def runTest(self):
"""
test runner routine that loads data expectedResults.h5 hdf file and
runs individual models/settings as subTests
"""
expected_results = h5py.File(self.expectedResultsFile, 'r')
for subTest in expected_results.keys():
for case in list(expected_results[subTest].keys()):
if case.startswith('sensi2'):
model_name = subTest + '_o2'
else:
model_name = subTest
with self.subTest(modelName=model_name, caseName=case):
print(f'running {model_name}::{case}')
def assert_fun(x):
return self.assertTrue(x)
model_swig_folder = \
os.path.join(os.path.dirname(__file__), '..',
'build', 'tests', 'cpputest',
f'external_{model_name}-prefix',
'src', f'external_{model_name}-build',
'swig')
sys.path.insert(0, model_swig_folder)
test_model_module = importlib.import_module(model_name)
self.model = test_model_module.getModel()
self.solver = self.model.getSolver()
amici.readModelDataFromHDF5(
self.expectedResultsFile, self.model.get(),
f'/{subTest}/{case}/options'
)
amici.readSolverSettingsFromHDF5(
self.expectedResultsFile, self.solver.get(),
f'/{subTest}/{case}/options'
)
edata = None
if 'data' in expected_results[subTest][case].keys():
edata = amici.readSimulationExpData(
self.expectedResultsFile,
f'/{subTest}/{case}/data', self.model.get()
)
rdata = amici.runAmiciSimulation(self.model, self.solver,
edata)
check_derivative_opts = dict()
if model_name == 'model_nested_events':
check_derivative_opts['rtol'] = 1e-2
elif model_name == 'model_events':
check_derivative_opts['atol'] = 1e-3
if edata \
and self.solver.getSensitivityMethod() \
and self.solver.getSensitivityOrder() \
and len(self.model.getParameterList()) \
and not model_name.startswith('model_neuron') \
and not case.endswith('byhandpreeq'):
check_derivatives(self.model, self.solver, edata,
assert_fun, **check_derivative_opts)
verify_simulation_opts = dict()
if model_name.startswith('model_neuron'):
verify_simulation_opts['atol'] = 1e-5
verify_simulation_opts['rtol'] = 1e-2
if model_name.startswith('model_robertson') and \
case == 'sensiforwardSPBCG':
verify_simulation_opts['atol'] = 1e-3
verify_simulation_opts['rtol'] = 1e-3
verify_simulation_results(
rdata, expected_results[subTest][case]['results'],
assert_fun, **verify_simulation_opts
)
if model_name == 'model_steadystate' and \
case == 'sensiforwarderrorint':
edata = amici.amici.ExpData(self.model.get())
if edata and model_name != 'model_neuron_o2' and not (
model_name == 'model_robertson' and
case == 'sensiforwardSPBCG'
):
# Test runAmiciSimulations: ensure running twice
# with same ExpData yields same results
if isinstance(edata, amici.amici.ExpData):
edatas = [edata, edata]
else:
edatas = [edata.get(), edata.get()]
rdatas = amici.runAmiciSimulations(
self.model, self.solver, edatas, num_threads=2
)
verify_simulation_results(
rdatas[0],
expected_results[subTest][case]['results'],
assert_fun, **verify_simulation_opts
)
verify_simulation_results(
rdatas[1],
expected_results[subTest][case]['results'],
assert_fun, **verify_simulation_opts
)
self.assertRaises(
RuntimeError,
self.model.getParameterByName,
'thisParameterDoesNotExist'
)
if case.startswith('sensi2'):
model_name = sub_test + '_o2'
else:
model_name = sub_test
model_swig_folder = \
os.path.join(os.path.dirname(__file__), '..', '..', 'build', 'tests',
'cpputest', f'external_{model_name}-prefix',
'src', f'external_{model_name}-build', 'swig')
test_model_module = amici.import_model_module(
module_name=model_name, module_path=model_swig_folder)
model = test_model_module.getModel()
solver = model.getSolver()
amici.readModelDataFromHDF5(options_file, model.get(),
f'/{sub_test}/{case}/options')
amici.readSolverSettingsFromHDF5(options_file, solver.get(),
f'/{sub_test}/{case}/options')
edata = None
if 'data' in expected_results[sub_test][case].keys():
edata = amici.readSimulationExpData(expected_results_file,
f'/{sub_test}/{case}/data',
model.get())
rdata = amici.runAmiciSimulation(model, solver, edata)
check_derivative_opts = dict()
if model_name == 'model_nested_events':
check_derivative_opts['rtol'] = 1e-2
elif model_name == 'model_events':
def apply_model_settings(self, model: 'amici.Model'):
"""Apply settings to Model"""
amici.readModelDataFromHDF5(self.filename, model.get(),
'/amiciOptions')
if case.startswith('sensi2'):
model_name = sub_test + '_o2'
else:
model_name = sub_test
model_swig_folder = \
os.path.join(os.path.dirname(__file__), '..', '..', 'build', 'tests',
'cpputest', f'external_{model_name}-prefix',
'src', f'external_{model_name}-build', 'swig')
test_model_module = amici.import_model_module(
module_name=model_name, module_path=model_swig_folder)
model = test_model_module.getModel()
solver = model.getSolver()
amici.readModelDataFromHDF5(expected_results_file, model.get(),
f'/{sub_test}/{case}/options')
amici.readSolverSettingsFromHDF5(expected_results_file, solver.get(),
f'/{sub_test}/{case}/options')
edata = None
if 'data' in expected_results[sub_test][case].keys():
edata = amici.readSimulationExpData(expected_results_file,
f'/{sub_test}/{case}/data',
model.get())
rdata = amici.runAmiciSimulation(model, solver, edata)
check_derivative_opts = dict()
if model_name == 'model_nested_events':
check_derivative_opts['rtol'] = 1e-2
elif model_name == 'model_events':