def setUp(self):
self.resetdir = os.getcwd()
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()
def setUp(self):
self.resetdir = os.getcwd()
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()
self.solver.setSensitivityOrder(amici.SensitivityOrder_first)
self.solver.setSensitivityMethod(amici.SensitivityMethod_forward)
self.edata = get_data(self.model)
self.edata.fixedParametersPresimulation = ()
self.edata_preeq = amici.ExpData(self.edata)
self.edata_preeq.setTimepoints([0])
self.edata_sim = amici.ExpData(self.edata)
self.edata_sim.fixedParametersPreequilibration = ()
self.pscales = [
amici.ParameterScaling_log10, amici.ParameterScaling_ln,
amici.ParameterScaling_none,
amici.parameterScalingFromIntVector([
amici.ParameterScaling_log10, amici.ParameterScaling_ln,
amici.ParameterScaling_none, amici.ParameterScaling_log10,
amici.ParameterScaling_ln, amici.ParameterScaling_none
])
]
self.plists = [
[3, 1, 2, 4],
[0, 1, 2, 3, 4, 5],
[5, 3, 2, 0, 4, 1],
[1, 2, 3, 4, 5],
[1, 1, 1],
]
def setUp(self):
sys.path.insert(
0,
os.path.join(os.path.dirname(__file__), '..', 'python', 'examples',
'example_presimulation'))
from createModel import 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()
def compare_to_pysb_simulation(self):
examples = [
tyson_oscillator.model, robertson.model,
expression_observables.model, bax_pore_sequential.model,
bax_pore.model, bngwiki_egfr_simple.model
]
for example in examples:
example.name = example.name.replace('pysb.examples.', '')
with self.subTest(example=example.name):
## pysb part
tspan = np.linspace(0, 100, 101)
sim = ScipyOdeSimulator(example,
tspan=tspan,
integrator_options={
'rtol': 1e-8,
'atol': 1e-8
},
compiler='python')
pysb_simres = sim.run()
## amici part
amici.pysb2amici(example, example.name, verbose=False)
sys.path.insert(0, example.name)
amici_model_module = importlib.import_module(example.name)
model_pysb = amici_model_module.getModel()
model_pysb.setTimepoints(tspan)
solver = model_pysb.getSolver()
rdata = amici.runAmiciSimulation(model_pysb, solver)
# check agreement of species simulation
self.assertTrue(
np.isclose(rdata['x'], pysb_simres.species, 1e-4,
1e-4).all())
def test_compare_to_sbml_import(self):
constant_parameters = ['DRUG_0', 'KIN_0']
# -------------- PYSB -----------------
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=constant_parameters)
sys.path.insert(0, model.name)
import test_model_presimulation_pysb as modelModulePYSB
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',
'model_presimulation.xml')
sbmlImporter = amici.SbmlImporter(sbmlFile)
observables = amici.assignmentRules2observables(
sbmlImporter.sbml, # the libsbml model object
filter_function=lambda variable: variable.getName() == 'pPROT_obs'
)
outdir = 'test_model_presimulation_sbml'
sbmlImporter.sbml2amici('test_model_presimulation_sbml',
outdir,
verbose=False,
observables=observables,
constantParameters=constant_parameters)
sys.path.insert(0, outdir)
import test_model_presimulation_sbml as modelModuleSBML
model_sbml = modelModuleSBML.getModel()
rdata_sbml = get_results(model_sbml, edata)
for field in rdata_pysb:
if field not in ['ptr', 't_steadystate', 'numsteps',
'newton_numsteps', 'numrhsevals',
'numerrtestfails', 'order', 'J', 'xdot',
'wrms_steadystate', ]:
with self.subTest(field=field):
if rdata_pysb[field] is None:
self.assertIsNone(
rdata_sbml[field],
)
elif rdata_sbml[field] is None:
self.assertIsNone(
rdata_pysb[field],
)
else:
self.assertTrue(np.isclose(
rdata_sbml[field],
rdata_pysb[field],
atol=1e-6, rtol=1e-6
).all())
def test_compare_to_pysb_simulation(self):
sys.path.insert(0, os.path.dirname(pysb.examples.__file__))
pysb_models = [
'tyson_oscillator', 'robertson', 'expression_observables',
'bax_pore_sequential', 'bax_pore', 'bngwiki_egfr_simple',
'bngwiki_enzymatic_cycle_mm', 'bngwiki_simple', 'earm_1_0',
'earm_1_3', 'move_connected', 'michment', 'kinase_cascade',
'hello_pysb', 'fricker_2010_apoptosis', 'explicit',
'fixed_initial',
]
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..',
'tests', 'pysb_test_models'))
custom_models = [
'bngwiki_egfr_simple_deletemolecules',
]
atol = 1e-8
rtol = 1e-8
for example in pysb_models + custom_models:
with self.subTest(example=example):
if example == 'earm_1_3' \
and platform.sys.version_info[0] == 3 \
and platform.sys.version_info[1] < 7:
continue
# load example
pysb.SelfExporter.cleanup() # reset pysb
pysb.SelfExporter.do_export = True
module = importlib.import_module(example)
pysb_model = module.model
pysb_model.name = pysb_model.name.replace('pysb.examples.', '')
# avoid naming clash for custom pysb models
pysb_model.name += '_amici'
# pysb part
tspan = np.linspace(0, 100, 101)
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)
model_pysb = amici_model_module.getModel()
model_pysb.setTimepoints(tspan)
solver = model_pysb.getSolver()
solver.setMaxSteps(int(1e5))
solver.setAbsoluteTolerance(atol)
solver.setRelativeTolerance(rtol)
rdata = amici.runAmiciSimulation(model_pysb, solver)
# check agreement of species simulation
self.assertTrue(np.isclose(
rdata['x'],
pysb_simres.species,
1e-4, 1e-4
).all())