From a65b4054fcb0a233ff298d813b9fd78371555c38 Mon Sep 17 00:00:00 2001
From: Daniel Weindl <daniel.weindl@uni-bonn.de>
Date: Mon, 21 Sep 2026 19:29:35 +0200
Subject: [PATCH] get_model_for_condition: don't remove rate rules for
 condition-table overrides

`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>
---
 petab/v1/sbml.py      | 10 +++++++++-
 tests/v1/test_sbml.py | 10 +++++++++-
 2 files changed, 18 insertions(+), 2 deletions(-)

diff --git a/petab/v1/sbml.py b/petab/v1/sbml.py
index e8ed10aa..dc6f594b 100644
--- a/petab/v1/sbml.py
+++ b/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.",
diff --git a/tests/v1/test_sbml.py b/tests/v1/test_sbml.py
index 5cbb1568..469524c5 100644
--- a/tests/v1/test_sbml.py
+++ b/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"
     )