Remove option to keep unmodeled species in ThinLayer

The 'remove_unmodeled_species' parameter was removed from BaseThinLayer and related tests. Unmodeled species are now always removed during optimization, simplifying the API and test logic.

Author: JR-1991

pyenzyme/thinlayers/base.py

@@ -36,7 +36,6 @@ def __init__(
         enzmldoc: v2.EnzymeMLDocument,
         measurement_ids: Optional[List[str]] = None,
         df_per_measurement: bool = False,
-        remove_unmodeled_species: bool = True,
     ):
         assert isinstance(enzmldoc, v2.EnzymeMLDocument)
         assert isinstance(measurement_ids, list) or measurement_ids is None
@@ -49,9 +48,6 @@ def __init__(
         if measurement_ids is None:
             measurement_ids = [meas.id for meas in enzmldoc.measurements]
 
-        if remove_unmodeled_species:
-            enzmldoc = self._remove_unmodeled_species(enzmldoc)
-
         self.enzmldoc = enzmldoc.model_copy(deep=True)
         self.fitted_doc = enzmldoc.model_copy(deep=True)
         self.measurement_ids = measurement_ids

pyenzyme/thinlayers/psyces.py

@@ -309,9 +309,10 @@ def _get_experimental_data(self):
 
         Populates the inits, experimental_data, and cols attributes.
         """
+        enzmldoc = self._remove_unmodeled_species(self.enzmldoc)
         self.inits = [
             InitMap.from_measurement(measurement, self.df_map[measurement.id])
-            for measurement in self.enzmldoc.measurements
+            for measurement in enzmldoc.measurements
             if measurement.id in self.measurement_ids
         ]
 

tests/unit/test_thinlayer.py

@@ -29,18 +29,19 @@ def test_remove_unmodeled_species_reaction(self):
         reaction.add_to_products(species_id="Product", stoichiometry=1)
 
         # Remove unmodeled species
-        thinlayer = MockThinLayer(enzmldoc, remove_unmodeled_species=True)
+        thinlayer = MockThinLayer(enzmldoc)
+        tl_enzmldoc = thinlayer.optimize()
 
-        assert len(thinlayer.enzmldoc.small_molecules) == 2, (
-            f"Unmodeled small molecules should be removed, but {len(thinlayer.enzmldoc.small_molecules)} remain."
+        assert len(tl_enzmldoc.small_molecules) == 2, (
+            f"Unmodeled small molecules should be removed, but {len(tl_enzmldoc.small_molecules)} remain."
         )
-        assert len(thinlayer.enzmldoc.measurements) == 2, (
-            f"Unmodeled measurements should be removed, but {len(thinlayer.enzmldoc.measurements)} remain."
+        assert len(tl_enzmldoc.measurements) == 2, (
+            f"Unmodeled measurements should be removed, but {len(tl_enzmldoc.measurements)} remain."
         )
 
         measurement_has_unmodeled: list[str] = []
 
-        for measurement in thinlayer.enzmldoc.measurements:
+        for measurement in tl_enzmldoc.measurements:
             for species_data in measurement.species_data:
                 if species_data.species_id == "Unmodeled":
                     measurement_has_unmodeled.append(measurement.id)
@@ -74,18 +75,19 @@ def test_remove_unmodeled_species_odes(self):
         )
 
         # Remove unmodeled species
-        thinlayer = MockThinLayer(enzmldoc, remove_unmodeled_species=True)
+        thinlayer = MockThinLayer(enzmldoc)
+        tl_enzmldoc = thinlayer.optimize()
 
-        assert len(thinlayer.enzmldoc.small_molecules) == 2, (
-            f"Unmodeled small molecules should be removed, but {len(thinlayer.enzmldoc.small_molecules)} remain."
+        assert len(tl_enzmldoc.small_molecules) == 2, (
+            f"Unmodeled small molecules should be removed, but {len(tl_enzmldoc.small_molecules)} remain."
         )
-        assert len(thinlayer.enzmldoc.measurements) == 2, (
-            f"Unmodeled measurements should be removed, but {len(thinlayer.enzmldoc.measurements)} remain."
+        assert len(tl_enzmldoc.measurements) == 2, (
+            f"Unmodeled measurements should be removed, but {len(tl_enzmldoc.measurements)} remain."
         )
 
         measurement_has_unmodeled: list[str] = []
 
-        for measurement in thinlayer.enzmldoc.measurements:
+        for measurement in tl_enzmldoc.measurements:
             for species_data in measurement.species_data:
                 if species_data.species_id == "Unmodeled":
                     measurement_has_unmodeled.append(measurement.id)
@@ -94,44 +96,6 @@ def test_remove_unmodeled_species_odes(self):
             f"Unmodeled species should be removed, but appears in measurements {measurement_has_unmodeled}."
         )
 
-    def test_leave_unmodeled_species(self):
-        """
-        Test that unmodeled species are preserved when remove_unmodeled_species=False.
-
-        This test verifies that:
-        - All species are kept in the document regardless of modeling status
-        - Empty measurements are still removed
-        - Measurements with unmodeled species are preserved
-        """
-        enzmldoc = self._create_enzmldoc()
-
-        # Add reaction with only Substrate and Product (Unmodeled remains unmodeled)
-        reaction = enzmldoc.add_to_reactions(id="R1", name="R1")
-        reaction.add_to_reactants(species_id="Substrate", stoichiometry=1)
-        reaction.add_to_products(species_id="Product", stoichiometry=1)
-
-        # Keep unmodeled species
-        thinlayer = MockThinLayer(enzmldoc, remove_unmodeled_species=False)
-
-        assert len(thinlayer.enzmldoc.small_molecules) == 3, (
-            f"Unmodeled small molecules should not be removed, but {len(thinlayer.enzmldoc.small_molecules)} remain."
-        )
-
-        assert len(thinlayer.enzmldoc.measurements) == 3, (
-            f"Empty measurements should be removed, but {len(thinlayer.enzmldoc.measurements)} remain."
-        )
-
-        measurement_has_unmodeled: list[str] = []
-
-        for measurement in thinlayer.enzmldoc.measurements:
-            for species_data in measurement.species_data:
-                if species_data.species_id == "Unmodeled":
-                    measurement_has_unmodeled.append(measurement.id)
-
-        assert len(measurement_has_unmodeled) == 2, (
-            f"Unmodeled species should not be removed, but appears in measurements {measurement_has_unmodeled}."
-        )
-
     def _create_enzmldoc(self) -> EnzymeMLDocument:
         """
         Create a test EnzymeML document with various measurement scenarios.
@@ -190,7 +154,7 @@ def integrate(self, *args, **kwargs):
 
     def optimize(self, *args, **kwargs):
         """Mock optimization method that does nothing."""
-        pass
+        return self._remove_unmodeled_species(self.enzmldoc)
 
     def write(self, *args, **kwargs):
         """Mock write method that does nothing."""