def test_solver_hdf5_roundtrip(sbml_example_presimulation_module):
"""TestCase class for AMICI HDF5 I/O"""
model = sbml_example_presimulation_module.getModel()
solver = model.getSolver()
_modify_solver_attrs(solver)
hdf5file = 'solverSettings.hdf5'
amici.writeSolverSettingsToHDF5(solver, hdf5file, 'ssettings')
new_solver = model.getSolver()
# check that we changed everything
for attr in dir(solver):
if not attr.startswith('set'):
continue
assert getattr(solver, attr.replace('set', 'get'))() \
!= getattr(new_solver, attr.replace('set', 'get'))(), attr
amici.readSolverSettingsFromHDF5(hdf5file, new_solver, 'ssettings')
# check that reading in settings worked
for attr in dir(solver):
if not attr.startswith('set'):
continue
assert getattr(solver, attr.replace('set', 'get'))() \
== pytest.approx(
getattr(new_solver, attr.replace('set', 'get'))()), attr
os.remove(hdf5file)
def __setstate__(self, state: Dict):
self.__dict__.update(state)
model = amici_petab_import.import_petab_problem(self.petab_problem)
solver = model.getSolver()
_fd, _file = tempfile.mkstemp()
try:
# write solver settings to temporary file
with open(_fd, 'wb', closefd=False) as f:
f.write(state['amici_solver_settings'])
# read in solver settings
try:
amici.readSolverSettingsFromHDF5(_file, solver)
except AttributeError as err:
if not err.args:
err.args = ('', )
err.args += ("Unpickling an AmiciObjective requires an AMICI "
"installation with HDF5 support.", )
raise
finally:
# close file descriptor and remove temporary file
os.close(_fd)
os.remove(_file)
self.amici_model = model
self.amici_solver = solver
def __setstate__(self, state: Dict):
if state['amici_object_builder'] is None:
raise NotImplementedError(
"AmiciObjective does not support __setstate__ without "
"an `amici_object_builder`.")
self.__dict__.update(state)
# note: attributes not defined in the builder are lost
model = self.amici_object_builder.create_model()
solver = self.amici_object_builder.create_solver(model)
edatas = self.amici_object_builder.create_edatas(model)
try:
# write solver settings to temporary file
_file = tempfile.mkstemp()[1]
with open(_file, 'wb') as f:
f.write(state['amici_solver_settings'])
# read in solver settings
amici.readSolverSettingsFromHDF5(_file, solver)
# remove temporary file
os.remove(_file)
except AttributeError as err:
if not err.args:
err.args = ('', )
err.args += ("Amici must have been compiled with hdf5 support", )
raise
self.amici_model = model
self.amici_solver = solver
self.edatas = edatas
def __setstate__(self, state: Dict) -> None:
self.__dict__.update(state)
petab_importer = state['petab_importer']
# note: attributes not defined in the importer are lost
model = petab_importer.create_model()
solver = petab_importer.create_solver(model)
edatas = petab_importer.create_edatas(model)
amici.readSolverSettingsFromHDF5(state['amici_solver'], solver)
os.remove(state['amici_solver'])
self.amici_model = model
self.amici_solver = solver
self.edatas = edatas
def __setstate__(self, state: Dict) -> None:
if state['amici_object_builder'] is None:
raise NotImplementedError(
"AmiciObjective does not support __setstate__ without "
"an `amici_object_builder`.")
self.__dict__.update(state)
# note: attributes not defined in the builder are lost
model = self.amici_object_builder.create_model()
solver = self.amici_object_builder.create_solver(model)
edatas = self.amici_object_builder.create_edatas(model)
_fd, _file = tempfile.mkstemp()
try:
# write solver settings to temporary file
with open(_fd, 'wb', closefd=False) as f:
f.write(state['amici_solver_settings'])
# read in solver settings
try:
amici.readSolverSettingsFromHDF5(_file, solver)
except AttributeError as err:
if not err.args:
err.args = ('', )
err.args += ("Unpickling an AmiciObjective requires an AMICI "
"installation with HDF5 support.", )
raise
finally:
# close file descriptor and remove temporary file
os.close(_fd)
os.remove(_file)
self.amici_model = model
self.amici_solver = solver
self.edatas = edatas
self.apply_custom_timepoints()
amici.set_model_settings(
self.amici_model,
state['AMICI_model_settings'],
)
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'
)
def apply_solver_settings(self, solver: 'amici.Solver'):
"""Apply settings to Solver"""
amici.readSolverSettingsFromHDF5(self.filename, solver.get(),
'/amiciOptions')
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':
check_derivative_opts['atol'] = 1e-3
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':
check_derivative_opts['atol'] = 1e-3