Author: tille Date: 2015-05-11 18:54:12 +0000 (Mon, 11 May 2015) New Revision: 19215
Added: trunk/packages/python-biopython/trunk/debian/patches/fix_broken_test.patch Modified: trunk/packages/python-biopython/trunk/debian/changelog trunk/packages/python-biopython/trunk/debian/patches/series Log: Apply fix for broken test from Upstream Git Modified: trunk/packages/python-biopython/trunk/debian/changelog =================================================================== --- trunk/packages/python-biopython/trunk/debian/changelog 2015-05-11 15:14:35 UTC (rev 19214) +++ trunk/packages/python-biopython/trunk/debian/changelog 2015-05-11 18:54:12 UTC (rev 19215) @@ -1,6 +1,7 @@ python-biopython (1.65+dfsg-1) UNRELEASED; urgency=medium * New upstream version + * Apply fix for broken test from Upstream Git -- Andreas Tille <[email protected]> Sat, 09 May 2015 07:13:03 +0200 Added: trunk/packages/python-biopython/trunk/debian/patches/fix_broken_test.patch =================================================================== --- trunk/packages/python-biopython/trunk/debian/patches/fix_broken_test.patch (rev 0) +++ trunk/packages/python-biopython/trunk/debian/patches/fix_broken_test.patch 2015-05-11 18:54:12 UTC (rev 19215) @@ -0,0 +1,53 @@ +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) ++ Modified: trunk/packages/python-biopython/trunk/debian/patches/series =================================================================== --- trunk/packages/python-biopython/trunk/debian/patches/series 2015-05-11 15:14:35 UTC (rev 19214) +++ trunk/packages/python-biopython/trunk/debian/patches/series 2015-05-11 18:54:12 UTC (rev 19215) @@ -1 +1,2 @@ remove_mathml-qname.patch +fix_broken_test.patch _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
