[med-svn] r20397 - in trunk/packages/python-biopython/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Thu Nov 5 18:09:02 UTC 2015
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 <tille at debian.org> 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 <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
-
---- 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 <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/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
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