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Optional warning in fill_in_parameters #2578

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Nov 10, 2024
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Optional warning in fill_in_parameters #2578

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22 changes: 19 additions & 3 deletions python/sdist/amici/petab/conditions.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@ def fill_in_parameters(
scaled_parameters: bool,
parameter_mapping: ParameterMapping,
amici_model: AmiciModel,
warn_unused: bool = True,
) -> None:
"""Fill fixed and dynamic parameters into the edatas (in-place).

Expand All @@ -59,9 +60,15 @@ def fill_in_parameters(
Parameter mapping for all conditions.
:param amici_model:
AMICI model.
:param warn_unused:
Whether a warning should be emitted if not all problem parameters
were used. I.e., if there are parameters in `problem_parameters`
that are not in `parameter_mapping`.
"""
if unused_parameters := (
set(problem_parameters.keys()) - parameter_mapping.free_symbols
if warn_unused and (
unused_parameters := (
set(problem_parameters.keys()) - parameter_mapping.free_symbols
)
):
warnings.warn(
"The following problem parameters were not used: "
Expand Down Expand Up @@ -223,6 +230,7 @@ def create_parameterized_edatas(
scaled_parameters: bool = False,
parameter_mapping: ParameterMapping = None,
simulation_conditions: pd.DataFrame | dict = None,
warn_unused: bool = True,
) -> list[amici.ExpData]:
"""Create list of :class:amici.ExpData objects with parameters filled in.

Expand All @@ -244,6 +252,11 @@ def create_parameterized_edatas(
:param simulation_conditions:
Result of :func:`petab.get_simulation_conditions`. Can be provided to
save time if this has been obtained before.
:param warn_unused:
Whether a warning should be emitted if not all problem parameters
were used. I.e., if there are parameters in `problem_parameters`
that are not in `parameter_mapping` or in the generated parameter
mapping.

:return:
List with one :class:`amici.amici.ExpData` per simulation condition,
Expand Down Expand Up @@ -282,6 +295,7 @@ def create_parameterized_edatas(
scaled_parameters=scaled_parameters,
parameter_mapping=parameter_mapping,
amici_model=amici_model,
warn_unused=warn_unused,
)

return edatas
Expand Down Expand Up @@ -387,7 +401,9 @@ def create_edatas(

:return:
List with one :class:`amici.amici.ExpData` per simulation condition,
with filled in timepoints and data.
with filled in timepoints and data, but without parameter values
(see :func:`create_parameterized_edatas` or
:func:`fill_in_parameters` for that).
"""
if simulation_conditions is None:
simulation_conditions = (
Expand Down
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