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Merged
dweindl merged 1 commit into from
Oct 9, 2025
Merged

Fix #2969 #2973

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86 changes: 43 additions & 43 deletions tests/performance/test.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -29,26 +29,26 @@ def parse_args():
def check_results(rdata):
diagnostics = [
"numsteps",
"numstepsB",
"numrhsevals",
"numrhsevalsB",
"numerrtestfails",
"numerrtestfailsB",
"numnonlinsolvconvfails",
"numnonlinsolvconvfailsB",
"numsteps_b",
"num_rhs_evals",
"num_rhs_evals_b",
"num_err_test_fails",
"num_err_test_fails_b",
"num_non_lin_solv_conv_fails",
"num_non_lin_solv_conv_fails_b",
"preeq_status",
"preeq_numsteps",
"preeq_numstepsB",
"preeq_numsteps_b",
"preeq_cpu_time",
"preeq_cpu_timeB",
"preeq_cpu_time_b",
"cpu_time_total",
"cpu_time",
"cpu_timeB",
"cpu_time_b",
"posteq_status",
"posteq_cpu_time",
"posteq_cpu_timeB",
"posteq_cpu_time_b",
"posteq_numsteps",
"posteq_numstepsB",
"posteq_numsteps_b",
]
for d in diagnostics:
print(d, rdata[d])
Expand Down Expand Up @@ -94,40 +94,40 @@ def compile_model(model_dir_source: Path, model_dir_compiled: Path):

def prepare_simulation(arg, model, solver, edata):
if arg == "forward_simulation":
solver.setSensitivityMethod(amici.SensitivityMethod.none)
solver.setSensitivityOrder(amici.SensitivityOrder.none)
solver.set_sensitivity_method(amici.SensitivityMethod.none)
solver.set_sensitivity_order(amici.SensitivityOrder.none)
elif arg == "forward_sensitivities":
model.setParameterList(list(range(100)))
solver.setSensitivityMethod(amici.SensitivityMethod.forward)
solver.setSensitivityOrder(amici.SensitivityOrder.first)
model.set_parameter_list(list(range(100)))
solver.set_sensitivity_method(amici.SensitivityMethod.forward)
solver.set_sensitivity_order(amici.SensitivityOrder.first)
elif arg == "adjoint_sensitivities":
solver.setSensitivityMethod(amici.SensitivityMethod.adjoint)
solver.setSensitivityOrder(amici.SensitivityOrder.first)
solver.set_sensitivity_method(amici.SensitivityMethod.adjoint)
solver.set_sensitivity_order(amici.SensitivityOrder.first)
elif arg == "forward_simulation_non_optimal_parameters":
tmp_par = model.getParameters()
model.setParameters([0.1 for _ in tmp_par])
solver.setSensitivityMethod(amici.SensitivityMethod.none)
solver.setSensitivityOrder(amici.SensitivityOrder.none)
tmp_par = model.get_parameters()
model.set_parameters([0.1 for _ in tmp_par])
solver.set_sensitivity_method(amici.SensitivityMethod.none)
solver.set_sensitivity_order(amici.SensitivityOrder.none)
elif arg == "adjoint_sensitivities_non_optimal_parameters":
tmp_par = model.getParameters()
model.setParameters([0.1 for _ in tmp_par])
solver.setSensitivityMethod(amici.SensitivityMethod.adjoint)
solver.setSensitivityOrder(amici.SensitivityOrder.first)
tmp_par = model.get_parameters()
model.set_parameters([0.1 for _ in tmp_par])
solver.set_sensitivity_method(amici.SensitivityMethod.adjoint)
solver.set_sensitivity_order(amici.SensitivityOrder.first)
elif arg == "forward_steadystate_sensitivities_non_optimal_parameters":
tmp_par = model.getParameters()
model.setParameters([0.1 for _ in tmp_par])
solver.setSensitivityMethod(amici.SensitivityMethod.forward)
solver.setSensitivityOrder(amici.SensitivityOrder.first)
model.setSteadyStateSensitivityMode(
tmp_par = model.get_parameters()
model.set_parameters([0.1 for _ in tmp_par])
solver.set_sensitivity_method(amici.SensitivityMethod.forward)
solver.set_sensitivity_order(amici.SensitivityOrder.first)
model.set_steady_state_sensitivity_mode(
amici.SteadyStateSensitivityMode.newtonOnly
)
edata.setTimepoints([float("inf")])
elif arg == "adjoint_steadystate_sensitivities_non_optimal_parameters":
tmp_par = model.getParameters()
model.setParameters([0.1 for _ in tmp_par])
solver.setSensitivityMethod(amici.SensitivityMethod.adjoint)
solver.setSensitivityOrder(amici.SensitivityOrder.first)
edata.setTimepoints([float("inf")])
tmp_par = model.get_parameters()
model.set_parameters([0.1 for _ in tmp_par])
solver.set_sensitivity_method(amici.SensitivityMethod.adjoint)
solver.set_sensitivity_order(amici.SensitivityOrder.first)
edata.set_timepoints([float("inf")])
else:
print("Unknown argument:", arg)
sys.exit(1)
Expand All @@ -153,17 +153,17 @@ def main():
model_module = amici.import_model_module(
model_name, model_dir_compiled
)
model = model_module.getModel()
solver = model.getSolver()
model = model_module.get_model()
solver = model.create_solver()
# TODO
edata = amici.ExpData(model)
edata.setTimepoints([1e8])
edata.setObservedData([1.0])
edata.setObservedDataStdDev([1.0])
edata.set_timepoints([1e8])
edata.set_observed_data([1.0])
edata.set_observed_data_std_dev([1.0])

prepare_simulation(arg, model, solver, edata)

rdata = amici.runAmiciSimulation(model, solver, edata)
rdata = amici.run_simulation(model, solver, edata)

check_results(rdata)

Expand Down
6 changes: 3 additions & 3 deletions tests/sbml/testSBMLSuiteJax.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,17 +34,17 @@ def __init__(self, jax_model: object, importer: amici.SbmlImporter):
self.jax_model = jax_model
self.importer = importer

def getParameterIds(self):
def get_parameter_ids(self):
return list(self.jax_model.parameter_ids)

def getParameterById(self, pid: str):
def get_parameter_by_id(self, pid: str):
return float(
self.jax_model.parameters[
list(self.jax_model.parameter_ids).index(pid)
]
)

def getExpressionIds(self):
def get_expression_ids(self):
return list(self.jax_model.expression_ids)


Expand Down
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