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 <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
