def VersionDict(): '''Return dict of version strings.''' import tesbml, tesedml, tecombine return { 'tellurium': getTelluriumVersion(), 'roadrunner': roadrunner.getVersionStr(roadrunner.VERSIONSTR_BASIC), 'antimony': antimony.__version__, 'phrasedml': phrasedml.__version__, 'tesbml': libsbml.getLibSBMLDottedVersion(), 'tesedml': tesedml.__version__, 'tecombine': tecombine.__version__ }
def getVersionInfo(): print "telluirum Version: ", getTelluriumVersion() print "RoadRunner version:", roadrunner.getVersionStr() print "Antimony version:", antimony.__version__ print "No information on sbnw viewer"
# -*- coding: utf-8 -*- """ Created on Tue Apr 21 12:47:12 2015 @author: phantom """ import roadrunner as rr import tellurium as te import csv import time from sys import stderr, stdout csvwriter = csv.writer(stdout, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL) csvwriter.writerow([rr.getVersionStr()]) csvwriter.writerow(['Name', 'Run_time']) r = rr.RoadRunner(r'C:\Users\phantom\Documents\devel\src\rr-benchmarking\jean_marie\Jean_Marie_AMPA16_RobHow_v6.xml') #print(r.rv()) name = 'JeanMarie' for n in range(3): #print te.sbmlToAntimony(r.getCurrentSBML()) startTime = time.time() m = r.simulate(0, 5000000, 10000) #r.plot() endTime = time.time() csvwriter.writerow([name, endTime-startTime])
def gatherInfo(self): """ Gathers information about relevant versions and paths into a dictionary. """ import subprocess import os import bionetgen import numpy import pandas import roadrunner self.logger.debug("Gathering info", loc=f"{__file__} : BNGInfo.gatherInfo()") self.info = {} # Add some description for the following information self.info[ "\nThe following are related to BioNetGen and its execution"] = "" self.logger.debug("BNG info", loc=f"{__file__} : BNGInfo.gatherInfo()") # Get BNG version with open( os.path.join(*[ os.path.dirname(bionetgen.__file__), "assets", "BNGVERSION" ]), "r", ) as f: read_data = f.read() self.info["BNG version"] = read_data[10:15] # Get BNG2.pl path self.info["BNG2.pl path"] = (self.config.get("bionetgen", "bngpath") + " (the main executable for BNG)") self.logger.debug("Perl info", loc=f"{__file__} : BNGInfo.gatherInfo()") # Get Perl version # Read in CLI text result = subprocess.run(["perl", "-v"], stdout=subprocess.PIPE) text = str(result.stdout) # Find start & end indices num_start = text.find("(v") + 2 num_end = text.find(")") # Save version info self.info["Perl version"] = text[ num_start:num_end] + " (used to run BNG2.pl)" self.logger.debug("PyBNG info", loc=f"{__file__} : BNGInfo.gatherInfo()") # Get CLI version with open( os.path.join(*[ os.path.dirname(bionetgen.__file__), "assets", "VERSION" ]), "r", ) as f: read_data = f.read() self.info["CLI version"] = read_data # Get pyBNG path self.info["pyBNG path"] = (os.path.dirname(bionetgen.__file__) + " (the PyBNG installation)") self.logger.debug( "Info on installed python libraries", loc=f"{__file__} : BNGInfo.gatherInfo()", ) # Add some description for the following information self.info["\nThe following libraries are required by PyBioNetGen"] = "" # Get numpy version self.info["numpy version"] = numpy.version.version # Get pandas version self.info["pandas version"] = pandas.__version__ # Get libRoadRunner version text = roadrunner.getVersionStr() self.info["libRoadRunner version"] = text[0:5] return self.info
#!/usr/bin/python ############################################################ # Test the roadrunner installation/python bindings # # Usage: # ./roadrunner_test.sh 2>&1 | tee ./logs/roadrunner_test.log # # To select a branch/tag/commit to build from change the # checkout command for roadrunner. # # @author: Matthias Koenig # @date: 2016-01-06 ############################################################ import roadrunner print roadrunner.getVersionStr() import roadrunner.testing roadrunner.testing.runTester()
""" The LibRoadRunner SBML Simulation Engine, (c) 2009-2014 Andy Somogyi and Herbert Sauro LibRoadRunner is an SBML JIT compiler and simulation engine with a variety of analysis functions. LibRoadRunner is a self contained library which is designed to be integrated into existing simulation platforms or may be used a stand alone simulation and analysis package. """ import roadrunner from roadrunner import * __version__ = roadrunner.getVersionStr() def runTests(testDir=None): import testing return testing.tester.runTester(testDir)
# -*- coding: utf-8 -*- """ Performing simulation with event driven peak. @author: Matthias Koenig @date: 2015-05-28 """ from __future__ import print_function import os import roadrunner from roadrunner import SelectionRecord print(roadrunner.getVersionStr()) import antimony model_txt = """ model time_peak() // Reactions J0: $PP_S -> 2 S3; K1 * PP_S; // Species initializations: var species S3; S3 = 0.5; // S4 := sin(time) PP_S = 0.0; // Rule for S1 K1 = 0.5; t_peak = 2; t_duration = 0.5; mu = t_peak + 0.5*t_duration;
# -*- coding: utf-8 -*- import roadrunner as rr import csv import time from sys import stdout csvwriter = csv.writer(stdout, delimiter=',', quotechar='"', quoting=csv.QUOTE_MINIMAL) csvwriter.writerow([rr.getVersionStr()]) csvwriter.writerow(['Name', 'Run_time']) print('Load Model ...') r = rr.RoadRunner(r'Galactose_v107_Nc20_galchallenge_noevents.xml') r.selections = r.selections + ["[PP__gal]", '[PV__gal]'] name = 'Koenig_Liver' for n in range(3): # reset the model ! for repeated simulation r.reset() # perform integration absTol = 1E-8 relTol = 1E-8 absTol = absTol * min( r.model.getCompartmentVolumes()) # absTol relative to the amounts tend = 100 tsteps = 1000