def _execute_case(case):
"""Run a single PEtab test suite case"""
case = petabtests.test_id_str(case)
logger.info(f"Case {case}")
# case folder
case_dir = os.path.join(petabtests.CASES_DIR, case)
# load solution
solution = petabtests.load_solution(case, 'sbml')
gt_chi2 = solution[petabtests.CHI2]
gt_llh = solution[petabtests.LLH]
gt_simulation_dfs = solution[petabtests.SIMULATION_DFS]
tol_chi2 = solution[petabtests.TOL_CHI2]
tol_llh = solution[petabtests.TOL_LLH]
tol_simulations = solution[petabtests.TOL_SIMULATIONS]
# import petab problem
yaml_file = os.path.join(case_dir, petabtests.problem_yaml_name(case))
# unique folder for compiled amici model
output_folder = f'amici_models/model_{case}'
# import and create objective function
importer = pypesto.petab.PetabImporter.from_yaml(
yaml_file, output_folder=output_folder)
model = importer.create_model(generate_sensitivity_code=False)
obj = importer.create_objective(model=model)
# the scaled parameters
problem_parameters = importer.petab_problem.x_nominal_scaled
# simulate
ret = obj(problem_parameters, sensi_orders=(0, ), return_dict=True)
# extract results
rdatas = ret['rdatas']
chi2 = sum(rdata['chi2'] for rdata in rdatas)
llh = -ret['fval']
simulation_df = amici.petab_objective.rdatas_to_measurement_df(
rdatas, model, importer.petab_problem.measurement_df)
petab.check_measurement_df(simulation_df,
importer.petab_problem.observable_df)
simulation_df = simulation_df.rename(
columns={petab.MEASUREMENT: petab.SIMULATION})
simulation_df[petab.TIME] = simulation_df[petab.TIME].astype(int)
# check if matches
chi2s_match = petabtests.evaluate_chi2(chi2, gt_chi2, tol_chi2)
llhs_match = petabtests.evaluate_llh(llh, gt_llh, tol_llh)
simulations_match = petabtests.evaluate_simulations([simulation_df],
gt_simulation_dfs,
tol_simulations)
# log matches
logger.log(
logging.INFO if chi2s_match else logging.ERROR,
f"CHI2: simulated: {chi2}, expected: {gt_chi2},"
f" match = {chi2s_match}",
)
logger.log(
logging.INFO if simulations_match else logging.ERROR,
f"LLH: simulated: {llh}, expected: {gt_llh}, "
f"match = {llhs_match}",
)
logger.log(
logging.INFO if simulations_match else logging.ERROR,
f"Simulations: match = {simulations_match}",
)
if not all([llhs_match, chi2s_match, simulations_match]):
logger.error(f"Case {case} failed.")
raise AssertionError(f"Case {case}: Test results do not match "
"expectations")
logger.info(f"Case {case} passed.")
def _execute_case(case):
"""Run a single PEtab test suite case"""
case = petabtests.test_id_str(case)
logger.info(f"Case {case}")
# case folder
case_dir = os.path.join(petabtests.CASES_DIR, case)
# load solution
solution = petabtests.load_solution(case)
gt_chi2 = solution[petabtests.CHI2]
gt_llh = solution[petabtests.LLH]
gt_simulation_dfs = solution[petabtests.SIMULATION_DFS]
tol_chi2 = solution[petabtests.TOL_CHI2]
tol_llh = solution[petabtests.TOL_LLH]
tol_simulations = solution[petabtests.TOL_SIMULATIONS]
# unique folder for compiled amici model
output_folder = f'amici_models/model_{case}'
# import petab problem
yaml_file = os.path.join(case_dir, petabtests.problem_yaml_name(case))
# create problem
petab_problem = petab.Problem.from_yaml(yaml_file)
# compile amici
amici_model = amici.petab_import.import_petab_problem(
petab_problem=petab_problem, model_output_dir=output_folder)
solver = amici_model.getSolver()
# import to pyabc
importer = pyabc.petab.AmiciPetabImporter(petab_problem, amici_model,
solver)
model = importer.create_model(return_rdatas=True)
# simulate
problem_parameters = petab_problem.x_nominal_free_scaled
ret = model(problem_parameters)
llh = ret['llh']
# extract results
rdatas = ret['rdatas']
chi2 = sum(rdata['chi2'] for rdata in rdatas)
simulation_df = amici.petab_objective.rdatas_to_measurement_df(
rdatas, amici_model, importer.petab_problem.measurement_df)
petab.check_measurement_df(simulation_df,
importer.petab_problem.observable_df)
simulation_df = simulation_df.rename(
columns={petab.MEASUREMENT: petab.SIMULATION})
simulation_df[petab.TIME] = simulation_df[petab.TIME].astype(int)
# check if matches
chi2s_match = petabtests.evaluate_chi2(chi2, gt_chi2, tol_chi2)
llhs_match = petabtests.evaluate_llh(llh, gt_llh, tol_llh)
simulations_match = petabtests.evaluate_simulations([simulation_df],
gt_simulation_dfs,
tol_simulations)
# log matches
logger.log(
logging.INFO if chi2s_match else logging.ERROR,
f"CHI2: simulated: {chi2}, expected: {gt_chi2},"
f" match = {chi2s_match}")
logger.log(
logging.INFO if simulations_match else logging.ERROR,
f"LLH: simulated: {llh}, expected: {gt_llh}, "
f"match = {llhs_match}")
logger.log(logging.INFO if simulations_match else logging.ERROR,
f"Simulations: match = {simulations_match}")
# FIXME case 7, 16 fail due to amici/#963
if not all([llhs_match, simulations_match]) \
or (not chi2s_match and case not in ['0007', '0016']):
# chi2s_match ignored until fixed in amici
logger.error(f"Case {case} failed.")
raise AssertionError(f"Case {case}: Test results do not match "
"expectations")
logger.info(f"Case {case} passed.")
if case.startswith('0006') and model_type != "pysb":
petab.flatten_timepoint_specific_output_overrides(problem)
model_output_dir = f'amici_models/model_{case}'
model = import_petab_problem(problem,
model_output_dir=model_output_dir,
force_compile=True)
# simulate
ret = simulate_petab(problem, model, log_level=logging.DEBUG)
rdatas = ret['rdatas']
chi2 = sum(rdata['chi2'] for rdata in rdatas)
llh = ret['llh']
simulation_df = rdatas_to_measurement_df(rdatas, model,
problem.measurement_df)
petab.check_measurement_df(simulation_df, problem.observable_df)
simulation_df = simulation_df.rename(
columns={petab.MEASUREMENT: petab.SIMULATION})
simulation_df[petab.TIME] = simulation_df[petab.TIME].astype(int)
solution = petabtests.load_solution(case, model_type)
gt_chi2 = solution[petabtests.CHI2]
gt_llh = solution[petabtests.LLH]
gt_simulation_dfs = solution[petabtests.SIMULATION_DFS]
if case.startswith('0006'):
# account for flattening
gt_simulation_dfs[0].loc[:, petab.OBSERVABLE_ID] = ('obs_a__10__c0',
'obs_a__15__c0')
tol_chi2 = solution[petabtests.TOL_CHI2]
tol_llh = solution[petabtests.TOL_LLH]
tol_simulations = solution[petabtests.TOL_SIMULATIONS]
def _test_case(case):
"""Run a single PEtab test suite case"""
case = petabtests.test_id_str(case)
logger.debug(f"Case {case}")
# load
case_dir = os.path.join(petabtests.CASES_DIR, case)
# import petab problem
yaml_file = os.path.join(case_dir, petabtests.problem_yaml_name(case))
problem = petab.Problem.from_yaml(yaml_file)
# compile amici model
model_output_dir = f'amici_models/model_{case}'
model = import_petab_problem(
problem, model_output_dir=model_output_dir)
# simulate
chi2s_match = llhs_match = simulations_match = False
ret = simulate_petab(problem, model, log_level=logging.DEBUG)
rdatas = ret['rdatas']
chi2 = sum(rdata['chi2'] for rdata in rdatas)
llh = ret['llh']
simulation_df = rdatas_to_measurement_df(rdatas, model,
problem.measurement_df)
petab.check_measurement_df(simulation_df, problem.observable_df)
simulation_df = simulation_df.rename(
columns={petab.MEASUREMENT: petab.SIMULATION})
simulation_df[petab.TIME] = simulation_df[petab.TIME].astype(int)
solution = petabtests.load_solution(case)
gt_chi2 = solution[petabtests.CHI2]
gt_llh = solution[petabtests.LLH]
gt_simulation_dfs = solution[petabtests.SIMULATION_DFS]
tol_chi2 = solution[petabtests.TOL_CHI2]
tol_llh = solution[petabtests.TOL_LLH]
tol_simulations = solution[petabtests.TOL_SIMULATIONS]
chi2s_match = petabtests.evaluate_chi2(chi2, gt_chi2, tol_chi2)
llhs_match = petabtests.evaluate_llh(llh, gt_llh, tol_llh)
simulations_match = petabtests.evaluate_simulations(
[simulation_df], gt_simulation_dfs, tol_simulations)
logger.log(logging.DEBUG if chi2s_match else logging.ERROR,
f"CHI2: simulated: {chi2}, expected: {gt_chi2},"
f" match = {chi2s_match}")
logger.log(logging.DEBUG if simulations_match else logging.ERROR,
f"LLH: simulated: {llh}, expected: {gt_llh}, "
f"match = {llhs_match}")
logger.log(logging.DEBUG if simulations_match else logging.ERROR,
f"Simulations: match = {simulations_match}")
# FIXME case 7 fails due to #963
if case not in ['0007', '0016']:
check_derivatives(problem, model)
# FIXME case 7 fails due to #963
if not all([llhs_match, simulations_match]) \
or (not chi2s_match and case not in ['0007', '0016']):
# chi2s_match ignored until fixed in amici
logger.error(f"Case {case} failed.")
raise AssertionError(f"Case {case}: Test results do not match "
"expectations")
logger.info(f"Case {case} passed.")