def test_file_with_directory_name_exists(self):
with self.assertRaises(DirectoryError):
temp = tempfile.NamedTemporaryFile()
model = create_decay()
solverSSAC = SSACSolver(model, temp.name)
solverODEC = ODECSolver(model, temp.name)
solverTAUC = TauLeapingCSolver(model, temp.name)
solverHYBC = TauHybridCSolver(model, temp.name)
def old_check_cpp_support(self):
try:
model = create_decay()
solver = SSACSolver(model=model)
results = model.run(solver=solver, cpp_support=True)
return True
except Exception as e:
from gillespy2.core import log
log.warn('Unable to use C++ optimized SSA: {0}. The performance of ' \
'this package can be significantly increased if you install/configure GCC on ' \
'this machine.'.format(e))
return False
class TestVariableSolvers(unittest.TestCase):
model = create_decay()
solverSSAC = SSACSolver(model, variable=True)
solverODEC = ODECSolver(model, variable=True)
solverTAUC = TauLeapingCSolver(model, variable=True)
solverHYBC = TauHybridCSolver(model, variable=True)
solverlist = [solverSSAC, solverODEC, solverTAUC, solverHYBC]
def test_create(self):
model = create_decay()
solverSSAC = SSACSolver(model)
solverODEC = ODECSolver(model)
solverTAUC = TauLeapingCSolver(model)
solverHYBC = TauHybridCSolver(model)
def test_file_with_directory_name_exists(self):
with self.assertRaises(DirectoryError):
temp = tempfile.NamedTemporaryFile()
model = create_decay()
solverSSAC = SSACSolver(model, temp.name)
solverODEC = ODECSolver(model, temp.name)
solverTAUC = TauLeapingCSolver(model, temp.name)
solverHYBC = TauHybridCSolver(model, temp.name)
def test_run_example_precompiled(self):
for solver in self.solverlist:
results = self.model.run(solver=solver)
def test_change_species(self):
initial_value = self.model.listOfSpecies['Sp'].initial_value
for solver in self.solverlist:
results = self.model.run(solver=solver, variables={'Sp': 3})
with self.subTest(msg='Test changed species simulation'):
self.assertEqual(results['Sp'][0], 3)
with self.subTest(msg='Test changed species model integrity'):
self.assertEqual(self.model.listOfSpecies['Sp'].initial_value,
initial_value)
def test_change_parameter(self):
initial_expression = self.model.listOfParameters['k1'].expression
for solver in self.solverlist:
results = self.model.run(solver=solver, variables={'k1': 0})
with self.subTest(msg='Test changed parameter simulation'):
self.assertEqual(results['Sp'][-1], results['Sp'][0])
with self.subTest(msg='Test changed parameter model integrity'):
self.assertEqual(self.model.listOfParameters['k1'].expression,
initial_expression)
def test_invalid_variable(self):
with self.assertRaises(SimulationError):
for solver in self.solverlist:
results = self.model.run(solver=solver,
variables={'foobar': 0})
def ssaSolver(model, data, run_timeout):
'''
Run the model with the best GillesPy2 SSASolver.
Attributes
----------
model : GillesPy2 Model
Model to be run.
data : dict
Simulation settings to use for the run.
run_timeout : int
Number of seconds until the simulation times out.
'''
solver = SSACSolver(model=model)
seed = data['seed']
if (seed == -1):
seed = None
results = model.run(solver=solver,
timeout=run_timeout,
number_of_trajectories=data['realizations'],
seed=seed)
return results
def test_create(self):
model = create_decay()
solverSSAC = SSACSolver(model)
solverODEC = ODECSolver(model)
solverTAUC = TauLeapingCSolver(model)
solverHYBC = TauHybridCSolver(model)
reactants={Y: 1},
products={},
rate=kd)
# nonlinear Y term:
rxn5 = gillespy2.Reaction(
name='Y nonlin',
reactants={Y: 1},
products={},
propensity_function='Y/(a0 + a1*(Y/vol)+a2*Y*Y/(vol*vol))')
model.add_reaction([rxn1, rxn2, rxn3, rxn4, rxn5])
return model
# Model simulation.
# .............................................................................
if __name__ == '__main__':
# A simulation in GillesPy2 is performed by first instantiating the model
# to be simulated, and then invoking the "run" method on that object.
# The results of the simulation are the output of "run".
import time
from gillespy2 import SSACSolver
tic = time.time()
for _ in range(10):
tyson_model = create_tyson_2_state()
solver = SSACSolver(model=tyson_model)
trajectories = tyson_model.run(solver=solver)
print((time.time() - tic) / 10)
def test_run_example_precompiled(self):
model = Example()
solver = SSACSolver(model)
results = model.run(solver=solver)
def test_file_with_directory_name_exists(self):
with self.assertRaises(DirectoryError):
temp = tempfile.NamedTemporaryFile()
model = Example()
solver = SSACSolver(model, temp.name)
def test_create(self):
model = Example()
solver = SSACSolver(model)