[med-svn] r7518 - in trunk/packages/python-cogent/trunk/debian: . patches

Steffen Möller moeller at alioth.debian.org
Sun Aug 21 22:53:57 UTC 2011 

Author: moeller
Date: 2011-08-21 22:53:57 +0000 (Sun, 21 Aug 2011)
New Revision: 7518

Modified:
   trunk/packages/python-cogent/trunk/debian/changelog
   trunk/packages/python-cogent/trunk/debian/control
   trunk/packages/python-cogent/trunk/debian/patches/fix_python_shebang_line.patch
Log:
Update to 1.5.1 of python-cogent


Modified: trunk/packages/python-cogent/trunk/debian/changelog
===================================================================
--- trunk/packages/python-cogent/trunk/debian/changelog	2011-08-21 21:41:29 UTC (rev 7517)
+++ trunk/packages/python-cogent/trunk/debian/changelog	2011-08-21 22:53:57 UTC (rev 7518)
@@ -1,3 +1,10 @@
+python-cogent (1.5.1-1) unstable; urgency=low
+
+  * New upstream version.
+  * Reformatted debian/control description
+
+ -- Steffen Moeller <moeller at debian.org>  Sun, 21 Aug 2011 21:14:08 +0200
+
 python-cogent (1.5-3) unstable; urgency=low
 
   * debian/control:

Modified: trunk/packages/python-cogent/trunk/debian/control
===================================================================
--- trunk/packages/python-cogent/trunk/debian/control	2011-08-21 21:41:29 UTC (rev 7517)
+++ trunk/packages/python-cogent/trunk/debian/control	2011-08-21 22:53:57 UTC (rev 7518)
@@ -16,9 +16,12 @@
 Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, libjs-jquery
 Description: framework for genomic biology
  PyCogent is a software library for genomic biology. It is a fully
- integrated and thoroughly tested framework for: controlling third-party
- applications; devising workflows; querying databases; conducting novel
- probabilistic analyses of biological sequence evolution; and generating
- publication quality graphics. It is distinguished by many unique built-in
- capabilities (such as true codon alignment) and the frequent addition
- of entirely new methods for the analysis of genomic data.
+ integrated and thoroughly tested framework for:
+ * controlling third-party applications,
+ * devising workflows; querying databases,
+ * conducting novel probabilistic analyses of biological sequence
+   evolution, and
+ * generating publication quality graphics.
+ It is distinguished by many unique built-in capabilities (such as true codon
+ alignment) and the frequent addition of entirely new methods for the analysis
+ of genomic data.

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	2011-08-21 21:41:29 UTC (rev 7517)
+++ trunk/packages/python-cogent/trunk/debian/patches/fix_python_shebang_line.patch	2011-08-21 22:53:57 UTC (rev 7518)
@@ -1,67 +1,60 @@
-Index: python-cogent-1.4.1/cogent/align/dp_calculation.py
+Index: PyCogent-1.5.1/cogent/align/dp_calculation.py
 ===================================================================
---- python-cogent-1.4.1.orig/cogent/align/dp_calculation.py	2010-06-25 18:29:53.790029187 +0200
-+++ python-cogent-1.4.1/cogent/align/dp_calculation.py	2010-06-25 18:29:58.700028486 +0200
+--- 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
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env/python
 +#!/usr/bin/python
  
  from cogent.maths.markov import SiteClassTransitionMatrix
  from cogent.recalculation.definition import PositiveParamDefn, \
-Index: python-cogent-1.4.1/cogent/data/molecular_weight.py
+Index: PyCogent-1.5.1/cogent/data/molecular_weight.py
 ===================================================================
---- python-cogent-1.4.1.orig/cogent/data/molecular_weight.py	2010-06-25 18:29:27.460027576 +0200
-+++ python-cogent-1.4.1/cogent/data/molecular_weight.py	2010-06-25 18:29:33.790026526 +0200
+--- 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
 @@ -1,4 +1,4 @@
 -#!/usr/bin/env Python
 +#!/usr/bin/python
  """Data for molecular weight calculations on proteins and nucleotides."""
  
  __author__ = "Rob Knight"
-Index: python-cogent-1.4.1/cogent/format/text_tree.py
+Index: PyCogent-1.5.1/cogent/format/text_tree.py
 ===================================================================
---- python-cogent-1.4.1.orig/cogent/format/text_tree.py	2010-06-25 18:26:20.110027538 +0200
-+++ python-cogent-1.4.1/cogent/format/text_tree.py	2010-06-25 18:26:30.180027920 +0200
+--- 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
 @@ -1,4 +1,4 @@
 -#!/bin/env python
 +#!/usr/bin/python
  # file text_tree.py
  """Simple base text representation of phylo tree."""
  
-Index: python-cogent-1.4.1/cogent/phylo/maximum_likelihood.py
+Index: PyCogent-1.5.1/cogent/recalculation/__init__.py
 ===================================================================
---- python-cogent-1.4.1.orig/cogent/phylo/maximum_likelihood.py	2010-06-25 18:27:03.970027345 +0200
-+++ python-cogent-1.4.1/cogent/phylo/maximum_likelihood.py	2010-06-25 18:27:48.590027730 +0200
+--- 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
 @@ -1,4 +1,4 @@
--#!/usr/bin/env python'
-+#!/usr/bin/python
- from tree_space import TreeEvaluator, ancestry2tree
- from least_squares import WLS
- from math import exp
-@@ -68,4 +68,4 @@
-         return LogLikelihoodScoredTreeCollection(results)
-     
- 
--    
-\ No newline at end of file
-+    
-Index: python-cogent-1.4.1/cogent/recalculation/__init__.py
-===================================================================
---- python-cogent-1.4.1.orig/cogent/recalculation/__init__.py	2010-06-25 18:28:36.420027396 +0200
-+++ python-cogent-1.4.1/cogent/recalculation/__init__.py	2010-06-25 18:28:42.280028115 +0200
-@@ -1,4 +1,4 @@
 -#!/usr/bin/envthon
 +#!/usr/bin/python
  __all__ = ['array', 'calculation', 'definition', 'scope', 'setting']
  
  __author__ = "Peter Maxwell"
-Index: python-cogent-1.4.1/cogent/recalculation/setting.py
+Index: PyCogent-1.5.1/cogent/recalculation/setting.py
 ===================================================================
---- python-cogent-1.4.1.orig/cogent/recalculation/setting.py	2010-06-25 18:27:33.160026774 +0200
-+++ python-cogent-1.4.1/cogent/recalculation/setting.py	2010-06-25 18:27:42.830027966 +0200
+--- 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
 @@ -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
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python'
++#!/usr/bin/python
+ from tree_space import TreeEvaluator, ancestry2tree
+ from least_squares import WLS
+ from math import exp

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