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 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
""" 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)
