debian/0000755000000000000000000000000012151631072007164 5ustar debian/control0000644000000000000000000000436112150605151010571 0ustar Source: python-cogent Section: python Priority: extra Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille , Thorsten Alteholz Build-Depends: debhelper (>= 9), python-all-dev (>= 2.6), python-support, python-numpy (>= 1.3.0), python-sphinx, cython Standards-Version: 3.9.4 Homepage: http://pycogent.sourceforge.net/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/python-cogent/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/python-cogent/trunk/ Package: python-cogent Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends} Suggests: python-cogent-doc 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. Package: python-cogent-dbg Architecture: any Section: debug Depends: python-cogent (= ${binary:Version}), ${misc:Depends} Description: debug information for pycogent PyCogent is a software library for genomic biology. . 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. . This package is needed to improve significantly the bug reports that users may feel inclined to send. Package: python-cogent-doc Architecture: all Section: doc Depends: ${misc:Depends}, libjs-jquery, libjs-underscore Suggests: python-cogent (= ${binary:Version}) Description: docs for python-cogent PyCogent is a software library for genomic biology. . 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. . This package contains documentation and examples. debian/python-cogent-doc.install0000644000000000000000000000005612150605151014114 0ustar doc/_build/* usr/share/doc/python-cogent-doc/ debian/python-cogent.dirs0000644000000000000000000000001011630726332012641 0ustar usr/lib debian/README.source0000644000000000000000000000025311412043501011334 0ustar python-cogent for Debian -------------------------- All source is left intact, except for obvious adjustments to the shebang line to have it point to /usr/bin/python. debian/rules0000755000000000000000000000217212151631034010244 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 PKG := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') %: dh $@ --with python2 override_dh_clean: #These files are rebuilt on-the-fly for f in `find -name '*.c'` ; do \ head -n 1 "$$f" | grep -q '^/\* Generated by Cython' && rm "$$f" ; \ done rm -rf build build-stamp rm -rf doc/_build dh_clean override_dh_auto_build: dh_auto_build cd doc; $(MAKE) html # remove superfluous files and dirs rm -f doc/_build/doctrees/COGENT_LICENSE.doctree rm -f doc/_build/html/_sources/COGENT_LICENSE.txt rm -f doc/_build/html/_static/jquery.js rm -f doc/_build/html/_static/underscore.js rm -rf doc/_build/html/_images/math/ override_dh_shlibdeps: dh_shlibdeps dh_numpy override_dh_compress: dh_compress --exclude=.js --exclude=.fasta --exclude=.txt --exclude=.pdb override_dh_installdocs: dh_installdocs rm -rf debian/$(PKG)/usr/share/doc/$(PKG)/html/_sources override_dh_strip: dh_strip --dbg-package=python-cogent-dbg get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs debian/watch0000644000000000000000000000007111412043501010204 0ustar version=3 http://sf.net/pycogent/PyCogent-([.0-9]+)\.tgz debian/upstream0000644000000000000000000000134011751750156010757 0ustar Reference: Author: Knight, Rob and Maxwell, Peter and Birmingham, Amanda and Carnes, Jason and Caporaso, J Gregory and Easton, Brett C and Eaton, Michael and Hamady, Micah and Lindsay, Helen and Liu, Zongzhi and Lozupone, Catherine and McDonald, Daniel and Robeson, Michael and Sammut, Raymond and Smit, Sandra and Wakefield, Matthew J and Widmann, Jeremy and Wikman, Shandy and Wilson, Stephanie and Ying, Hua and Huttley, Gavin A Title: "PyCogent: a toolkit for making sense from sequence" Journal: Genome Biology Year: 2007 Volume: 8 Number: 8 Pages: R171 DOI: 10.1186/gb-2007-8-8-r171 PMID: 17708774 URL: http://genomebiology.com/2007/8/8/R171 eprint: http://genomebiology.com/content/pdf/gb-2007-8-8-r171.pdf debian/copyright0000644000000000000000000000445411533144302011124 0ustar This work was packaged for Debian by: Sri Girish Srinivasa Murthy and Steffen Moeller on Fri, 25 Jun 2010 17:23:58 +0200 It was downloaded from Files: * Upstream authors: Andreas Wilm Andrew Butterfield Amanda Birmingham Brett Easton Catherine Lozuopone Daniel McDonald Edward Lang Felix Schill Gavin Huttley Greg Caporaso Helen Lindsay Hua Ying Jeremy Widmann Jens Reeder Jesse Zaneveld Julia Goodrich Justin Kuczynski Kyle Bittinger Kristian Rother Matthrew Wakefield Marcin Cieslik Micah Hamady Mike Robeson Peter Maxwell Rob Knight Sandra Smit Shandy Wikman Stephanie Wilson Tianlin Wang Von Bing Yap Zongzhi Liu Copyright: Copyright 2007-2009, The Cogent Project License: GPL-2 Files: cogent/maths/matrix_invert.c cogent/maths/eigen.c (partly) Upstream author: Z. Yang Copyright: (C) 1993 Z. Yang and the University College London License: According to a mail to the Debian Med mailing list http://lists.debian.org/debian-med/2011/03/msg00006.html the author agreed to dual licensing of these two files with the original license of the PAML project: Redistribution is ok as long with proper copyright notice. It is free to use/modify/redistribute only for academia. Others need to contact the authors. and GPL-2. For the Debian packaging we choose GPL-2. Files: debian/* The Debian packaging is: Copyright (C) 2010 Sri Girish Srinivasa Murthy and Steffen Moeller and is licensed under the same copyright, see `/usr/share/common-licenses/GPL-2'. debian/pyversions0000644000000000000000000000000511533167616011336 0ustar 2.4- debian/source/0000755000000000000000000000000012150436622010467 5ustar debian/source/format0000644000000000000000000000001412125621110011663 0ustar 3.0 (quilt) debian/python-cogent.install0000644000000000000000000000001011630726332013346 0ustar usr/lib debian/changelog0000644000000000000000000001067612151631072011050 0ustar python-cogent (1.5.3-2) unstable; urgency=low * debian/rules: Add -f option to rm statements to not fail if files to be remove do not exist Closes: #710339 -- Andreas Tille Thu, 30 May 2013 13:02:05 +0200 python-cogent (1.5.3-1) unstable; urgency=low * New upstream * debian/control: use dh 9 * debian/control: set standard to 3.9.4 (no changes) * debian/rules: add get-orig-source target * debian/rules: remove some superfluous files [ Tim Booth ] * Added back python2 helper and invoked dh_numpy to sort deps * Split out docs into separate package * Added extra cleanup to dh_clean -- Thorsten Alteholz Sun, 16 May 2013 18:00:00 +0200 python-cogent (1.5.1-3) UNRELEASED; urgency=low * debian/upstream: Added citations -- Andreas Tille Mon, 07 May 2012 15:39:14 +0200 python-cogent (1.5.1-2) unstable; urgency=low * Explicitly added python-numpy as dependency to binary ... where is the dh_shlibdeps? Many thanks to Jakub (Closes: #640262). * Added build-dependency on cython after look in setup.py * Some further formatting in debian/control * Added -dbg package * Fiddled with debian/*.install to actually install the libraries and fill that -dbg package. * Added dependency to underscore.js -- Steffen Moeller Sun, 04 Sep 2011 10:49:49 +0200 python-cogent (1.5.1-1) unstable; urgency=low * New upstream version. * Reformatted debian/control description -- Steffen Moeller Sun, 21 Aug 2011 21:14:08 +0200 python-cogent (1.5-3) unstable; urgency=low * debian/control: - Remove Sri Girish Srinivasa Murthy from Uploaders - Standards-Version: 3.9.2 (no changes needed) - python-all-dev (>= 2.6) to be able to use dh_python2 * debhelper 8 (control+compat) * debian/rules: dh_python2 Finally closes: #596540 -- Andreas Tille Wed, 27 Apr 2011 09:16:52 +0200 python-cogent (1.5-2) unstable; urgency=low * debian/copyright: Clarified license of two single non-free files -> package can go to main * debian/control: - Added myself to uploaders - python-central -> python-support - Build-Depends: python-sphinx to create doc in HTML format - Depends: libjs-jquery to enable using Debian packaged version of this JS library * debian/rules: - Short dh syntax to simplyfy the following tasks - Build html doc from rst - avoid compressing used files * Removed README.Debian because the non-free issue is solved * debian/links: Link against Debian's jquery.js -- Andreas Tille Tue, 01 Mar 2011 11:30:18 +0100 python-cogent (1.5-1) unstable; urgency=low * Bumped standard to 3.9.1, no changes required. * New upstream version. - major additions to Cookbook - added AlleleFreqs attribute to ensembl Variation objects. - added getGeneByStableId method to genome objects. - added Introns attribute to Transcript objects and an Intron class. - added Mann-Whitney test and a Monte-Carlo version - exploratory and confirmatory period estimation techniques (suitable for symbolic and continuous data) - Information theoretic measures (AIC and BIC) added - drawing of trees with collapsed nodes - progress display indicator support for terminal and GUI apps - added parser for illumina HiSeq2000 and GAiix sequence files as cogent.parse.illumina_sequence.MinimalIlluminaSequenceParser. - added parser to FASTQ files, one of the output options for illumina's workflow, also added cookbook demo. - added functionality for parsing of SFF files without the Roche tools in cogent.parse.binary_sff - thousand fold performance improvement to nmds - >10-fold performance improvements to some Table operations -- Steffen Moeller Sat, 04 Dec 2010 22:30:35 +0100 python-cogent (1.4.1-1.2) unstable; urgency=low * Non-maintainer upload. * Mark package as auto-buildable -- Moritz Muehlenhoff Wed, 13 Oct 2010 20:56:27 +0200 python-cogent (1.4.1-1.1) unstable; urgency=low * Non-maintainer upload. * Replace build-dependency on python2.5-dev with python-all-dev. Closes: #596325. -- Matthias Klose Sun, 12 Sep 2010 15:18:44 +0200 python-cogent (1.4.1-1) unstable; urgency=low * Initial release (Closes: #587161) -- Sri Girish Srinivasa Murthy Sat, 24 Jul 2010 00:53:31 +0200 debian/patches/0000755000000000000000000000000012150436622010616 5ustar debian/patches/fix_python_shebang_line.patch0000644000000000000000000000544612150411760016531 0ustar Author: Steffen Moeller 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 @@ -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 @@ -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 @@ -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 @@ -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 @@ -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/patches/series0000644000000000000000000000003612125621110012020 0ustar fix_python_shebang_line.patch debian/python-cogent-doc.doc-base0000644000000000000000000000224512150605151014125 0ustar Document: python-cogent-doc Title: PyCogent documentation Author: PyCogent Team Abstract: 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. . Our primary goal is to provide a collection of rigourously validated tools for the manipulation and analysis of genome biology data sets. The project is routinely employed in numerous labs across the world and has provided essential capabilities for many high profile publications, e.g. Nature 2009 457:480-4, PNAS 2008 105:17994-9, Science 2008 320:1647-51, Nature 2008 453: 175-83 and Nat Genet 2007 39: 1261-5. Section: Science/Biology Format: HTML Index: /usr/share/doc/python-cogent-doc/html/index.html Files: /usr/share/doc/python-cogent-doc/html/*.html debian/compat0000644000000000000000000000000212150605151010360 0ustar 9