debian/0000755000000000000000000000000012213273625007171 5ustar debian/epigrass.manpages0000644000000000000000000000001311416562007012514 0ustar debian/*.1 debian/control0000644000000000000000000000416312157554224010604 0ustar Source: epigrass Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Torsten Werner , Varun Hiremath , Charles Plessy , Andreas Tille , Thorsten Alteholz Build-Depends: debhelper (>= 9), python (>= 2.6), python-setuptools, python-support, python-virtualenv, python-sqlsoup, python-redis Standards-Version: 3.9.4 Homepage: http://pypi.python.org/pypi/epigrass/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/epigrass/trunk/ Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/epigrass/trunk/ Package: epigrass Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, python-sqlobject (>= 0.12.4-2), python-visual, python-qt4-gl, python-qwt5-qt4 (>= 5.2.0), python-numpy, python-gdal, python-formencode, python-mysqldb, python-pysqlite2, python-matplotlib, python-networkx, python-pkg-resources, python-sqlalchemy, python-sqlsoup, python-redis, redis-server Suggests: grass, epigrass-doc, kate Description: scientific tool for simulations and scenario analysis in network epidemiology Epigrass is a software for visualizing, analyzing and simulating of epidemic processes on geo-referenced networks. . EpiGrass can interact with the GRASS GIS from which it can obtain maps and other geo-referenced information. However, EpiGrass does not require an installation of the GRASS GIS for most of its features. Package: epigrass-doc Architecture: all Section: doc Depends: ${misc:Depends} Enhances: epigrass Description: Documentation for EpiGrass, a network epidemiology tool Epigrass is a software for visualizing, analyzing and simulating of epidemic processes on geo-referenced networks. . EpiGrass can interact with the GRASS GIS from which it can obtain maps and other geo-referenced information. However, EpiGrass does not require an installation of the GRASS GIS for most of its features. . This package contains the documentation. debian/epigrass.10000644000000000000000000000140511416562007011067 0ustar .TH epigrass 1 "December 4, 2006" .SH NAME epigrass - scientific tool for simulations and scenario analysis in network epidemiology .SH DESCRIPTION .PP Epigrass is a software for visualizing, analyzing and simulating of epidemic processes on geo-referenced networks. EpiGrass can interact with the GRASS GIS from which it can obtain maps and other geo-referenced information. However, EpiGrass does not require an installation of the GRASS GIS for most of its features. .PP .SH DOCUMENTATION HTML documentation is available here: http://epigrass.sourceforge.net/userguide/index.html .SH HOMEPAGE http://model-builder.sourceforge.net/ .SH AUTHOR This manual page was written by Varun Hiremath , for the Debian project (but may be used by others). debian/epirunner.10000644000000000000000000000172711416562007011270 0ustar .TH EPIRUNNER "1" "March 2010" "epirunner 2.0a1" "User Commands" .SH NAME epirunner \- command line version of Epigrass .SH SYNOPSIS .B epirunner [\fIoptions\fR] \fIyour_model.epg\fR .SH DESCRIPTION This is a command line version of Epigrass. With it you can run models without invoking the GUI. It’s great for batch simulations and for remote use. .SH OPTIONS .TP \fB\-\-version\fR show program's version number and exit .TP \fB\-h\fR, \fB\-\-help\fR show this help message and exit .TP \fB\-b\fR , \fB\-\-backend=\fR Define which datastorage backend to use .TP \fB\-u\fR DBUSER, \fB\-\-dbusername\fR=\fIDBUSER\fR MySQL user name .TP \fB\-p\fR DBPASS, \fB\-\-password\fR=\fIDBPASS\fR MySQL password for user .TP \fB\-H\fR DBHOST, \fB\-\-dbhost\fR=\fIDBHOST\fR MySQL hostname or IP address .SH SEE ALSO epigrass(1) .SH AUTHOR This manual page was written by Andreas Tille , for the Debian project (but may be used by others). debian/README.source0000644000000000000000000000033411416562007011347 0ustar This packages uses a patch system. Please read /usr/share/doc/quilt/README.source for more informations. New upstream releases are temporarly stored in the Python Package Index, but will come back to SourceForge later. debian/epgeditor.10000644000000000000000000000112212213273612011225 0ustar .TH epgeditor 1 "March 26, 2010" .SH NAME epgeditor - graphical editor of .epg models for epigrass .SH SYNOPSIS .B epgeditor \fIyour_model.epg\fR .SH DESCRIPTION .PP Epigrass is a software for visualizing, analyzing and simulating of epidemic processes on geo-referenced networks. Epgeditor is graphical editor of .epg models. A easy way to edit already existing models. It contains detailed explanations of every section of the EPG file. .SH SEE ALSO epigrass(1) .SH AUTHOR This manual page was written by Andreas Tille , for the Debian project (but may be used by others). debian/epigrass-doc.doc-base0000644000000000000000000000065212146711423013151 0ustar Document: epigrass Title: Epigrass Documentation Author: Flavio Codeco Coelho Abstract: Epigrass is a framework for the construction and simulation of complex network epidemiology models. At least this is its main vocation. However, Epigrass can be used to simulate any dynamical system on a set of nodes (connected into a network or not!). Section: Text Format: PDF Files: /usr/share/doc/epigrass-doc/Epigrass.pdf.gz debian/rules0000755000000000000000000000041412146711423010246 0ustar #!/usr/bin/make -f %: dh $@ --with python2 # override_dh_clean: # *.pyc files should be cleaned in principle, but are part of upstream tarball # rm -f Epigrass/*.pyc get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --destdir=../tarballs debian/watch0000644000000000000000000000040311416562007010216 0ustar version=3 # opts="dversionmangle=s/([\d.abc]+)~dfsg/$1/" \ http://pypi.python.org/packages/source/e/epigrass/epigrass-(.*).tar.gz # Sources will come back on SourceForge later. In the meantime, they are there: # http://sf.net/epigrass/ epigrass-(.*).tar.gz \ debian/upstream0000644000000000000000000000111711724071634010756 0ustar Contact: Flavio Codeco Coelho Homepage: http://epigrass.sourceforge.net/ Name: EpiGrass Watch: http://pypi.python.org/packages/source/e/epigrass/epigrass-(.*).tar.gz Reference: author: Coelho, Flavio and Cruz, Oswaldo and Codeco, Claudia DOI: 10.1186/1751-0473-3-3 title: "Epigrass: a tool to study disease spread in complex networks" journal: Source Code for Biology and Medicine volume: 3 year: 2008 number: 1 pages: 3 PMID: 18302744 URL: http://www.scfbm.org/content/3/1/3 ISSN: 1751-0473 debian/copyright0000644000000000000000000000302412157554224011127 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: EpiGrass Upstream-Contact: Flávio Codeço Coelho , Cláudia Torres Codeço Source: http://pypi.python.org/pypi/epigrass/ Files: * Copyright: © 2006-2010, Flávio Codeço Coelho License: GPL-2+ This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . On Debian systems, you can find the GPL license version 2 in: /usr/share/common-licenses/GPL-2 Files: Epigrass/pylabQtcanvas.py Copyright: © 2005, Florent Rougon License: PD This file is an example program for matplotlib. It may be used and modified with no restriction; raw copies as well as modified versions may be distributed without limitation. Files: debian/* Copyright: © 2006–2008, Varun Hiremath © 2007, Torsten Werner © 2008–2009, Charles Plessy © 2009-2011, Andreas Tille © 2013, Thorsten Alteholz License: GPL-2+ see above debian/pyversions0000644000000000000000000000000511162722325011326 0ustar 2.4- debian/source/0000755000000000000000000000000012166732140010470 5ustar debian/source/format0000644000000000000000000000001411416562007011676 0ustar 3.0 (quilt) debian/epigrass.desktop0000644000000000000000000000036212157554224012406 0ustar [Desktop Entry] Name=Epigrass Comment=Epidemics Simulator GenericName=Epidemics Simulator Exec=epigrass Icon=/usr/share/pixmaps/egigrass.png Type=Application StartupNotify=false Terminal=false Categories=Education;Science; Keywords=Medicine; debian/changelog0000644000000000000000000001512712213273625011051 0ustar epigrass (2.3.1-1) unstable; urgency=low [ Thorsten Alteholz ] * new upstream version * debian/control: change VCS-* according to lintian * debian/control: new dependency on redis-server needed * debian/copyright: take care of lintian complaints * debian/epigrass.desktop: add keywords from debtags of package [ Andreas Tille ] * Adapted patches to latest upstream version (remove redis-version.patch) * Upload new version since python-sqlsoup is available Closes: #717738 * Fixed typo in manpage -- Andreas Tille Mon, 09 Sep 2013 09:10:02 +0200 epigrass (2.2.2-1) unstable; urgency=low * new upstream version * debian/control: Standards-Version: 3.9.4 (no changes needed) * debian/control: swith to dh 9 * debian/rules: make get-orig-source compatible with svn-buildpackage * debian/control: remove duplicate Depends: on python-visual * debian/control: remove dependency on quilt * debian/control: add new dependency on python-visual * debian/copyright: add correct Format: line -- Thorsten Alteholz Thu, 16 May 2013 17:00:00 +0200 epigrass (2.0.4-3) unstable; urgency=low * debian/control: Homepage has changed to http://pypi.python.org/pypi/epigrass/ * debian/copyright: - some adaptations to DEP5 - New download location * debian/epigrass.links: Link to usable icon for desktop file Closes: #640005 -- Andreas Tille Fri, 28 Oct 2011 15:28:35 +0200 epigrass (2.0.4-2) unstable; urgency=low * debian/control: Depends: python-pkg-resources Closes: #640098 * Standards-Version: 3.9.2 (no changes needed) * Fixed Vcs fields * Debhelper 8 (control+compat) * debian/rules: Switch to dh_python2 -- Andreas Tille Fri, 28 Oct 2011 14:54:25 +0200 epigrass (2.0.4-1) unstable; urgency=low * New upstream version * debian/control: - Standards-Version: 3.9.1 (no changes needed) - Removed XS-Python-Version fields which is unneeded if using pysupport -- Andreas Tille Tue, 23 Nov 2010 11:55:45 +0100 epigrass (2.0.3-1) unstable; urgency=low * New upstream version * Upstream source now includes source for the PDF documentation and thus there is no need for stripping the source tarball any more. -> rm debian/orig-tar.sh, adapted debian/watch -> rm debian/README.Debian which talks about missing source for doc * debian/patches/desktop.diff: removed, because debian/epigras.desktop is used anyway instead of the patched upstream desktop file * debian/control: additional package epigrass-doc - Standards-Version: 3.9.0 (no changes needed) - Increased versioned debhelper dependency to >= 7.1 - Increase version numnber of python-sqlobject to >= 0.12.4-2 before in a former version egg info was broken - Depends: python-networkx * Replace debian/references by debian/upstream-metadata.yaml * debian/rules: Do not try to edit pyshared files -- Andreas Tille Fri, 09 Jul 2010 14:46:45 +0200 epigrass (2.0.1~dfsg-1) unstable; urgency=low * New upstream version * Standards-Version: 3.8.4 (no changes needed) * debian/orig-tar.sh: Do not only exclude sourceless PDF file but also remove cruft (*.pyc, *~) from tarball which is deleted by clean target anyway and breaks build process if it remains in tarball * debian/patches/series: Do not apply setup.diff any more because the affected line is commented in new upstream setup.py so it seems to become useless * Standards-Version: 3.8.4 (no changes needed) * Depends: python-sqlobject (>= 0.12) * debian/source/format: 3.0 (quilt) * debian/{epirunner,epgeditor}.1: Man pages for new tools -- Andreas Tille Thu, 25 Mar 2010 08:04:17 +0100 epigrass (2.0b3~dfsg-2) unstable; urgency=low * Fixed watch file * Standards-Version: 3.8.3 (no changes needed) * Bumped versioned Depends python-qwt5-qt4 (>= 5.2.0) (otherwise epigrass is crashing) -- Andreas Tille Tue, 06 Oct 2009 14:18:27 +0200 epigrass (2.0b3~dfsg-1) unstable; urgency=low [ Charles Plessy ] * New upstream release (LP: #271789). * debian/control: - Switch to debhelper 7 (also in debian/compat). - Dropped versionned dependency on CDBS (satisfied even in oldstable) - Incremented Standards-Version to 3.8.1 to reflect concordance with latest Policy (added README.source). - Added myself to the Uploaders. - Suggests: grass. - Depends: python-qt4-gl (instead of python-qt3) and python-qwt5-qt4. * debian/watch: updated to look in the Python Package Index. * debian/patches refreshed and documented: - desktop.diff: added MedicalSoftware category and kept Education because at least one Main Category must be supported. - setup.diff (deletion of sourceless documentation). - sqlite3.diff (purpose not understood yet). * debian/copyright updated and converted to machine-readable format * debian/reference copied from http://www.scfbm.org/content/3/1/3/citation and abstract (CC-BY-2.0) removed. [ Andreas Tille ] * Added myself to Uploaders * debian/watch: dversionmangle * debian/orig-tar.sh: Append '~dfsg' to upstream version [ Varun Hiremath ] * debian/control: Add versioned depends on python-qwt5-qt4 (>= 5.1.0.dfsg-2), which fixes a bug related to Qwt import. -- Varun Hiremath Thu, 07 May 2009 22:51:36 -0400 epigrass (1.5.1-4) unstable; urgency=low * debian/control: - Depends on python-matplotlib (Closes: #509863, LP: #295625). - Added myself to Uploaders. -- Charles Plessy Sun, 28 Dec 2008 13:32:04 +0100 epigrass (1.5.1-3) unstable; urgency=low * Change Build-Depends: python-central (>= 0.6.0) (Closes: #472034) * debian/rules: Support new directory structure of python-central -- Varun Hiremath Sat, 22 Mar 2008 21:12:49 +0530 epigrass (1.5.1-2) unstable; urgency=low * Move package to debian-med on alioth * Set Debian-Med Packaging Team as Maintainer * Add myself and Torsten to Uploaders * Set new Vcs-{Svn, Browser} and Homepage headers * Bump Standards-Version to 3.7.3 * Add desktop.diff patch to fix upstream desktop file * Add some missing dependencies * Cleanup debian/rules -- Varun Hiremath Wed, 27 Feb 2008 21:59:52 +0530 epigrass (1.5.1-1) unstable; urgency=low * new upstream version -- Torsten Werner Fri, 05 Oct 2007 21:32:41 +0200 epigrass (1.4.7-1) unstable; urgency=low * Initial release (Closes: #401577) -- Varun Hiremath Mon, 4 Dec 2006 23:54:51 +0530 debian/patches/0000755000000000000000000000000012213273273010617 5ustar debian/patches/sqlite3.diff0000644000000000000000000000052012213273273013032 0ustar Author: Author: V. Hiremath Puropose: ? Forwarded: no License: same as Epigrass itself. --- a/Epigrass/manager.py +++ b/Epigrass/manager.py @@ -19,7 +19,9 @@ import report as Rp import epigdal import json import __version__ -import sqlite3, MySQLdb +import MySQLdb +from pysqlite2 import dbapi2 as sqlite3 + #import pycallgraph debian/patches/series0000644000000000000000000000001512213273216012025 0ustar sqlite3.diff debian/compat0000644000000000000000000000000212146711423010365 0ustar 9 debian/epigrass.install0000644000000000000000000000012012157554224012373 0ustar usr debian/epigrass.desktop usr/share/applications demos usr/share/doc/epigrass debian/epigrass-doc.docs0000644000000000000000000000002711353133525012420 0ustar docs/build/latex/*.pdf debian/epigrass.links0000644000000000000000000000010611672621061012044 0ustar usr/share/pyshared/Epigrass/egicon.png usr/share/pixmaps/egigrass.png