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# amici part
outdir = pysb_model.name
if pysb_model.name in ['move_connected_amici']:
self.assertRaises(
Exception,
amici.pysb2amici,
*[pysb_model, outdir],
**{'verbose': False, 'compute_conservation_laws': True}
)
compute_conservation_laws = False
else:
compute_conservation_laws = True
amici.pysb2amici(
pysb_model,
outdir,
verbose=False,
compute_conservation_laws=compute_conservation_laws
)
sys.path.insert(0, outdir)
amici_model_module = importlib.import_module(pysb_model.name)
model_pysb = amici_model_module.getModel()
model_pysb.setTimepoints(tspan)
solver = model_pysb.getSolver()
solver.setMaxSteps(int(1e5))
solver.setAbsoluteTolerance(atol)
sim = ScipyOdeSimulator(
pysb_model,
tspan=tspan,
integrator_options={'rtol': rtol, 'atol': atol},
compiler='python'
)
pysb_simres = sim.run()
# amici part
outdir = pysb_model.name
if pysb_model.name in ['move_connected_amici']:
self.assertRaises(
Exception,
amici.pysb2amici,
*[pysb_model, outdir],
**{'verbose': False, 'compute_conservation_laws': True}
)
compute_conservation_laws = False
else:
compute_conservation_laws = True
amici.pysb2amici(
pysb_model,
outdir,
verbose=False,
compute_conservation_laws=compute_conservation_laws
)
sys.path.insert(0, outdir)
amici_model_module = importlib.import_module(pysb_model.name)
self.default_path = copy.copy(sys.path)
pysb.SelfExporter.cleanup() # reset pysb
pysb.SelfExporter.do_export = True
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..',
'python', 'examples',
'example_presimulation'))
if 'createModelPresimulation' in sys.modules:
importlib.reload(sys.modules['createModelPresimulation'])
model_module = sys.modules['createModelPresimulation']
else:
model_module = importlib.import_module('createModelPresimulation')
model = copy.deepcopy(model_module.model)
model.name = 'test_model_presimulation_pysb'
amici.pysb2amici(model,
model.name,
verbose=False,
observables=['pPROT_obs'],
constant_parameters=['DRUG_0', 'KIN_0'])
sys.path.insert(0, model.name)
import test_model_presimulation_pysb as modelModulePYSB
self.model = modelModulePYSB.getModel()
self.solver = self.model.getSolver()
pysb.SelfExporter.cleanup() # reset pysb
pysb.SelfExporter.do_export = True
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..',
'python', 'examples',
'example_presimulation'))
if 'createModelPresimulation' in sys.modules:
importlib.reload(sys.modules['createModelPresimulation'])
model_module = sys.modules['createModelPresimulation']
else:
model_module = importlib.import_module('createModelPresimulation')
model = copy.deepcopy(model_module.model)
model.name = 'test_model_presimulation_pysb'
outdir = model.name
amici.pysb2amici(model,
outdir,
verbose=False,
observables=['pPROT_obs'],
constant_parameters=['DRUG_0', 'KIN_0'])
sys.path.insert(0, outdir)
modelModulePYSB = importlib.import_module(outdir)
self.model = modelModulePYSB.getModel()
self.model.setReinitializeFixedParameterInitialStates(True)
self.solver = self.model.getSolver()
self.solver.setSensitivityOrder(amici.SensitivityOrder_first)
self.solver.setSensitivityMethod(amici.SensitivityMethod_forward)
self.edata = get_data(self.model)
self.edata.t_presim = 2
pysb.SelfExporter.cleanup() # reset pysb
pysb.SelfExporter.do_export = True
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..',
'python', 'examples',
'example_presimulation'))
if 'createModelPresimulation' in sys.modules:
importlib.reload(sys.modules['createModelPresimulation'])
model_module = sys.modules['createModelPresimulation']
else:
model_module = importlib.import_module('createModelPresimulation')
model = copy.deepcopy(model_module.model)
model.name = 'test_model_presimulation_pysb'
outdir_pysb = model.name
amici.pysb2amici(model,
outdir_pysb,
verbose=False,
observables=['pPROT_obs'],
constant_parameters=constant_parameters)
sys.path.insert(0, outdir_pysb)
modelModulePYSB = importlib.import_module(outdir_pysb)
model_pysb = modelModulePYSB.getModel()
edata = get_data(model_pysb)
rdata_pysb = get_results(model_pysb, edata)
# -------------- SBML -----------------
sbmlFile = os.path.join(os.path.dirname(__file__), '..', 'python',
'examples', 'example_presimulation',