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 <[email protected]> +Author: Peter Cock <[email protected]> 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 <[email protected]> +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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
