debian/0000755000000000000000000000000012152357570007175 5ustar debian/compat0000644000000000000000000000000211420212742010357 0ustar 7 debian/PyMB.10000644000000000000000000001206311420212742010054 0ustar .TH model-builder 1 "December 4, 2006" .SH NAME model-builder - graphical ODE simulator .SH DESCRIPTION .PP Model Builder is a graphical ODE simulator. It allows the user to define, simulate and analyze arbitrary systems of Ordinary Diferential Equations. .PP .SH Features .PP * Equation-based model definition. No need to learn to program to define and run your models. Just type-in you differential equations .PP * Graphic output of simulation. You can save the graphics in the most common formats: png, svg, pdf, etc. .PP * Spreadsheet view of the results. From the spreadsheet you can make customized plots from your variables. You can also export your data to a .csv text file .PP * Latex rendering of your system of equations. Check you equation in clear mathematical notation. .PP * Intuitive graphical interface. .PP * Uncertainty analysis module. Implements a straightforward interface for the Bayesian Melding method. .PP * Sensitivity analysis. Find out how sensitive your model is to variations in parameter values. .PP .SH GETTING STARTED The best way to get started with ModelBuilder is open one of the models included with the distribution and look at it . Yes, it's that simple. So, if you have already intalled it, start Model-Builder by typing in the console: $ PyMB followed by . This will start Model-Buider . From now on I will assume that you know what a system of differential equations is, otherwise you probably should not be using Model-Builder. The larger box on the main frame, labeled "Differential Equations" is where we are going to start. On this text box you will write your system of equations (or a single equation) The syntax is that of python for mathematical expressions and functions and there are some conventions also, which I will explain below: .PP * First of all, Model-Builder expects only the right-hand-side (RHS) of you equations to be present one per line in the equations box. The LHS is assumed to be of the form dy(t)/dt, dy_i/dt where i is an index to the the number of equations in your model. This number i will be used to refer to the state variables of the model ( y[i] ). This index, i, MUST start at 0, so if your model has 3 equations, their state variables will be y[0], y[1], and y[2] . .PP * Another convention is the reference to model parameters. Any number of parameters may be included in the equations by the using this nomeclature: p[0], p[1], and so on. These parameter must the be specified one per line and in ascending order in the "Parameters" box. So the first line would be the definition of p[0], the second of p[1] and so forth. .PP * The mathematical expressions that make up the equations and the parameters may include any function of the numpy python module. This allows for the easy contruction of models with a level of sophistication higher than that of a simple algebraic expression. Time may be referenced in the equations or parameter expressions by the variable "t". So if you want a parameter that is a function of time, you can simply write in the parameter box. .PP * The user familiar with python will also be able to include more advanced structures in the model specification, such as Lambda functions for instance. Well, with that out of the way, it remains to explain the rest of the interface which is pretty much self-explanatory: .PP * The initial values box should include one number for each equation (line) in the equations box. The numbers should be separated by spaces. .PP * The start time is the time value at which the equations begin to be evaluated. The values of the state variables at this point in time are those specified in the initial conditions. .PP * End time: You can figure this one out... .PP * Time step: this is the time-step used in reporting the output of the simulation. The actual time step used by the numeric integrator is variable and chosen on the fly. Its normally much finer that what you specify here. .PP * Critical time steps. Most user wil leave this box empty. .PP * First Step: The size of the first step. Leave at 0 for automatic determination. .PP * Min Step Size and Max Step Size: Respectively the minimum and maximum value for step sizes as chosen by variable step size algorithm. Leave at zero for automatic determination. .PP * Full Output check box: If this box is checked a lot of useful information about the integration is included in the output. Check out the output spreadsheet to see what they are. .PP * Show convergence message: if this box is checked, ModelBuilder will print "Integration successful" to the console after the integration is completed. Useful for debugging purposes only. Uncheck if you are doing uncertainty analyses. as it will slow things down. .PP * Once you are done entering the necessary information for you model, Just press the start button to calculate your model. Enjoy! .PP .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/patches/0000755000000000000000000000000012013305205010604 5ustar debian/patches/setup.diff0000644000000000000000000000216511420212742012606 0ustar Description: Fix installation files diff -urN Model-Builder-0.4.0.orig/setup.py Model-Builder-0.4.0/setup.py --- Model-Builder-0.4.0.orig/setup.py 2007-04-10 20:57:25.000000000 +0530 +++ Model-Builder-0.4.0/setup.py 2007-04-10 21:06:09.000000000 +0530 @@ -33,5 +33,5 @@ entry_points = {'gui_scripts':['PyMB = model_builder.PyMB:main',]}, packages = ['model_builder','model_builder/Bayes'], package_data = {'':['MB*','*.pdf','*.desktop'],'model_builder':['Docs/*.pdf', 'model-builder.desktop']}, - data_files=[('/usr/share/pixmaps',['model_builder/MB.ico']),('/usr/share/applications',['model_builder/model-builder.desktop']),('/usr/share/model-builder/examples',glob.glob("model_builder/Examples/*.ode")),('/usr/share/model-builder/docs',['model_builder/Docs/Quick-start.pdf'])], + data_files=[('/usr/share/pixmaps',['model_builder/MB.ico']),('/usr/share/applications',['model_builder/model-builder.desktop']),('/usr/share/doc/model-builder/examples',glob.glob("model_builder/Examples/*.ode")),('/usr/share/model-builder/help',glob.glob('model_builder/*.html')+glob.glob('model_builder/MB.*'))], ) debian/patches/use_wx2.8.diff0000644000000000000000000001701112013305064013203 0ustar Description: use wxversion 2.8 instead of 2.6 Index: model-builder-0.4.1/model_builder/about.py =================================================================== --- model-builder-0.4.1.orig/model_builder/about.py 2008-01-22 13:57:53.000000000 -0500 +++ model-builder-0.4.1/model_builder/about.py 2012-08-16 20:01:47.599831181 -0400 @@ -1,6 +1,6 @@ #Boa:Dialog:wxDialog1 import wxversion -wxversion.select('2.6') +wxversion.select('2.8') import wx import wx.html import webbrowser Index: model-builder-0.4.1/model_builder/icones.py =================================================================== --- model-builder-0.4.1.orig/model_builder/icones.py 2006-12-08 14:49:14.000000000 -0500 +++ model-builder-0.4.1/model_builder/icones.py 2012-08-16 20:01:47.599831181 -0400 @@ -3,7 +3,7 @@ # This file was generated by /usr/bin/img2py-2.6 # import wxversion -wxversion.select('2.6') +wxversion.select('2.8') from wx import ImageFromStream, BitmapFromImage import cStringIO, zlib Index: model-builder-0.4.1/model_builder/lhsframe_glade.py =================================================================== --- model-builder-0.4.1.orig/model_builder/lhsframe_glade.py 2006-12-08 14:48:44.000000000 -0500 +++ model-builder-0.4.1/model_builder/lhsframe_glade.py 2012-08-16 20:01:47.603831062 -0400 @@ -2,7 +2,7 @@ # -*- coding: ISO-8859-1 -*- # generated by wxGlade 0.3.5.1 on Thu Aug 31 11:12:37 2006 import wxversion -wxversion.select('2.6') +wxversion.select('2.8') import wx import wx.grid Index: model-builder-0.4.1/model_builder/lhsframe.py =================================================================== --- model-builder-0.4.1.orig/model_builder/lhsframe.py 2008-01-22 13:39:01.000000000 -0500 +++ model-builder-0.4.1/model_builder/lhsframe.py 2012-08-16 20:01:47.603831062 -0400 @@ -12,7 +12,7 @@ # New field: Whatever #----------------------------------------------------------------------------- import wxversion -wxversion.select('2.6') +wxversion.select('2.8') import wx import os,cPickle from Bayes import lhs, Melding as meld Index: model-builder-0.4.1/model_builder/odexml.py =================================================================== --- model-builder-0.4.1.orig/model_builder/odexml.py 2007-06-25 13:13:50.000000000 -0400 +++ model-builder-0.4.1/model_builder/odexml.py 2012-08-16 20:01:47.603831062 -0400 @@ -13,7 +13,7 @@ from xml.dom import minidom, Node import __version__ as V import wxversion -wxversion.select('2.6') +wxversion.select('2.8') import wx, sys, os from numpy import array Index: model-builder-0.4.1/model_builder/PlotFigure.py =================================================================== --- model-builder-0.4.1.orig/model_builder/PlotFigure.py 2007-03-26 15:47:31.000000000 -0400 +++ model-builder-0.4.1/model_builder/PlotFigure.py 2012-08-16 20:01:47.603831062 -0400 @@ -3,7 +3,7 @@ # Name: PlotFigure.py # Purpose: Plotting frame that contains the plots generated by Model Buider # -# Author: Flavio C. Coelho +# Author: Flavio C. Coelho # # Created: 2004/09/01 # RCS-ID: $Id: PlotFigure.py,v 1.1 2004/01/13 10:51:43 fccoelho Exp $ @@ -22,7 +22,7 @@ from matplotlib.figure import Figure from matplotlib.axes import Subplot -import matplotlib.numerix as numpy +#import matplotlib.numerix as numpy #from RandomArray import * #from numpy.random.old import * from pylab import * @@ -30,7 +30,7 @@ from numpy import * import wxversion -wxversion.select('2.6') +wxversion.select('2.8') import wx def create(parent): @@ -160,10 +160,10 @@ a.clabel(cs1l,fmt = 'Nullcline %2.1f',inline=0, colors = 'r', fontsize=14) a.clabel(cs2l,fmt = 'dx/dt=%2.1f',inline=0, colors = 'r', fontsize=14) a.clabel(cs3l,fmt = 'dy/dt=%2.1f',inline=0, colors = 'r', fontsize=14) - + def plotSpecg(self,x, name): """ - Makes a Spectrogram plot of x + Makes a Spectrogram plot of x """ # Use this line if using a toolbar a = self.fig.add_subplot(111) @@ -173,10 +173,10 @@ a.set_xlabel('time') a.set_ylabel('frequency') a.set_title('Spectrogram of %s'%name) - + def plotSpec(self,x, name): """ - Makes a power spectrum plot of x + Makes a power spectrum plot of x """ # Use this line if using a toolbar a = self.fig.add_subplot(111) @@ -186,7 +186,7 @@ a.set_xlabel('frequency') a.set_ylabel('Power(dB)') a.set_title('Power Spectrum of %s'%name) - + def plot_data(self, x,y,leg=None): """ This function will plot the time series as output by odeint. Index: model-builder-0.4.1/model_builder/PyMB.py =================================================================== --- model-builder-0.4.1.orig/model_builder/PyMB.py 2012-08-16 20:01:47.491834404 -0400 +++ model-builder-0.4.1/model_builder/PyMB.py 2012-08-16 20:01:47.603831062 -0400 @@ -27,7 +27,7 @@ #----------------------------------------------------------------------------- import wxversion -wxversion.select('2.6') +wxversion.select('2.8') import wx import wxFrame1 Index: model-builder-0.4.1/model_builder/quivVarFrame.py =================================================================== --- model-builder-0.4.1.orig/model_builder/quivVarFrame.py 2006-12-08 14:47:37.000000000 -0500 +++ model-builder-0.4.1/model_builder/quivVarFrame.py 2012-08-16 20:01:47.603831062 -0400 @@ -12,7 +12,7 @@ #----------------------------------------------------------------------------- #Boa:MiniFrame:quivVarFrame import wxversion -wxversion.select('2.6') +wxversion.select('2.8') import wx import wx.lib.buttons import PlotFigure as PF Index: model-builder-0.4.1/model_builder/uncertaintyMiniFrame.py =================================================================== --- model-builder-0.4.1.orig/model_builder/uncertaintyMiniFrame.py 2006-12-08 14:47:18.000000000 -0500 +++ model-builder-0.4.1/model_builder/uncertaintyMiniFrame.py 2012-08-16 20:01:47.603831062 -0400 @@ -25,7 +25,7 @@ #----------------------------------------------------------------------------- #Boa:MiniFrame:uncertaintyMiniFrame import wxversion -wxversion.select('2.6') +wxversion.select('2.8') import wx import wx.gizmos from Numeric import * Index: model-builder-0.4.1/model_builder/wxFrame1.py =================================================================== --- model-builder-0.4.1.orig/model_builder/wxFrame1.py 2012-08-16 20:01:47.563832256 -0400 +++ model-builder-0.4.1/model_builder/wxFrame1.py 2012-08-16 20:02:10.819138176 -0400 @@ -26,7 +26,7 @@ #Boa:Frame:wxFrame1 from __future__ import division import wxversion -wxversion.select('2.6') +wxversion.select('2.8') import wx import wx.stc #from Numeric import * @@ -321,7 +321,7 @@ self.SetAutoLayout(True) self.SetBestFittingSize(wx.Size(730, 480)) self.SetMaxSize(wx.Size(730, 480)) - self.SetIcon(wx.Icon('MB.ico',wx.BITMAP_TYPE_ICO)) + self.SetIcon(wx.Icon('/usr/share/pixmaps/MB.ico',wx.BITMAP_TYPE_ICO)) self.Bind(wx.EVT_CLOSE, self.OnWxFrame1Close) self.statusBar1 = wx.StatusBar(id=wxID_WXFRAME1STATUSBAR1, Index: model-builder-0.4.1/model_builder/wxFrame2.py =================================================================== --- model-builder-0.4.1.orig/model_builder/wxFrame2.py 2007-03-26 09:44:16.000000000 -0400 +++ model-builder-0.4.1/model_builder/wxFrame2.py 2012-08-16 20:01:47.603831062 -0400 @@ -25,7 +25,7 @@ #Boa:Frame:wxFrame2 import wxversion -wxversion.select('2.6') +wxversion.select('2.8') import wx import wx.grid from numpy import * debian/patches/show.diff0000644000000000000000000000115511420212742012424 0ustar Description: Fix issues with displaying the PyMB window Index: model-builder-0.4.1/model_builder/PyMB.py =================================================================== --- model-builder-0.4.1.orig/model_builder/PyMB.py 2008-01-27 17:02:48.000000000 +0530 +++ model-builder-0.4.1/model_builder/PyMB.py 2008-01-27 17:02:55.000000000 +0530 @@ -56,7 +56,7 @@ self.main = wxFrame1.create(None) # needed when running from Boa under Windows 9X self.SetTopWindow(self.main) - self.main.Show();self.main.Hide();self.main.Show() + self.main.Show(); return True def main(): debian/patches/series0000644000000000000000000000011011420212742012015 0ustar show.diff setup.diff MB_help_path.diff desktop_file.diff use_wx2.8.diff debian/patches/MB_help_path.diff0000644000000000000000000000110411420212742013760 0ustar Description: Fix install directory Index: model-builder-0.4.1/model_builder/wxFrame1.py =================================================================== --- model-builder-0.4.1.orig/model_builder/wxFrame1.py 2008-01-22 23:59:46.000000000 +0530 +++ model-builder-0.4.1/model_builder/wxFrame1.py 2008-01-27 16:31:37.000000000 +0530 @@ -1419,7 +1419,7 @@ return self.OnMenu1items1Menu(event) def OnMenu3MbhelpMenu(self, event): - helpviewer.main(['','MB.hhp']) + helpviewer.main(['','/usr/share/model-builder/help/MB.hhp']) class Future: """ debian/patches/desktop_file.diff0000644000000000000000000000121611420212742014112 0ustar Description: Fix desktop file Index: model-builder-0.4.1/model_builder/model-builder.desktop =================================================================== --- model-builder-0.4.1.orig/model_builder/model-builder.desktop 2008-01-27 16:47:00.000000000 +0530 +++ model-builder-0.4.1/model_builder/model-builder.desktop 2008-01-27 16:50:31.000000000 +0530 @@ -1,5 +1,4 @@ [Desktop Entry] -Encoding=UTF-8 Name=Model Builder Comment=Graphical ODE simulator GenericName=Graphical ODE simulator @@ -8,4 +7,4 @@ Type=Application StartupNotify=false Terminal=false -Categories=Science;Math;Engineering; +Categories=Education;Science;Math;Engineering; debian/rules0000755000000000000000000000145012152363634010253 0ustar #!/usr/bin/make -f DEB_PYTHON2_MODULE_PACKAGES=model-builder DEB_COMPRESS_INCLUDE := .ode DEB_COMPRESS_INCLUDE := .pdf include /usr/share/cdbs/1/rules/debhelper.mk include /usr/share/cdbs/1/class/python-distutils.mk DEB_PYTHON_INSTALL_ARGS_ALL += --install-layout=deb SITE=$(DEB_DESTDIR)/usr/share/pyshared/model_builder/ makebuilddir/model-builder:: if [ -e model_builder/Docs/Quick-start.pdf ]; then \ echo "Quick-start.pdf shouldn't be part of the tarball because of licensing issues!"; \ exit 1; \ fi binary-predeb/model-builder:: chmod 644 $(DEB_DESTDIR)/usr/share/doc/model-builder/examples/* chmod 644 $(SITE)/Examples/* grep -rl "^#!.*" $(SITE) | xargs sed -i 's/^#!.*//' sed -i '1s#python.*#python#' $(DEB_DESTDIR)/usr/bin/PyMB get-orig-source: -uscan --upstream-version 0 --rename debian/docs0000644000000000000000000000000710534322212010030 0ustar README debian/control0000644000000000000000000000147612152357755010615 0ustar Source: model-builder Section: math Priority: optional Maintainer: Varun Hiremath Build-Depends: debhelper (>=7), cdbs (>= 0.4.90~), python-all (>= 2.6.6-3~), python-setuptools Build-Depends-Indep: python-numpy Standards-Version: 3.9.0 Homepage: http://model-builder.sourceforge.net/ Vcs-Svn: https://bollin.googlecode.com/svn/model-builder/ Vcs-Browser: http://bollin.googlecode.com/svn/model-builder/ Package: model-builder Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, python-numpy, python-scipy, python-wxtools, python-wxgtk2.8, python-matplotlib, python-pkg-resources Description: graphical ODE simulator Model Builder is a graphical tool for designing, simulating and analyzing Mathematical model consisting of a system of ordinary differential equations(ODEs). debian/changelog0000644000000000000000000000653312152357570011056 0ustar model-builder (0.4.1-6.1) unstable; urgency=low * Non-maintainer upload. * Convert to dh_python2 (Closes: #616908). -- Luca Falavigna Sat, 01 Jun 2013 13:47:47 +0200 model-builder (0.4.1-6) unstable; urgency=high * Update patches/use_wx2.8.diff: - disable import of matplotlib.numerix, which is not used and no longer available (Closes: #684681) - fix the MB.ico icon load path -- Varun Hiremath Thu, 16 Aug 2012 20:03:58 -0400 model-builder (0.4.1-5) unstable; urgency=low * Add use_wx2.8.diff patch to use wx 2.8 instead of 2.6 (Closes: #588443) * Bump Standards-Version to 3.9.0 * Remove Torsten Werner from Uploaders, as requested * Switahc to source format 3.0 (quilt) * Update the patches; add descriptions * Update the manpage - fix lintian errors -- Varun Hiremath Fri, 16 Jul 2010 21:49:31 -0400 model-builder (0.4.1-4) unstable; urgency=low * Change Build-Depends: python-central (>= 0.6.0). (Closes: #472047) * Fix copyright file. -- Torsten Werner Fri, 21 Mar 2008 20:26:27 +0100 model-builder (0.4.1-3) unstable; urgency=low * Use python-pkg-resources instead of python-setuptools for the runtime dependency (Closes: #468726) -- Varun Hiremath Mon, 10 Mar 2008 16:04:17 +0530 model-builder (0.4.1-2) unstable; urgency=low * debian/control: Build-Depend and Depend on python-numpy instead of python-numpy-ext and python-numpy-dev virtual packages provided by python-numpy (Closes: #463208) -- Varun Hiremath Wed, 30 Jan 2008 16:23:01 +0530 model-builder (0.4.1-1) unstable; urgency=low * New upstream release * Bump Standards-Version to 3.7.3 * Bump debhelper compat to 6 * Add Homepage header and replace XS-Vcs with Vcs * Add debian/orig-tar.sh to create orig.tar.gz * debian/rules: add get-orig-source target * Add patches/desktop_file.diff to fix desktop file category and remove encoding field * Add patches/show.diff to fix problems while loading model-builder -- Varun Hiremath Sun, 27 Jan 2008 16:54:52 +0530 model-builder (0.4.0-2) unstable; urgency=low * Support all python versions. (Closes: #427317) * Change Architecture: all. * Clean up Build-Depends a bit. -- Torsten Werner Sun, 3 Jun 2007 10:41:19 +0200 model-builder (0.4.0-1) unstable; urgency=low * New upstream release -- Varun Hiremath Tue, 10 Apr 2007 17:05:04 +0530 model-builder (0.3.5-3) unstable; urgency=low * Add python-matplotlib and python-setuptools to Depends (Closes: #410660) -- Varun Hiremath Mon, 12 Feb 2007 21:46:37 +0530 model-builder (0.3.5-2) unstable; urgency=low [ Varun Hiremath ] * Remove Quick-start.pdf from upstream source, merged in manpage. [ Torsten Werner ] * Test for Quick-start.pdf in debian/rules. -- Torsten Werner Sat, 13 Jan 2007 16:58:37 +0100 model-builder (0.3.5-1) unstable; urgency=low [ Varun Hiremath ] * Initial release (Closes: #393250) * Fix the MB.hhp path problem. * Move all help files to /usr/share/model-builder/help/ [ Torsten Werner ] * Move documentation and examples to /usr/share/doc/model-builder/. -- Varun Hiremath Fri, 22 Dec 2006 21:24:43 +0530 debian/README.Debian-source0000644000000000000000000000057110747064323012536 0ustar model-builder ============= The upstream supplied source package contains pdf files without source which have been removed from the orig tarball. Use the rules/get-orig-source target to create the orig.tar.gz. For more details on repackaging of upstream sources please see the debian/orig-tar.sh file. -- Varun Hiremath , Sun, 27 Jan 2008 16:22:54 +0530 debian/copyright0000644000000000000000000000211010771006071011112 0ustar This package was debianized by Varun Hiremath on Tue, 17 Oct 2006 19:45:12 +0530. It was downloaded from http://model-builder.sourceforge.net/ Upstream Author: Flávio Codeço Coelho Copyright: © 2003-2006, Flávio Codeço Coelho © 2004, Antonio Guilherme Pacheco License: 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 in: /usr/share/common-licenses/GPL The Debian packaging is (C) 2006, Varun Hiremath and is licensed under the GPL, see `/usr/share/common-licenses/GPL'. debian/source/0000755000000000000000000000000012013305205010455 5ustar debian/source/format0000644000000000000000000000001411420212742011667 0ustar 3.0 (quilt) debian/watch0000644000000000000000000000013510747064323010224 0ustar version=3 http://sf.net/model-builder/ Model-Builder-(.*)\.tar\.gz debian debian/orig-tar.sh debian/orig-tar.sh0000755000000000000000000000060310747064323011256 0ustar #!/bin/sh -e # called by uscan with '--upstream-version' DIR=model-builder-$2.orig # remove pds without source tar -z -x -f $3 mv Model-Builder-$2 $DIR (cd $DIR; rm model_builder/Docs/Quick-start.pdf) tar -c -z -f $3 $DIR rm -rf $DIR # move to directory 'tarballs' if [ -r .svn/deb-layout ]; then . .svn/deb-layout mv $3 $origDir echo "moved $3 to $origDir" fi debian/manpages0000644000000000000000000000001710535061467010711 0ustar debian/PyMB.1