[med-svn] r19215 - in trunk/packages/python-biopython/trunk/debian: . patches

[Andreas Tille]

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 <tille at debian.org>  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 <notifications at github.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
+
+--- 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