[med-svn] r16810 - trunk/packages/python-cogent/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2014-04-25 19:24:19 +0000 (Fri, 25 Apr 2014)
New Revision: 16810

Modified:
   trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit.patch
   trunk/packages/python-cogent/trunk/debian/patches/fix_python_shebang_line.patch
   trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps.patch
Log:
Refreshed patches


Modified: trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit.patch
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit.patch	2014-04-25 19:20:55 UTC (rev 16809)
+++ trunk/packages/python-cogent/trunk/debian/patches/accept_newer_cdhit.patch	2014-04-25 19:24:19 UTC (rev 16810)
@@ -4,8 +4,8 @@
  a temporary file sitting around.  This patch has only been quickly tested and
  there may be deeper issues.
 
---- a/cogent/app/cd_hit.py
-+++ b/cogent/app/cd_hit.py
+--- PyCogent-1.5.3.orig/cogent/app/cd_hit.py
++++ PyCogent-1.5.3/cogent/app/cd_hit.py
 @@ -257,7 +257,10 @@
      # perform cleanup
      res.cleanUp()

Modified: trunk/packages/python-cogent/trunk/debian/patches/fix_python_shebang_line.patch
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/fix_python_shebang_line.patch	2014-04-25 19:20:55 UTC (rev 16809)
+++ trunk/packages/python-cogent/trunk/debian/patches/fix_python_shebang_line.patch	2014-04-25 19:24:19 UTC (rev 16810)
@@ -1,59 +1,47 @@
 Author: Steffen Moeller <moeller at debian.org>
 Description: fix path to python interpreter
-Index: PyCogent-1.5.1/cogent/align/dp_calculation.py
-===================================================================
---- PyCogent-1.5.1.orig/cogent/align/dp_calculation.py	2011-06-06 18:10:17.000000000 +0200
-+++ PyCogent-1.5.1/cogent/align/dp_calculation.py	2011-08-22 00:16:56.362987354 +0200
+--- PyCogent-1.5.3.orig/cogent/align/dp_calculation.py
++++ PyCogent-1.5.3/cogent/align/dp_calculation.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env/python
 +#!/usr/bin/python
  
  from cogent.maths.markov import SiteClassTransitionMatrix
  from cogent.recalculation.definition import PositiveParamDefn, \
-Index: PyCogent-1.5.1/cogent/data/molecular_weight.py
-===================================================================
---- PyCogent-1.5.1.orig/cogent/data/molecular_weight.py	2011-06-06 18:10:17.000000000 +0200
-+++ PyCogent-1.5.1/cogent/data/molecular_weight.py	2011-08-22 00:16:56.362987354 +0200
+--- PyCogent-1.5.3.orig/cogent/data/molecular_weight.py
++++ PyCogent-1.5.3/cogent/data/molecular_weight.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env Python
 +#!/usr/bin/python
  """Data for molecular weight calculations on proteins and nucleotides."""
  
  __author__ = "Rob Knight"
-Index: PyCogent-1.5.1/cogent/format/text_tree.py
-===================================================================
---- PyCogent-1.5.1.orig/cogent/format/text_tree.py	2011-06-06 18:10:17.000000000 +0200
-+++ PyCogent-1.5.1/cogent/format/text_tree.py	2011-08-22 00:16:56.362987354 +0200
+--- PyCogent-1.5.3.orig/cogent/format/text_tree.py
++++ PyCogent-1.5.3/cogent/format/text_tree.py
 @@ -1,4 +1,4 @@
 -#!/bin/env python
 +#!/usr/bin/python
  # file text_tree.py
  """Simple base text representation of phylo tree."""
  
-Index: PyCogent-1.5.1/cogent/recalculation/__init__.py
-===================================================================
---- PyCogent-1.5.1.orig/cogent/recalculation/__init__.py	2011-06-06 18:10:17.000000000 +0200
-+++ PyCogent-1.5.1/cogent/recalculation/__init__.py	2011-08-22 00:16:56.362987354 +0200
+--- PyCogent-1.5.3.orig/cogent/recalculation/__init__.py
++++ PyCogent-1.5.3/cogent/recalculation/__init__.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/envthon
 +#!/usr/bin/python
  __all__ = ['array', 'calculation', 'definition', 'scope', 'setting']
  
  __author__ = "Peter Maxwell"
-Index: PyCogent-1.5.1/cogent/recalculation/setting.py
-===================================================================
---- PyCogent-1.5.1.orig/cogent/recalculation/setting.py	2011-06-06 18:10:17.000000000 +0200
-+++ PyCogent-1.5.1/cogent/recalculation/setting.py	2011-08-22 00:16:56.362987354 +0200
+--- PyCogent-1.5.3.orig/cogent/recalculation/setting.py
++++ PyCogent-1.5.3/cogent/recalculation/setting.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python'
 +#!/usr/bin/python
  """Instances of these classes are assigned to different parameter/scopes
  by a parameter controller"""
  
-Index: PyCogent-1.5.1/cogent/phylo/maximum_likelihood.py
-===================================================================
---- PyCogent-1.5.1.orig/cogent/phylo/maximum_likelihood.py	2011-08-22 00:17:10.787058879 +0200
-+++ PyCogent-1.5.1/cogent/phylo/maximum_likelihood.py	2011-08-22 00:17:24.395127334 +0200
+--- PyCogent-1.5.3.orig/cogent/phylo/maximum_likelihood.py
++++ PyCogent-1.5.3/cogent/phylo/maximum_likelihood.py
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env python'
 +#!/usr/bin/python

Modified: trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps.patch
===================================================================
--- trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps.patch	2014-04-25 19:20:55 UTC (rev 16809)
+++ trunk/packages/python-cogent/trunk/debian/patches/parsinsert_not_in_caps.patch	2014-04-25 19:24:19 UTC (rev 16810)
@@ -3,8 +3,8 @@
 Description: make script compatible with spelling of Debian's
  parsinsert package
 
---- a/cogent/app/parsinsert.py
-+++ b/cogent/app/parsinsert.py
+--- PyCogent-1.5.3.orig/cogent/app/parsinsert.py
++++ PyCogent-1.5.3/cogent/app/parsinsert.py
 @@ -28,7 +28,7 @@
  class ParsInsert(CommandLineApplication):
      """ParsInsert application Controller"""