[med-svn] r20101 - in trunk/packages/python-biopython/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-09-23 11:45:24 +0000 (Wed, 23 Sep 2015)
New Revision: 20101

Added:
   trunk/packages/python-biopython/trunk/debian/patches/fix_test_phyml_tool.patch
Modified:
   trunk/packages/python-biopython/trunk/debian/changelog
   trunk/packages/python-biopython/trunk/debian/clean
   trunk/packages/python-biopython/trunk/debian/control
   trunk/packages/python-biopython/trunk/debian/patches/series
Log:
Build-Depends & Suggests: phylip + fixed test_phyml_tool


Modified: trunk/packages/python-biopython/trunk/debian/changelog
===================================================================
--- trunk/packages/python-biopython/trunk/debian/changelog	2015-09-23 08:49:52 UTC (rev 20100)
+++ trunk/packages/python-biopython/trunk/debian/changelog	2015-09-23 11:45:24 UTC (rev 20101)
@@ -1,3 +1,11 @@
+python-biopython (1.65+dfsg-2) UNRELEASED; urgency=medium
+
+  * Build-Depends & Suggests: phylip + fixed test_phyml_tool
+    Closes: #799820
+  * debian/clean: Remove test results occuring now since phylip can be used
+
+ -- Andreas Tille <tille at debian.org>  Wed, 23 Sep 2015 10:34:47 +0200
+
 python-biopython (1.65+dfsg-1) unstable; urgency=medium
 
   * New upstream version

Modified: trunk/packages/python-biopython/trunk/debian/clean
===================================================================
--- trunk/packages/python-biopython/trunk/debian/clean	2015-09-23 08:49:52 UTC (rev 20100)
+++ trunk/packages/python-biopython/trunk/debian/clean	2015-09-23 11:45:24 UTC (rev 20101)
@@ -4,4 +4,8 @@
 Tests/Clustalw/temp*
 Tests/Graphics/*.*
 Tests/output.*
+Tests/Phylip/interlaced2.phy_phyml_*
+Tests/TreeConstruction/bootstrap_consensus.tre
+Tests/TreeConstruction/pars1.tre
+Tests/TreeConstruction/pars2.tre
 debian/tmp_tests

Modified: trunk/packages/python-biopython/trunk/debian/control
===================================================================
--- trunk/packages/python-biopython/trunk/debian/control	2015-09-23 08:49:52 UTC (rev 20100)
+++ trunk/packages/python-biopython/trunk/debian/control	2015-09-23 11:45:24 UTC (rev 20101)
@@ -23,6 +23,7 @@
                mafft,
                muscle,
                ncbi-blast+,
+               phylip,
                phyml,
                prank,
                probcons,
@@ -65,6 +66,7 @@
           fasttree,
           mafft,
           muscle,
+          phylip,
           phyml,
           prank,
           probcons,
@@ -114,6 +116,7 @@
           fasttree,
           mafft,
           muscle,
+          phylip,
           phyml,
           prank,
           probcons,

Added: trunk/packages/python-biopython/trunk/debian/patches/fix_test_phyml_tool.patch
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/fix_test_phyml_tool.patch	                        (rev 0)
+++ trunk/packages/python-biopython/trunk/debian/patches/fix_test_phyml_tool.patch	2015-09-23 11:45:24 UTC (rev 20101)
@@ -0,0 +1,18 @@
+Author: Andreas Tille <tille at debian.org>
+Bug-Debian: https://bugs.debian.org/799820
+Forwarded: yes
+Last-Update: Wed, 23 Sep 2015 10:34:47 +0200
+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
+@@ -47,7 +47,7 @@ class AppTests(unittest.TestCase):
+             self.assertTrue(len(out) > 0)
+             self.assertEqual(len(err), 0)
+             # Check the output tree
+-            tree = Phylo.read(EX_PHYLIP + '_phyml_tree.txt', 'newick')
++            tree = Phylo.read(EX_PHYLIP + '_phyml_tree', 'newick')
+             self.assertEqual(tree.count_terminals(), 4)
+         finally:
+             # Clean up generated files

Modified: trunk/packages/python-biopython/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/series	2015-09-23 08:49:52 UTC (rev 20100)
+++ trunk/packages/python-biopython/trunk/debian/patches/series	2015-09-23 11:45:24 UTC (rev 20101)
@@ -1,3 +1,4 @@
 remove_mathml-qname.patch
 fix_broken_test.patch
 privacy_breach.patch
+fix_test_phyml_tool.patch