diff --git a/python/sdist/amici/petab/petab_problem.py b/python/sdist/amici/petab/petab_problem.py index 6be89a6c67..bb6806fbd3 100644 --- a/python/sdist/amici/petab/petab_problem.py +++ b/python/sdist/amici/petab/petab_problem.py @@ -14,7 +14,7 @@ class AmiciPetabProblem: """Manage experimental conditions based on a PEtab problem definition. - Create :class:`ExpData` objects from a PEtab problem definition, handle + Create :class:`ExpData` objects from a PEtab problem definition, and handle parameter scales and parameter mapping. :param petab_problem: PEtab problem definition. @@ -24,13 +24,13 @@ class AmiciPetabProblem: :param scaled_parameters: Whether the provided parameters are on PEtab `parameterScale` or not. :param simulation_conditions: Simulation conditions to use for simulation. - It Can be used to subset the conditions in the PEtab problem. - All subsequent operations will only be performed based on that subset. + It can be used to subset the conditions in the PEtab problem. + All subsequent operations will only be performed on that subset. By default, all conditions are used. - :param store_edatas: Whether to create and store all ExpData objects for - all conditions upfront. If set to False, ExpData objects will be - created and disposed of on the fly during simulation. This can save - memory if many conditions are simulated. + :param store_edatas: Whether to create and store all `ExpData` objects for + all conditions upfront. If set to ``False``, `ExpData` objects will be + created and disposed of on the fly during simulation. The latter saves + memory if the given PEtab problem comprises many simulation conditions. """ def __init__( @@ -148,14 +148,14 @@ def get_edata( ) -> amici.ExpData: """Get ExpData object for a given condition. - NOTE: If `store_edatas=True` was passed to the constructor and the + NOTE: If ``store_edatas=True`` was passed to the constructor and the returned object is modified, the changes will be reflected in the - internal ExpData objects. Also, if parameter values of - AmiciPetabProblem are changed, all ExpData objects will be updated. + internal `ExpData` objects. Also, if parameter values of + `AmiciPetabProblem` are changed, all `ExpData` objects will be updated. Create a deep copy if you want to avoid this. - :param condition_id: PEtab Condition ID - :param preequilibration_condition_id: PEtab Preequilibration condition ID + :param condition_id: PEtab condition ID + :param preequilibration_condition_id: PEtab preequilibration condition ID :return: ExpData object """ # exists or has to be created? @@ -173,10 +173,10 @@ def get_edata( def get_edatas(self): """Get all ExpData objects. - NOTE: If `store_edatas=True` was passed to the constructor and the + NOTE: If ``store_edatas=True`` was passed to the constructor and the returned objects are modified, the changes will be reflected in the - internal ExpData objects. Also, if parameter values of - AmiciPetabProblem are changed, all ExpData objects will be updated. + internal `ExpData` objects. Also, if parameter values of + `AmiciPetabProblem` are changed, all `ExpData` objects will be updated. Create a deep copy if you want to avoid this. :return: List of ExpData objects @@ -202,8 +202,8 @@ def _create_edata( ) -> amici.ExpData: """Create ExpData object for a given condition. - :param condition_id: PEtab Condition ID - :param preequilibration_condition_id: PEtab Preequilibration condition ID + :param condition_id: PEtab condition ID + :param preequilibration_condition_id: PEtab preequilibration condition ID :return: ExpData object """ simulation_condition = pd.DataFrame(