[med-svn] r20109 - in trunk/packages/python-biopython/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-09-23 19:59:21 +0000 (Wed, 23 Sep 2015)
New Revision: 20109

Added:
   trunk/packages/python-biopython/trunk/debian/patches/fix_test_mafft_tool.patch
Modified:
   trunk/packages/python-biopython/trunk/debian/patches/fix_broken_test.patch
   trunk/packages/python-biopython/trunk/debian/patches/series
   trunk/packages/python-biopython/trunk/debian/rules
Log:
Fix for mafft test


Modified: trunk/packages/python-biopython/trunk/debian/patches/fix_broken_test.patch
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/fix_broken_test.patch	2015-09-23 14:50:42 UTC (rev 20108)
+++ trunk/packages/python-biopython/trunk/debian/patches/fix_broken_test.patch	2015-09-23 19:59:21 UTC (rev 20109)
@@ -1,4 +1,4 @@
-Author: Peter Cock <notifications at github.com>
+Author: Peter Cock <p.j.a.cock at googlemail.com>
 Last-Update: Mon, 11 May 2015 07:38:41 -0700
 Description: Corner case for absolute vs relative paths (issue #541) 
   https://github.com/biopython/biopython/commit/cf54c6c5a99be1127fdbd839ea01067ffc21f302?diff=unified

Added: trunk/packages/python-biopython/trunk/debian/patches/fix_test_mafft_tool.patch
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/fix_test_mafft_tool.patch	                        (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/patches/fix_test_mafft_tool.patch	2015-09-23 19:59:21 UTC (rev 20109)
@@ -0,0 +1,23 @@
+From: Author: Peter Cock <p.j.a.cock at googlemail.com>
+Last-Update: Wed, 23 Sep 2015 16:24:03 +0100
+Subject: Tweak test_Mafft_tool.py for Mafft v7.245
+ https://github.com/biopython/biopython/commit/dad073bc78109b926ea8de35f4140f9afc0953df
+
+---
+ Tests/test_Mafft_tool.py | 5 ++++-
+ 1 file changed, 4 insertions(+), 1 deletion(-)
+
+--- a/Tests/test_Mafft_tool.py
++++ b/Tests/test_Mafft_tool.py
+@@ -83,7 +83,10 @@ class MafftApplication(unittest.TestCase
+         self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
+         stdoutdata, stderrdata = cmdline()
+         self.assertTrue(stdoutdata.startswith(">gi|1348912|gb|G26680|G26680"))
+-        self.assertTrue("Progressive alignment ..." in stderrdata, stderrdata)
++        # Used to get "Progressive alignment ..." but in v7.245
++        # became "Progressive alignment 1/2..." and "Progressive alignment 2/2..."
++        self.assertTrue(("Progressive alignment ..." in stderrdata) or
++                        ("Progressive alignment 1/" in stderrdata), stderrdata)
+         self.assertTrue("$#=0" not in stderrdata)
+ 
+     def test_Mafft_with_options(self):

Modified: trunk/packages/python-biopython/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/series	2015-09-23 14:50:42 UTC (rev 20108)
+++ trunk/packages/python-biopython/trunk/debian/patches/series	2015-09-23 19:59:21 UTC (rev 20109)
@@ -2,3 +2,4 @@
 fix_broken_test.patch
 privacy_breach.patch
 fix_test_phyml_tool.patch
+fix_test_mafft_tool.patch

Modified: trunk/packages/python-biopython/trunk/debian/rules
===================================================================
--- trunk/packages/python-biopython/trunk/debian/rules	2015-09-23 14:50:42 UTC (rev 20108)
+++ trunk/packages/python-biopython/trunk/debian/rules	2015-09-23 19:59:21 UTC (rev 20109)
@@ -34,8 +34,8 @@
 # This would not trigger a failure but bloats the build log with irrelevant noise
 EXCLUDEDATABASE=BioSQL_MySQLdb BioSQL_psycopg2
 
-# FIXME: These tests are failing for unknown reasons and this needs to be investigated
-EXCLUDEFAILINGTESTS=Mafft_tool
+# No need to exclude any tests any more
+EXCLUDEFAILINGTESTS=
 
 # FIXME: Currently it is not sure for what architecture samtools will be available
 #        to anable a smooth migration to testing the build-dependency will be dropped