[med-svn] r3570 - in trunk/packages/python-biopython/trunk/debian: . patches
Philipp Benner
pbenner-guest at alioth.debian.org
Sun Jun 28 12:40:34 UTC 2009
Author: pbenner-guest
Date: 2009-06-28 12:40:33 +0000 (Sun, 28 Jun 2009)
New Revision: 3570
Modified:
trunk/packages/python-biopython/trunk/debian/changelog
trunk/packages/python-biopython/trunk/debian/control
trunk/packages/python-biopython/trunk/debian/patches/02-fix-wise-test.patch
trunk/packages/python-biopython/trunk/debian/patches/series
Log:
new upstream release
Modified: trunk/packages/python-biopython/trunk/debian/changelog
===================================================================
--- trunk/packages/python-biopython/trunk/debian/changelog 2009-06-27 18:28:17 UTC (rev 3569)
+++ trunk/packages/python-biopython/trunk/debian/changelog 2009-06-28 12:40:33 UTC (rev 3570)
@@ -1,10 +1,17 @@
-python-biopython (1.49-2) UNRELEASED; urgency=low
+python-biopython (1.51b-1) unstable; urgency=low
+ * New upstream release
* debian/control:
+ - moved python-martel back to section python (python packages do not
+ use section oldlibs)
+ * debian/patches/02-fix-wise-test.patch
+ - removed (merged with upstream)
+ * debian/control:
- Changed the description of python-biopython-sql according to Peter Cock's
suggestions.
+ [Charles Plessy]
- -- Charles Plessy <plessy at debian.org> Fri, 27 Mar 2009 13:55:10 +0900
+ -- Philipp Benner <pbenner at uni-osnabrueck.de> Sat, 27 Jun 2009 15:14:52 +0000
python-biopython (1.49-1) unstable; urgency=low
Modified: trunk/packages/python-biopython/trunk/debian/control
===================================================================
--- trunk/packages/python-biopython/trunk/debian/control 2009-06-27 18:28:17 UTC (rev 3569)
+++ trunk/packages/python-biopython/trunk/debian/control 2009-06-28 12:40:33 UTC (rev 3570)
@@ -12,7 +12,7 @@
# For the purpose of the tests
python-mysqldb, wise
XS-Python-Version: >= 2.3
-Standards-Version: 3.8.0
+Standards-Version: 3.8.2
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/python-biopython/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/python-biopython/trunk/
Homepage: http://biopython.org
@@ -67,7 +67,6 @@
Package: python-biopython-martel
Architecture: all
Priority: extra
-Section: oldlibs
Depends: ${python:Depends}, python-biopython
Provides: ${python:Provides}
Replaces: python2.3-biopython-martel (<< 1.42-1), python2.4-biopython-martel (<< 1.42-1)
Modified: trunk/packages/python-biopython/trunk/debian/patches/02-fix-wise-test.patch
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/02-fix-wise-test.patch 2009-06-27 18:28:17 UTC (rev 3569)
+++ trunk/packages/python-biopython/trunk/debian/patches/02-fix-wise-test.patch 2009-06-28 12:40:33 UTC (rev 3570)
@@ -1,80 +0,0 @@
-Author: Peter <biopython-bugzilla at maubp.freeserve.co.uk>
-Description: Wise output changed between 2.2.0 and 2.4.1.
- This patch makes the test pass for both versions.
-Forwarded: no
- This patch is an Upstream patch:
- http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Tests/test_Wise.py.diff?r2=1.7&cvsroot=biopython&r1=1.6&diff_format=u
-License: same as Biopython.
-
-===================================================================
-RCS file: /home/repository/biopython/biopython/Tests/test_Wise.py,v
-retrieving revision 1.6
-retrieving revision 1.7
-diff -u -r1.6 -r1.7
---- biopython/Tests/test_Wise.py 2008/11/07 11:51:18 1.6
-+++ biopython/Tests/test_Wise.py 2009/01/23 12:23:20 1.7
-@@ -3,7 +3,7 @@
- # license. Please see the LICENSE file that should have been included
- # as part of this package.
-
--__version__ = "$Revision: 1.6 $"
-+__version__ = "$Revision: 1.7 $"
-
- import cStringIO
- import doctest, unittest
-@@ -29,10 +29,12 @@
- sys.stdout = cStringIO.StringIO()
-
- def test_dnal(self):
-+ """Call dnal, and do a trivial check on its output."""
- Wise.align(["dnal"], ("seq1.fna", "seq2.fna"), kbyte=100000, dry_run=True)
- self.assert_(sys.stdout.getvalue().startswith("dnal -kbyte 100000 seq1.fna seq2.fna"))
-
- def test_psw(self):
-+ """Call psw, and do a trivial check on its output."""
- Wise.align(["psw"], ("seq1.faa", "seq2.faa"), dry_run=True, kbyte=4)
- self.assert_(sys.stdout.getvalue().startswith("psw -kbyte 4 seq1.faa seq2.faa"))
-
-@@ -41,8 +43,21 @@
-
- class TestWise(unittest.TestCase):
- def test_align(self):
-+ """Call dnal with optional arguments, and do a trivial check on the output."""
- temp_file = Wise.align(["dnal"], ("Wise/human_114_g01_exons.fna_01", "Wise/human_114_g02_exons.fna_01"), kbyte=100000, force_type="DNA", quiet=True)
-- self.assertEqual(temp_file.readline().rstrip(), "ENSG00000172135 AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCC")
-+ line = temp_file.readline().rstrip()
-+ if line == "Score 114" :
-+ #Wise 2.4.1 includes a score line, even in quiet mode, ignore this
-+ line = temp_file.readline().rstrip()
-+ if line == "ENSG00000172135 AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAGTGGGGTCCC" :
-+ #This is what we expect from wise 2.2.0 (and earlier)
-+ pass
-+ elif line == "ENSG00000172135 AGGGAAAGCCCCTAAGCTC--CTGATCTATGCTGCATCCAGTTTGCAAAG-TGGGGTCC" :
-+ #This is what we expect from wise 2.4.1
-+ pass
-+ else :
-+ #Bad!
-+ self.assert_(False, line)
-
- def run_tests(argv):
- test_suite = testing_suite()
-
-diff -u -r1.2 -r1.3
---- biopython/Tests/output/test_Wise 2005/10/23 21:24:51 1.2
-+++ biopython/Tests/output/test_Wise 2009/01/23 12:23:20 1.3
-@@ -1,11 +1,11 @@
- test_Wise
--test_dnal (test_Wise.TestWiseDryRun) ... ok
--test_psw (test_Wise.TestWiseDryRun) ... ok
--test_align (test_Wise.TestWise) ... ok
-+Call dnal, and do a trivial check on its output. ... ok
-+Call psw, and do a trivial check on its output. ... ok
-+Call dnal with optional arguments, and do a trivial check on the output. ... ok
- Doctest: Bio.Wise._build_align_cmdline ... ok
- Doctest: Bio.Wise.all_pairs ... ok
-
- ----------------------------------------------------------------------
--Ran 5 tests in 0.010s
-+Ran 5 tests in 0.070s
-
- OK
Modified: trunk/packages/python-biopython/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/series 2009-06-27 18:28:17 UTC (rev 3569)
+++ trunk/packages/python-biopython/trunk/debian/patches/series 2009-06-28 12:40:33 UTC (rev 3570)
@@ -1,2 +1 @@
01-enable-mmCIF.patch
-02-fix-wise-test.patch
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