[med-svn] r16391 - in trunk/packages/python-biopython/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2014-03-05 14:33:34 +0000 (Wed, 05 Mar 2014)
New Revision: 16391

Added:
   trunk/packages/python-biopython/trunk/debian/patches/
   trunk/packages/python-biopython/trunk/debian/patches/fix_test_emboss.patch
   trunk/packages/python-biopython/trunk/debian/patches/series
Modified:
   trunk/packages/python-biopython/trunk/debian/README.source
   trunk/packages/python-biopython/trunk/debian/control
   trunk/packages/python-biopython/trunk/debian/rules
Log:
Enable more testing and fix Emboss test


Modified: trunk/packages/python-biopython/trunk/debian/README.source
===================================================================
--- trunk/packages/python-biopython/trunk/debian/README.source	2014-03-05 10:36:44 UTC (rev 16390)
+++ trunk/packages/python-biopython/trunk/debian/README.source	2014-03-05 14:33:34 UTC (rev 16391)
@@ -41,4 +41,8 @@
              http://xxmotif.genzentrum.lmu.de/index.php?id=download
 
 
+The test test_Phylo_CDAO for Python3 also needs python3-rdflib, but this is
+currently only avialable in experimental, so this will be ignored for the
+moment.
+
  -- Andreas Tille <tille at debian.org>  Tue, 04 Mar 2014 11:16:02 +0100

Modified: trunk/packages/python-biopython/trunk/debian/control
===================================================================
--- trunk/packages/python-biopython/trunk/debian/control	2014-03-05 10:36:44 UTC (rev 16390)
+++ trunk/packages/python-biopython/trunk/debian/control	2014-03-05 14:33:34 UTC (rev 16391)
@@ -30,9 +30,16 @@
                python-mysqldb,
                python-matplotlib,
                python3-matplotlib,
+               python-numpy,
+               python3-numpy,
+               python-pil,
+               python3-pil,
                python-rdflib,
+               python-renderpm,
+               python3-renderpm,
                python-psycopg2,
                python3-psycopg2,
+               raxml,
                t-coffee,
                wise
 Standards-Version: 3.9.5

Added: trunk/packages/python-biopython/trunk/debian/patches/fix_test_emboss.patch
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/fix_test_emboss.patch	                        (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/patches/fix_test_emboss.patch	2014-03-05 14:33:34 UTC (rev 16391)
@@ -0,0 +1,11 @@
+--- a/Tests/test_Emboss.py
++++ b/Tests/test_Emboss.py
+@@ -73,6 +73,8 @@ def get_emboss_version():
+     assert stderr is None  # Send to stdout instead
+     for line in stdout.split("\n"):
+         if line.strip()=="Reports the current EMBOSS version number":
++           pass
++        elif line.strip()=="Report the current EMBOSS version number":
+             pass
+         elif line.startswith("Writes the current EMBOSS version number"):
+             pass

Added: trunk/packages/python-biopython/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/patches/series	2014-03-05 14:33:34 UTC (rev 16391)
@@ -0,0 +1 @@
+fix_test_emboss.patch

Modified: trunk/packages/python-biopython/trunk/debian/rules
===================================================================
--- trunk/packages/python-biopython/trunk/debian/rules	2014-03-05 10:36:44 UTC (rev 16390)
+++ trunk/packages/python-biopython/trunk/debian/rules	2014-03-05 14:33:34 UTC (rev 16391)
@@ -29,6 +29,8 @@
 		    ; do \
 	    mv Tests/test_$${avoid}.py Tests_avoid ; \
 	done
-	dh_auto_test -- --test --system=custom --test-args='env PYTHONPATH={build_dir} {interpreter} setup.py test'
+	# in the Debian package dialign it is not needed to set DIALIGN2_DIR but the test is verifying this dir 
+	# to run the EMBOSS test test_Emboss also requires to have the environment variable EMBOSS_ROOT set
+	dh_auto_test -- --test --system=custom --test-args='env DIALIGN2_DIR=/usr/share/dialign EMBOSS_ROOT=/usr/lib/emboss PYTHONPATH={build_dir} {interpreter} setup.py test'
 	mv Tests_avoid/* Tests
 	rmdir Tests_avoid