[med-svn] r3041 - in trunk/packages/python-biopython/trunk/debian: . patches

[plessy at alioth.debian.org]

Author: plessy
Date: 2009-01-23 12:46:31 +0000 (Fri, 23 Jan 2009)
New Revision: 3041

Added:
   trunk/packages/python-biopython/trunk/debian/patches/02-fix-wise-test.patch
Modified:
   trunk/packages/python-biopython/trunk/debian/changelog
   trunk/packages/python-biopython/trunk/debian/patches/series
Log:
Added a patch that prevents the tests from failing with Debian's version of Wise.


Modified: trunk/packages/python-biopython/trunk/debian/changelog
===================================================================
--- trunk/packages/python-biopython/trunk/debian/changelog	2009-01-23 07:30:47 UTC (rev 3040)
+++ trunk/packages/python-biopython/trunk/debian/changelog	2009-01-23 12:46:31 UTC (rev 3041)
@@ -24,6 +24,8 @@
     - debian/control: build-depends on quilt.
   * debian/python-biopython-doc.doc-base: corrected index name that was changed
     upstream.
+  * debian/patches/02-fix-wise-test.patch: prevents tests failing with Debian's
+    version of Wise.
   * debian/rules: perform tests after build.
 
  -- Charles Plessy <plessy at debian.org>  Thu, 15 Jan 2009 13:15:44 +0900

Added: trunk/packages/python-biopython/trunk/debian/patches/02-fix-wise-test.patch
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/02-fix-wise-test.patch	                        (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/patches/02-fix-wise-test.patch	2009-01-23 12:46:31 UTC (rev 3041)
@@ -0,0 +1,61 @@
+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()
+

Modified: trunk/packages/python-biopython/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/series	2009-01-23 07:30:47 UTC (rev 3040)
+++ trunk/packages/python-biopython/trunk/debian/patches/series	2009-01-23 12:46:31 UTC (rev 3041)
@@ -1 +1,2 @@
 01-enable-mmCIF.patch
+02-fix-wise-test.patch