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PEtab: Fix warning from fill_in_parameters with fixed parameters #1509

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merged 7 commits into from
Nov 19, 2024
Merged

PEtab: Fix warning from fill_in_parameters with fixed parameters #1509

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ade574a
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dweindl Nov 18, 2024
c966147
add paranoia
dilpath Nov 18, 2024
18f3aab
Update pypesto/objective/amici/amici_calculator.py
dilpath Nov 18, 2024
34a8b38
..
dweindl Nov 18, 2024
7d6d1d4
Merge remote-tracking branch 'upstream/develop' into fix_fillin_warning
dweindl Nov 19, 2024
256182e
revert
dweindl Nov 19, 2024
7ba3815
..
dweindl Nov 19, 2024
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22 changes: 21 additions & 1 deletion pypesto/objective/amici/amici.py
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Original file line number Diff line number Diff line change
Expand Up @@ -183,7 +183,12 @@ def __init__(
# (relevant for setting ``plist`` in ExpData later on)
self.parameter_mapping = parameter_mapping
# parameter mapping independent of fixed parameters
# (i.e., all objective parameters are included as parameter IDs,
# not as their values)
self._parameter_mapping_full = copy.deepcopy(parameter_mapping)
# IDs of fixed `Problem` parameters
self._fixed_parameter_ids = []

# If supported, enable `guess_steadystate` by default. If not
# supported, disable by default. If requested but unsupported, raise.
if (
Expand Down Expand Up @@ -478,8 +483,16 @@ def call_unprocessed(
edatas = self.edatas
if parameter_mapping is None:
parameter_mapping = self.parameter_mapping
# Some parameters may appear estimated in the original compiled model,
# but then are fixed during parameter estimation. These are removed
# from the parameter vector to avoid warnings about unused parameters.
x_dct_free = {
par_id: val
for par_id, val in x_dct.items()
if par_id not in self._fixed_parameter_ids
}
ret = self.calculator(
x_dct=x_dct,
x_dct=x_dct_free,
sensi_orders=sensi_orders,
mode=mode,
amici_model=self.amici_model,
Expand Down Expand Up @@ -679,6 +692,7 @@ def update_from_problem(
# and replace the IDs of all fixed parameters by their respective
# values.
self.parameter_mapping = copy.deepcopy(self._parameter_mapping_full)
self._fixed_parameter_ids = [self.x_ids[i] for i in x_fixed_indices]
if not len(x_fixed_indices):
return

Expand All @@ -693,3 +707,9 @@ def update_from_problem(
) in condition_mapping.map_sim_var.items():
if (val := id_to_val.get(mapped_to_par)) is not None:
condition_mapping.map_sim_var[model_par] = val
for (
model_par,
mapped_to_par,
) in condition_mapping.map_sim_fix.items():
if (val := id_to_val.get(mapped_to_par)) is not None:
condition_mapping.map_sim_fix[model_par] = val
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