From c06df1d6d94ff670953b453ec7aa3ff90b8470db Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Sun, 10 Nov 2024 10:26:15 +0100
Subject: [PATCH] Optional warning in `fill_in_parameters`

`amici.petab.conditions.fill_in_parameters` emits a warnings if parameters are supplied that don't occur in the parameter mapping.
This is to point out potential issues with the parameter mapping.
However, sometimes it's more convenient to silently ignore those extra parameters. Therefore, make this warning optional.
---
 python/sdist/amici/petab/conditions.py | 22 +++++++++++++++++++---
 1 file changed, 19 insertions(+), 3 deletions(-)

diff --git a/python/sdist/amici/petab/conditions.py b/python/sdist/amici/petab/conditions.py
index 08c2f90302..ab06e8850d 100644
--- a/python/sdist/amici/petab/conditions.py
+++ b/python/sdist/amici/petab/conditions.py
@@ -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).
 
@@ -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: "
@@ -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.
 
@@ -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,
@@ -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
@@ -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 = (