get_model_for_condition: don't remove rate rules for condition-table overrides (#520)

`get_model_for_condition` removed *any* SBML rule (including rate rules)
for a species/compartment/parameter overridden in the condition table.
For rate-rule targets, this turned dynamic species into constants
instead of just setting their initial value.

Only assignment rules are removed now; rate rules are left in place.

Fixes #197

Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>

Author: dweindl

petab/v1/sbml.py

@@ -307,7 +307,15 @@ def get_param_value(parameter_id: str):
         ]
 
     def remove_rules(target_id: str):
-        if sbml_model.removeRuleByVariable(target_id):
+        """Remove any assignment rule and initial assignment for
+        ``target_id`` so that its initial value can be set explicitly.
+        """
+        rule = sbml_model.getRuleByVariable(target_id)
+        if (
+            rule is not None
+            and rule.getTypeCode() == libsbml.SBML_ASSIGNMENT_RULE
+        ):
+            sbml_model.removeRuleByVariable(target_id)
             warn(
                 "An SBML rule was removed to set the component "
                 f"{target_id} to a constant value.",

tests/v1/test_sbml.py

@@ -17,9 +17,10 @@ def create_test_data():
         "\n".join(
             [
                 "compartment compartment_1 = 1",
-                *(f"species species_{i} = 10 * {i}" for i in range(1, 5)),
+                *(f"species species_{i} = 10 * {i}" for i in range(1, 6)),
                 *(f"parameter_{i} = {i}" for i in range(1, 4)),
                 "species_2 := 25",
+                "species_5' = 1",
             ]
         )
     )
@@ -32,6 +33,7 @@ def create_test_data():
             "species_2": [25],
             "species_3": ["parameter_1"],
             "species_4": ["not_a_model_parameter"],
+            "species_5": [55],
             "compartment_1": [2],
         }
     )
@@ -85,6 +87,12 @@ def check_model(condition_model):
         condition_model.getSpecies("species_4").getInitialConcentration()
         == 3.25
     )
+    assert (
+        condition_model.getSpecies("species_5").getInitialConcentration() == 55
+    )
+    assert condition_model.getRuleByVariable("species_5") is not None, (
+        "RateRule was removed although it should have been kept"
+    )
     assert len(condition_model.getListOfInitialAssignments()) == 0, (
         "InitialAssignment not removed"
     )