[med-svn] r19273 - in trunk/packages/python-cogent/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-05-21 06:51:16 +0000 (Thu, 21 May 2015)
New Revision: 19273

Added:
   trunk/packages/python-cogent/trunk/debian/patches/cd-hit.patch
Modified:
   trunk/packages/python-cogent/trunk/debian/changelog
   trunk/packages/python-cogent/trunk/debian/patches/series
Log:
Adapt to the naming scheme of cd-hit inside Debian


Modified: trunk/packages/python-cogent/trunk/debian/changelog
===================================================================
--- trunk/packages/python-cogent/trunk/debian/changelog	2015-05-21 06:42:36 UTC (rev 19272)
+++ trunk/packages/python-cogent/trunk/debian/changelog	2015-05-21 06:51:16 UTC (rev 19273)
@@ -7,8 +7,10 @@
   * DEP3
   * README.source removed since redundant
   * cme fix dpkg-control
+  * Adapt to the naming scheme of cd-hit inside Debian
+    Closes: #730515
 
- -- Andreas Tille <tille at debian.org>  Fri, 25 Apr 2014 20:40:39 +0200
+ -- Andreas Tille <tille at debian.org>  Thu, 21 May 2015 08:47:01 +0200
 
 python-cogent (1.5.3-2biolinux1) trusty; urgency=low
 

Added: trunk/packages/python-cogent/trunk/debian/patches/cd-hit.patch
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/cd-hit.patch	                        (rev 0)
+++ trunk/packages/python-cogent/trunk/debian/patches/cd-hit.patch	2015-05-21 06:51:16 UTC (rev 19273)
@@ -0,0 +1,52 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 21 May 2015 08:47:01 +0200
+Bug-Debian: http://bugs.debian.org/730515
+Description: cd-hit-est is cdhit-est in Debian
+ As the bug log shows cd-hit upstream was contacted about a consistent
+ naming scheme.  Since there was no answer I decided to keep the latest
+ upstream naming scheme of cd-hit and adapt pyython-cogent (which is known
+ to lag behind upstream changes (see raxml_unsupported_version.patch)
+
+--- a/cogent/app/cd_hit.py
++++ b/cogent/app/cd_hit.py
+@@ -201,7 +201,7 @@ class CD_HIT_EST(CD_HIT):
+     Use this version of CD-HIT if your MolType is PROTEIN
+     """
+ 
+-    _command = 'cd-hit-est'
++    _command = 'cdhit-est'
+     _input_handler = '_input_as_multiline_string'
+     _parameters = CD_HIT._parameters
+     _parameters.update({\
+--- a/tests/test_app/test_cd_hit.py
++++ b/tests/test_app/test_cd_hit.py
+@@ -58,24 +58,24 @@ class CD_HIT_EST_Tests(TestCase):
+         """CD_HIT_EST BaseCommand should return the correct BaseCommand"""
+         c = CD_HIT_EST()
+         self.assertEqual(c.BaseCommand,\
+-            ''.join(['cd "',getcwd(),'/"; ','cd-hit-est']))
++            ''.join(['cd "',getcwd(),'/"; ','cdhit-est']))
+         c.Parameters['-i'].on('seq.txt')
+         self.assertEqual(c.BaseCommand,\
+-            ''.join(['cd "',getcwd(),'/"; ','cd-hit-est -i "seq.txt"']))
++            ''.join(['cd "',getcwd(),'/"; ','cdhit-est -i "seq.txt"']))
+         c.Parameters['-c'].on(0.8)
+         self.assertEqual(c.BaseCommand,\
+-            ''.join(['cd "',getcwd(),'/"; ','cd-hit-est -c 0.8' +
++            ''.join(['cd "',getcwd(),'/"; ','cdhit-est -c 0.8' +
+             ' -i "seq.txt"']))
+ 
+     def test_changing_working_dir(self):
+         """CD_HIT_EST BaseCommand should change according to WorkingDir"""
+         c = CD_HIT_EST(WorkingDir='/tmp/cdhitest_test')
+         self.assertEqual(c.BaseCommand,\
+-            ''.join(['cd "','/tmp/cdhitest_test','/"; ','cd-hit-est']))
++            ''.join(['cd "','/tmp/cdhitest_test','/"; ','cdhit-est']))
+         c = CD_HIT_EST()
+         c.WorkingDir = '/tmp/cdhitest_test2'
+         self.assertEqual(c.BaseCommand,\
+-            ''.join(['cd "','/tmp/cdhitest_test2','/"; ','cd-hit-est']))
++            ''.join(['cd "','/tmp/cdhitest_test2','/"; ','cdhit-est']))
+ 
+         #removing the dirs is proof that they were created at the same time
+         #if the dirs are not there, an OSError will be raised

Modified: trunk/packages/python-cogent/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/series	2015-05-21 06:42:36 UTC (rev 19272)
+++ trunk/packages/python-cogent/trunk/debian/patches/series	2015-05-21 06:51:16 UTC (rev 19273)
@@ -6,3 +6,4 @@
 fasttree_not_in_caps.patch
 raxml_unsupported_version.patch
 # debug_tests.patch
+cd-hit.patch