From ca2a01c0c2a72ef158747ff521a286ccefaecc0e Mon Sep 17 00:00:00 2001 From: Daniel Weindl Date: Thu, 9 Oct 2025 08:38:16 +0200 Subject: [PATCH] Fix #2969 Missed a few lines in #2969. --- tests/performance/test.py | 86 +++++++++++++++++----------------- tests/sbml/testSBMLSuiteJax.py | 6 +-- 2 files changed, 46 insertions(+), 46 deletions(-) diff --git a/tests/performance/test.py b/tests/performance/test.py index efba89f81d..0ccb287167 100755 --- a/tests/performance/test.py +++ b/tests/performance/test.py @@ -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]) @@ -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) @@ -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) diff --git a/tests/sbml/testSBMLSuiteJax.py b/tests/sbml/testSBMLSuiteJax.py index 085cdddf97..77773c2da0 100644 --- a/tests/sbml/testSBMLSuiteJax.py +++ b/tests/sbml/testSBMLSuiteJax.py @@ -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)