/trunk/debian/changelog	2014-06-30 15:03:51 UTC (rev 17378)
+++ trunk/packages/velvet/trunk/debian/changelog	2014-06-30 19:25:09 UTC (rev 17379)
@@ -2,6 +2,8 @@
 
   * Drop more stuff from upstream source via Files-Excluded
   * cme fix dpkg-control
+  * Do not pack example data into another archive
+  * add autopkgtest (using new binary package velvet-tests)
 
  -- Andreas Tille <tille at debian.org>  Mon, 30 Jun 2014 13:56:46 +0200
 

Modified: trunk/packages/velvet/trunk/debian/control
===================================================================
--- trunk/packages/velvet/trunk/debian/control	2014-06-30 15:03:51 UTC (rev 17378)
+++ trunk/packages/velvet/trunk/debian/control	2014-06-30 19:25:09 UTC (rev 17379)
@@ -4,6 +4,7 @@
            Andreas Tille <tille at debian.org>
 Section: science
 Priority: optional
+Testsuite: autopkgtest
 Build-Depends: debhelper (>= 9),
                zlib1g-dev,
                help2man,
@@ -63,3 +64,22 @@
  .
  This package contains the example data distributed in the sources of Velvet,
  a de novo genomic assembler. 
+
+Package: velvet-tests
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: python
+Description: Test data for the Velvet sequence assembler
+ Velvet is a de novo genomic assembler specially designed for short read
+ sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and
+ Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near
+ Cambridge, in the United Kingdom.
+ .
+ Velvet currently takes in short read sequences, removes errors then produces
+ high quality unique contigs. It then uses paired read information, if
+ available, to retrieve the repeated areas between contigs.
+ .
+ This package contains the test data to run the unit tests of Velvet, a de novo
+ genomic assembler, that could be used as additional set of examples.
+
+

Modified: trunk/packages/velvet/trunk/debian/rules
===================================================================
--- trunk/packages/velvet/trunk/debian/rules	2014-06-30 15:03:51 UTC (rev 17378)
+++ trunk/packages/velvet/trunk/debian/rules	2014-06-30 19:25:09 UTC (rev 17379)
@@ -18,7 +18,6 @@
 	find -name '._*' -delete
 	rm -rf contrib/MetaVelvet*
 	rm -rf contrib/VelvetOptimiser*
-	rm -rf test_data.tar.*
 
 build_long_versions :
 	touch zlib
@@ -36,8 +35,6 @@
 	touch zlib # prevents the zlib in the ‘third-party’ folder to be built.
 	dh_auto_build -- OPENMP=1 CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
 	dh_auto_build -- color OPENMP=1 CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)"
-	#Pack the examples
-	tar -cvaf test_data.tar.xz data
 
 override_dh_install :
 	mkdir -p debian/$(pkg)/usr/share/man/man1/
@@ -59,9 +56,14 @@
 	[ ! -e debian/velvet-example/usr ] || \
 	    cp debian/VelvetOptimiser.README debian/velvet-example/usr/share/doc/velvet/contrib/
 
+override_dh_installexamples-indep:
+	dh_installexamples -i
+	xz -6 debian/velvet-example/usr/share/doc/velvet/examples/*
+	sed -i 's?=\.\./velvet?=/usr/bin/velvet?' debian/velvet-tests/usr/share/doc/velvet/tests/run-tests.functions
+
 #Prevent compression of user manual and sample code
 override_dh_compress :
-	dh_compress -X.pdf -X.c -X.pl -X.h
+	dh_compress -X.pdf -X.c -X.pl -X.h -X.xz
 
 override_dh_pysupport :
 	#Not needed, Python scripts are just for examples

Added: trunk/packages/velvet/trunk/debian/tests/control
===================================================================
--- trunk/packages/velvet/trunk/debian/tests/control	                        (rev 0)
+++ trunk/packages/velvet/trunk/debian/tests/control	2014-06-30 19:25:09 UTC (rev 17379)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, velvet-tests
+Restrictions: allow-stderr

Added: trunk/packages/velvet/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/velvet/trunk/debian/tests/run-unit-test	                        (rev 0)
+++ trunk/packages/velvet/trunk/debian/tests/run-unit-test	2014-06-30 19:25:09 UTC (rev 17379)
@@ -0,0 +1,12 @@
+#!/bin/sh -e
+
+pkg=velvet
+if [ "$ADTTMP" = "" ] ; then
+  ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/${pkg}/tests/* $ADTTMP
+gunzip [RS]*.gz
+chmod +x run-tests*
+./run-tests.sh
+# rm -f $ADTTMP/*

Modified: trunk/packages/velvet/trunk/debian/velvet-example.install
===================================================================
--- trunk/packages/velvet/trunk/debian/velvet-example.install	2014-06-30 15:03:51 UTC (rev 17378)
+++ trunk/packages/velvet/trunk/debian/velvet-example.install	2014-06-30 19:25:09 UTC (rev 17379)
@@ -1,2 +1,2 @@
 contrib	usr/share/doc/velvet
-test_data.tar.xz usr/share/doc/velvet/examples
+data/*	usr/share/doc/velvet/examples

Added: trunk/packages/velvet/trunk/debian/velvet-tests.install
===================================================================
--- trunk/packages/velvet/trunk/debian/velvet-tests.install	                        (rev 0)
+++ trunk/packages/velvet/trunk/debian/velvet-tests.install	2014-06-30 19:25:09 UTC (rev 17379)
@@ -0,0 +1 @@
+tests	usr/share/doc/velvet