[med-svn] r16702 - in trunk/packages/staden-io-lib/trunk/debian: . tests

Mon Apr 14 15:58:57 UTC 2014

Author: tille
Date: 2014-04-14 15:58:57 +0000 (Mon, 14 Apr 2014)
New Revision: 16702

Added:
   trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-examples.install
   trunk/packages/staden-io-lib/trunk/debian/tests/
   trunk/packages/staden-io-lib/trunk/debian/tests/control
   trunk/packages/staden-io-lib/trunk/debian/tests/run-unit-test
Modified:
   trunk/packages/staden-io-lib/trunk/debian/changelog
   trunk/packages/staden-io-lib/trunk/debian/control
   trunk/packages/staden-io-lib/trunk/debian/rules
Log:
use dh-autoreconf; Add autopkgtest using new staden-io-lib-examples package


Modified: trunk/packages/staden-io-lib/trunk/debian/changelog
===================================================================

--- trunk/packages/staden-io-lib/trunk/debian/changelog	2014-04-14 07:26:28 UTC (rev 16701)
+++ trunk/packages/staden-io-lib/trunk/debian/changelog	2014-04-14 15:58:57 UTC (rev 16702)
@@ -1,3 +1,12 @@
+staden-io-lib (1.13.5-2) UNRELEASED; urgency=medium
+
+  * use dh-autoreconf
+    Closes: 744664
+  * Add autopkgtest using new staden-io-lib-examples package
+    
+
+ -- Andreas Tille <tille at debian.org>  Mon, 14 Apr 2014 13:08:48 +0200
+
 staden-io-lib (1.13.5-1.1) unstable; urgency=medium
 
   * Non-maintainer upload.

Modified: trunk/packages/staden-io-lib/trunk/debian/control
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/control	2014-04-14 07:26:28 UTC (rev 16701)
+++ trunk/packages/staden-io-lib/trunk/debian/control	2014-04-14 15:58:57 UTC (rev 16702)
@@ -4,9 +4,10 @@
            Andreas Tille <tille at debian.org>,
            Thorsten Alteholz <debian at alteholz.de>
 Section: science
+XS-Testsuite: autopkgtest
 Priority: optional
 Build-Depends: debhelper (>= 9),
-               autotools-dev,
+               dh-autoreconf,
                zlib1g-dev,
                libcurl4-gnutls-dev | libcurl4-nss-dev,
                d-shlibs
@@ -58,3 +59,20 @@
  code to provide a general purpose trace file (and Experiment File) reading
  interface. It has been compiled and tested on a variety of unix systems,
  MacOS X and MS Windows.
+
+Package: staden-io-lib-examples
+Architecture: all
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: programs for maniuplating DNA sequencing files
+ The io_lib from the Staden package is a library of file reading and writing
+ code to provide a general purpose trace file (and Experiment File) reading
+ interface. It has been compiled and tested on a variety of unix systems,
+ MacOS X and MS Windows.
+ .
+ This package contains the programs that are distributed with the Staden io_lib
+ for manipulating and converting sequencing data files, and in particular files
+ to maniuplate short reads generated by second and third generation sequencers
+ and stored in SRF format.
+ .
+ This package contains example data and a test suite to test the data.

Modified: trunk/packages/staden-io-lib/trunk/debian/rules
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/rules	2014-04-14 07:26:28 UTC (rev 16701)
+++ trunk/packages/staden-io-lib/trunk/debian/rules	2014-04-14 15:58:57 UTC (rev 16702)
@@ -3,11 +3,12 @@
 libpkg=libstaden-read
 devpkg=$(libpkg)-dev
 #version=$(shell dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d- )
-#utils=staden-io-lib-utils
+srcname=staden-io-lib
+testdir=debian/$(srcname)-examples/usr/share/doc/$(srcname)/test
 #mandir=$(CURDIR)/debian/$(utils)/usr/share/man/man1/
 
 %:
-	dh $@ --with autotools_dev
+	dh $@ --with autoreconf
 
 override_dh_install:
 	dh_install
@@ -30,7 +31,18 @@
 	#	 --name='filter SRF files for various purposes' \
 	#	 --version-string="$(version)" \
 	#	 $(CURDIR)/debian/$(utils)/usr/bin/srf_filter > $(mandir)/srf_filter.1
+	mkdir -p $(testdir)
+        # fix path to staden-io-lib executable in examples
+	for tst in `ls tests/*.test` ; do \
+	    sed 's#$$top_builddir/progs/#/usr/bin/#' $${tst} > $(testdir)/`basename $${tst}` ; \
+	done
+	# remove autogenerated big data files
+	rm -f $(testdir)/data/ce\#*sorted.sam
 
+override_dh_fixperms:
+	dh_fixperms
+	chmod +x $(testdir)/*.test $(testdir)/*.pl
+
 override_dh_auto_clean:
 	dh_auto_clean
 	rm -f tests/.done tests/data/ce\#sorted.sam tests/data/ce\#unsorted.sam

Added: trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-examples.install
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-examples.install	                        (rev 0)
+++ trunk/packages/staden-io-lib/trunk/debian/staden-io-lib-examples.install	2014-04-14 15:58:57 UTC (rev 16702)
@@ -0,0 +1,2 @@
+tests/*.pl	usr/share/doc/staden-io-lib/test
+tests/data	usr/share/doc/staden-io-lib/test

Added: trunk/packages/staden-io-lib/trunk/debian/tests/control
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/tests/control	                        (rev 0)
+++ trunk/packages/staden-io-lib/trunk/debian/tests/control	2014-04-14 15:58:57 UTC (rev 16702)
@@ -0,0 +1,3 @@
+Tests: run-unit-test
+Depends: @, staden-io-lib-utils, smalt-examples
+Restrictions: allow-stderr

Added: trunk/packages/staden-io-lib/trunk/debian/tests/run-unit-test
===================================================================
--- trunk/packages/staden-io-lib/trunk/debian/tests/run-unit-test	                        (rev 0)
+++ trunk/packages/staden-io-lib/trunk/debian/tests/run-unit-test	2014-04-14 15:58:57 UTC (rev 16702)
@@ -0,0 +1,18 @@
+#!/bin/sh -e
+
+if [ "$ADTTMP" = "" ] ; then
+  ADTTMP=`mktemp -d /tmp/staden-io-lib-test.XXXXXX`
+fi
+cd $ADTTMP
+cp -a /usr/share/doc/staden-io-lib/test/* $ADTTMP
+gunzip data/*.gz
+
+TESTS=`ls *.test`
+OUTDIR=./test.out
+LOGFILE=`basename $0`.log
+
+mkdir -p $OUTDIR
+for tst in $TESTS ; do
+    srcdir=. outdir=$OUTDIR $tst > $LOGFILE
+done
+


Property changes on: trunk/packages/staden-io-lib/trunk/debian/tests/run-unit-test
___________________________________________________________________
Added: svn:executable
   + *


