Author: tille Date: 2015-11-05 18:09:01 +0000 (Thu, 05 Nov 2015) New Revision: 20397
Removed: trunk/packages/python-biopython/trunk/debian/patches/fix_broken_test.patch trunk/packages/python-biopython/trunk/debian/patches/fix_test_mafft_tool.patch Modified: trunk/packages/python-biopython/trunk/debian/changelog trunk/packages/python-biopython/trunk/debian/patches/fix_test_phyml_tool.patch trunk/packages/python-biopython/trunk/debian/patches/series Log: Remove patches applied upstream Modified: trunk/packages/python-biopython/trunk/debian/changelog =================================================================== --- trunk/packages/python-biopython/trunk/debian/changelog 2015-11-05 18:02:30 UTC (rev 20396) +++ trunk/packages/python-biopython/trunk/debian/changelog 2015-11-05 18:09:01 UTC (rev 20397) @@ -1,3 +1,9 @@ +python-biopython (1.66+dfsg-1) UNRELEASED; urgency=medium + + * New upstream version (some patches applied upstream) + + -- Andreas Tille <[email protected]> Wed, 04 Nov 2015 17:16:51 +0100 + python-biopython (1.65+dfsg-3) unstable; urgency=medium * Also run Tutorial test Deleted: trunk/packages/python-biopython/trunk/debian/patches/fix_broken_test.patch =================================================================== --- trunk/packages/python-biopython/trunk/debian/patches/fix_broken_test.patch 2015-11-05 18:02:30 UTC (rev 20396) +++ trunk/packages/python-biopython/trunk/debian/patches/fix_broken_test.patch 2015-11-05 18:09:01 UTC (rev 20397) @@ -1,53 +0,0 @@ -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 - ---- a/Tests/test_SeqIO_index.py -+++ b/Tests/test_SeqIO_index.py -@@ -257,16 +257,34 @@ if sqlite3: - expt_sff_files) - - def test_some_abs(self): -- """Check absolute filenames in index.""" -+ """Check absolute filenames in index. -+ -+ Unless the repository and tests themselves are under the temp -+ directory (as detected by ``tempfile``), we expect the index to -+ use absolute filenames. -+ """ - h, t = tempfile.mkstemp(prefix="index_test_", suffix=".idx") - os.close(h) - os.remove(t) - -- expt_sff_files = [os.path.abspath("Roche/E3MFGYR02_no_manifest.sff"), -- os.path.abspath("Roche/greek.sff"), -- os.path.abspath(os.path.join("Roche", "paired.sff"))] -- # All absolute paths... -- self.check(t, expt_sff_files, expt_sff_files) -+ abs_sff_files = [os.path.abspath("Roche/E3MFGYR02_no_manifest.sff"), -+ os.path.abspath("Roche/greek.sff"), -+ os.path.abspath(os.path.join("Roche", "paired.sff"))] -+ -+ if os.getcwd().startswith(os.path.dirname(t)): -+ # The tests are being run from within the temp directory, -+ # e.g. index filename /tmp/index_test_XYZ.idx -+ # and working directory of /tmp/biopython/Tests/ -+ # This means the indexing will use a RELATIVE path -+ # e.g. biopython/Tests/Roche/E3MFGYR02_no_manifest.sff -+ # not /tmp/biopython/Tests/Roche/E3MFGYR02_no_manifest.sff -+ expt_sff_files = [os.path.relpath(f, os.path.dirname(t)) -+ for f in abs_sff_files] -+ else: -+ expt_sff_files = abs_sff_files -+ -+ # Providing absolute paths... -+ self.check(t, abs_sff_files, expt_sff_files) - # Now try with mix of abs and relative paths... - self.check(t, - [os.path.abspath("Roche/E3MFGYR02_no_manifest.sff"), -@@ -646,3 +664,4 @@ for filename, format, alphabet in tests: - if __name__ == "__main__": - runner = unittest.TextTestRunner(verbosity=2) - unittest.main(testRunner=runner) -+ Deleted: trunk/packages/python-biopython/trunk/debian/patches/fix_test_mafft_tool.patch =================================================================== --- trunk/packages/python-biopython/trunk/debian/patches/fix_test_mafft_tool.patch 2015-11-05 18:02:30 UTC (rev 20396) +++ trunk/packages/python-biopython/trunk/debian/patches/fix_test_mafft_tool.patch 2015-11-05 18:09:01 UTC (rev 20397) @@ -1,23 +0,0 @@ -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/fix_test_phyml_tool.patch =================================================================== --- trunk/packages/python-biopython/trunk/debian/patches/fix_test_phyml_tool.patch 2015-11-05 18:02:30 UTC (rev 20396) +++ trunk/packages/python-biopython/trunk/debian/patches/fix_test_phyml_tool.patch 2015-11-05 18:09:01 UTC (rev 20397) @@ -5,8 +5,8 @@ Description: Fix test_phyml_tool.py Remove ".txt" extention that should not be there ---- python-biopython-1.65+dfsg.orig/Tests/test_phyml_tool.py -+++ python-biopython-1.65+dfsg/Tests/test_phyml_tool.py +--- a/Tests/test_phyml_tool.py ++++ b/Tests/test_phyml_tool.py @@ -47,7 +47,7 @@ class AppTests(unittest.TestCase): self.assertTrue(len(out) > 0) self.assertEqual(len(err), 0) Modified: trunk/packages/python-biopython/trunk/debian/patches/series =================================================================== --- trunk/packages/python-biopython/trunk/debian/patches/series 2015-11-05 18:02:30 UTC (rev 20396) +++ trunk/packages/python-biopython/trunk/debian/patches/series 2015-11-05 18:09:01 UTC (rev 20397) @@ -1,5 +1,3 @@ remove_mathml-qname.patch -fix_broken_test.patch privacy_breach.patch fix_test_phyml_tool.patch -fix_test_mafft_tool.patch _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
