added test script to source

Author: bgoli

testing/example_tests.py

@@ -0,0 +1,132 @@
+#! /usr/bin/env python
+"""
+StochPy - Stochastic modeling in Python (http://stochpy.sourceforge.net)
+
+Copyright (C) 2010-2025 T.R Maarlveld, B.G. Olivier, F.J. Bruggeman. All rights reserved.
+
+This file:
+Author: Brett G. Olivier (b.g.olivier@vu.nl)
+Address: Vrije Universiteit Amsterdam, Amsterdam, Netherlands.
+
+
+Permission to use, modify, and distribute this software is given under the
+terms of the StochPy (BSD style) license. 
+
+NO WARRANTY IS EXPRESSED OR IMPLIED.  USE AT YOUR OWN RISK.
+"""
+
+print('# StochPy Basic tests')
+
+print('## Import and load')
+
+import stochpy
+smod = stochpy.SSA()
+
+print('\nDone.\n\n## Basic Simulation with the Direct method')
+
+smod.DoStochSim(IsTrackPropensities=True)
+smod.data_stochsim.simulation_endtime
+smod.data_stochsim.simulation_timesteps
+smod.GetWaitingtimes()
+smod.PrintWaitingtimesMeans()
+
+print('\nDone.\n\n## Do some Plotting')
+
+smod.PlotSpeciesTimeSeries()
+smod.PlotWaitingtimesDistributions()
+smod.PlotPropensitiesTimeSeries()
+
+print('\nDone.\n\n## Write data to a text file')
+
+smod.Export2File()
+smod.Export2File(analysis='distribution')
+smod.Export2File(analysis='distribution',datatype='species')
+smod.Export2File(analysis='mean',datatype='species')
+smod.Export2File(analysis='std',datatype='species')
+smod.Export2File(analysis='autocorrelation',datatype='species')
+
+print('\nDone.\n\n## Show the means from the data of 3-th trajectory')
+
+smod.DoStochSim(trajectories=3) # multiple trajectories
+smod.data_stochsim.simulation_trajectory
+smod.PrintSpeciesMeans()
+smod.PrintSpeciesStandardDeviations()
+
+print('\nDone.\n\n## Switch to data from trajectory 1 and show the means of each species')
+
+smod.GetTrajectoryData(1)
+smod.PrintSpeciesMeans()
+smod.PrintSpeciesStandardDeviations()
+
+print('\nDone.\n\n## Do one long simulation')
+
+smod.DoStochSim(trajectories=1,end=1000000,mode='steps')
+smod.PrintSpeciesMeans()
+smod.PrintSpeciesStandardDeviations()
+
+print('\nDone.\n\n## Plot the PDF for different bin sizes')
+
+smod.PlotSpeciesDistributions()
+smod.PlotSpeciesDistributions(bin_size=5)  # larger bin size
+smod.PlotSpeciesDistributions(bin_size=10) # again a larger bin size
+smod.Export2File(analysis='distribution',datatype='species')
+
+print('\nDone.\n\n## Usage of the Reload Function: `Ksyn = 20, kdeg = 0.2`')
+
+smod.ChangeParameter('Ksyn',20.0)
+smod.ChangeParameter('Kdeg',0.2)
+smod.DoStochSim()
+smod.PrintSpeciesMeans()   # should be ~Ksyn/Kdeg
+
+print('\nDone.\n\n## Use another model to show the Interpolation features')
+
+smod.Model('dsmts-001-01.xml.psc')
+smod.DoStochSim(trajectories=1000,end=50,mode='time')
+smod.GetRegularGrid(n_samples=51)
+smod.PlotAverageSpeciesTimeSeries()
+smod.PrintAverageSpeciesTimeSeries()
+smod.Export2File(datatype='species',analysis='timeseries',IsAverage=True)
+
+print('\nDone.\n\n## Test each method for different models:')
+
+smod.Model('Autoreg.psc')
+smod.DoStochSim(trajectories=1,end=1000,mode='steps')
+smod.Method('NextReactionMethod')
+smod.DoStochSim(trajectories=1,end=1000,mode='steps')
+smod.data_stochsim.species
+smod.PlotWaitingtimesDistributions()
+smod.Method('FirstReactionMethod')
+smod.DoStochSim(trajectories=1,end=1000,mode='steps')
+smod.Method('TauLeaping')
+smod.DoStochSim(trajectories=1,end=1000,mode='steps')
+
+smod.Model('DecayingDimerizing.psc')
+smod.DoStochSim(method = 'Direct',trajectories=1,end=50,mode='time')
+smod.DoStochSim(method = 'NextReactionMethod',trajectories=1,end=50,mode='time')
+smod.DoStochSim(method = 'FirstReactionMethod',trajectories=1,end=50,mode='time')
+smod.PlotWaitingtimesDistributions()
+smod.DoStochSim(method = 'TauLeaping',trajectories=1,end=50,mode='time',epsilon=0.03)  # Should outperform all other implementations
+smod.PlotSpeciesTimeSeries()
+#smod.PlotWaitingtimesDistributions()   # Should give an error
+
+smod.Model('chain500.psc')
+smod.DoStochSim(method = 'Direct',trajectories=1,end=10000,mode='steps')
+smod.DoStochSim(method = 'NextReactionMethod',trajectories=1,end=10000,mode='steps') # should outperform the direct method and all other implementations
+
+print('\n### Use the Next Reaction Method to test a model with a time event\n')
+
+smod.Model('dsmts-003-03.xml.psc')
+smod.DoStochSim(method = 'NextReactionMethod')
+smod.DoTestsuite()
+
+print('\n### Use the First Reaction method to test a model with a concentration event\n')
+
+smod.Model('dsmts-003-04.xml.psc')
+smod.DoStochSim(method = 'FirstReactionMethod')
+smod.DoTestsuite()
+
+print('\n### Volume Models\n')
+
+smod.Model('dsmts-001-11.xml.psc')
+smod.DoStochSim(method = 'Direct',trajectories=1000,end=50,mode ='time')
+smod.PrintAverageSpeciesTimeSeries()