diff --git a/python/sdist/amici/petab/petab_problem.py b/python/sdist/amici/petab/petab_problem.py index 8a205cebdd..df5b59a02b 100644 --- a/python/sdist/amici/petab/petab_problem.py +++ b/python/sdist/amici/petab/petab_problem.py @@ -1,19 +1,11 @@ """PEtab-problem based simulations.""" import copy -from typing import Optional, Sequence, Union +from typing import Optional, Union import amici import pandas as pd import petab -from petab.C import ( - DATASET_ID, - NOISE_PARAMETERS, - OBSERVABLE_ID, - PREEQUILIBRATION_CONDITION_ID, - SIMULATION, - SIMULATION_CONDITION_ID, - TIME, -) +from petab.C import PREEQUILIBRATION_CONDITION_ID, SIMULATION_CONDITION_ID from .conditions import create_edatas, fill_in_parameters from .parameter_mapping import create_parameter_mapping @@ -27,8 +19,6 @@ class AmiciPetabProblem: :param petab_problem: PEtab problem definition. :param amici_model: AMICI model - :param amici_solver: AMICI solver (Solver with default options will be - used if not provided). :param problem_parameters: Problem parameters to use for simulation (default: PEtab nominal values and model values). :param scaled_parameters: Whether the provided parameters are on PEtab @@ -48,15 +38,12 @@ def __init__( petab_problem: petab.Problem, amici_model: amici.Model, problem_parameters: Optional[dict[str, float]] = None, - # move to a separate AmiciPetabProblemSimulator class? - amici_solver: Optional[amici.Solver] = None, scaled_parameters: Optional[bool] = False, simulation_conditions: Union[pd.DataFrame, list[dict]] = None, store_edatas: bool = True, ): - self._petab_problem = petab_problem + self._petab_problem = copy.deepcopy(petab_problem) self._amici_model = amici_model - self._amici_solver = amici_solver self._scaled_parameters = scaled_parameters self._simulation_conditions = simulation_conditions or ( @@ -94,7 +81,6 @@ def __init__( scaled_parameters=self._scaled_parameters, amici_model=self._amici_model, ) - self._create_edatas() else: self._parameter_mapping = None @@ -223,11 +209,6 @@ def _create_edata( raise AssertionError("Expected exactly one ExpData object.") return edatas[0] - @property - def solver(self): - """Get the solver.""" - return self._amici_solver or self._amici_model.getSolver() - def _create_edatas( self, ):