[med-svn] r22092 - in trunk/packages/conservation-code/trunk/debian: . patches

[Tatiana Malygina]

Author: latticetower-guest
Date: 2016-06-06 09:58:21 +0000 (Mon, 06 Jun 2016)
New Revision: 22092

Added:
   trunk/packages/conservation-code/trunk/debian/patches/fix_load_identity_matrix
Modified:
   trunk/packages/conservation-code/trunk/debian/changelog
   trunk/packages/conservation-code/trunk/debian/patches/series
Log:
fixed upstream - add import statementr when alignment matrix not found

Modified: trunk/packages/conservation-code/trunk/debian/changelog
===================================================================
--- trunk/packages/conservation-code/trunk/debian/changelog	2016-06-06 08:54:40 UTC (rev 22091)
+++ trunk/packages/conservation-code/trunk/debian/changelog	2016-06-06 09:58:21 UTC (rev 22092)
@@ -3,6 +3,8 @@
   * Team upload
   [ Tatiana Malygina ]
   * add draft autopkgtest
+  * fixed example file in test + added test with error in matrix path
+  * upstream fix - to load identity matrix without error when no alignment matrix is found
 
   [ Andreas Tille ]
   * install link to /usr/bin rather than copy of Python file

Added: trunk/packages/conservation-code/trunk/debian/patches/fix_load_identity_matrix
===================================================================
--- trunk/packages/conservation-code/trunk/debian/patches/fix_load_identity_matrix	                        (rev 0)
+++ trunk/packages/conservation-code/trunk/debian/patches/fix_load_identity_matrix	2016-06-06 09:58:21 UTC (rev 22092)
@@ -0,0 +1,13 @@
+Author: Tatiana Malygina <merlettaia at gmail.com>
+Last-Update: 2016-06-06
+Description: add import statement before identity method call
+--- conservation-code-20110309.0.orig/score_conservation.py
++++ conservation-code-20110309.0/score_conservation.py
+@@ -544,6 +544,7 @@
+ 
+     except IOError, e:
+ 	print( "Could not load similarity matrix: %s. Using identity matrix..." % sm_file, file=sys.stderr )
++	from numpy import identity
+ 	return identity(20)
+ 	
+     # if matrix is stored in lower tri form, copy to upper

Modified: trunk/packages/conservation-code/trunk/debian/patches/series
===================================================================
--- trunk/packages/conservation-code/trunk/debian/patches/series	2016-06-06 08:54:40 UTC (rev 22091)
+++ trunk/packages/conservation-code/trunk/debian/patches/series	2016-06-06 09:58:21 UTC (rev 22092)
@@ -6,3 +6,4 @@
 stockholm_format
 Python3-prints
 usage
+fix_load_identity_matrix