From 0d3c25a32ac8c19e2e0c088be9a4b9c1b38f21ce Mon Sep 17 00:00:00 2001
From: Branwen Snelling <branwen.snelling@crick.ac.uk>
Date: Wed, 19 Aug 2026 15:04:49 +0100
Subject: [PATCH 1/2] skip cond ids set by arrays for all periods

---
 petab/v2/converters.py | 12 ++++++------
 tests/v2/test_sciml.py | 37 +++++++++++++++++++++++++++++++++++++
 2 files changed, 43 insertions(+), 6 deletions(-)

diff --git a/petab/v2/converters.py b/petab/v2/converters.py
index e5e9c4f4..33f6f550 100644
--- a/petab/v2/converters.py
+++ b/petab/v2/converters.py
@@ -248,6 +248,12 @@ def _convert_experiment(self, experiment: Experiment) -> None:
                 #  or the only non-equilibration period (handled above)
                 continue
 
+            # Skip if condition ids are set by array data
+            if self._array_data_condition_ids and set(
+                period.condition_ids
+            ).issubset(self._array_data_condition_ids):
+                continue
+
             # Encode the period changes in the SBML model as events
             #  that trigger at the start of the period or,
             #  for the first period, as initial assignments.
@@ -258,12 +264,6 @@ def _convert_experiment(self, experiment: Experiment) -> None:
             #  single-period experiments.
             if i_period == 0:
                 exp_ind_id = self.get_experiment_indicator(experiment.id)
-                # Skip if condition ids are set by array data
-                # importers handle this
-                if self._array_data_condition_ids and set(
-                    period.condition_ids
-                ).issubset(self._array_data_condition_ids):
-                    continue
 
                 for change in self._new_problem.get_changes_for_period(period):
                     period0_assignments.setdefault(
diff --git a/tests/v2/test_sciml.py b/tests/v2/test_sciml.py
index f6cedc28..74ed2737 100644
--- a/tests/v2/test_sciml.py
+++ b/tests/v2/test_sciml.py
@@ -463,6 +463,43 @@ def test_genuinely_missing_output_parameter_still_reported():
     assert not any("net1_output2" in issue.message for issue in results)
 
 
+# ---------------------------------------------------------------------------
+# Experiment -> SBML conversion
+# ---------------------------------------------------------------------------
+
+def test_convert_experiments_with_array_data_condition_ids():
+    """Conditions defined only in array files are skipped in every period.
+    """
+    from petab.v2.converters import ExperimentsToSbmlConverter
+
+    problem = _get_test_problem()
+    assert not problem.conditions, "cond1 must not be in the condition table"
+    array_condition_ids = (
+        problem.extensions.sciml._get_array_data_condition_ids()
+    )
+    assert array_condition_ids == {"cond1"}
+
+    # Add preequilibration and simulation periods
+    periods = [(-float("inf"), "cond1"), (0.0, "cond1")]
+    problem.experiments[0].periods = [
+        ExperimentPeriod(time=time, condition_ids=[condition_id])
+        for time, condition_id in periods
+    ]
+
+    converted = ExperimentsToSbmlConverter(problem).convert()
+
+    # No events defined for conditions given by array data
+    sbml_model = converted.model.sbml_model
+    assigned_targets = {
+        ia.getSymbol() for ia in sbml_model.getListOfInitialAssignments()
+    } | {
+        ea.getVariable()
+        for event in sbml_model.getListOfEvents()
+        for ea in event.getListOfEventAssignments()
+    }
+    assert "net1_input2" not in assigned_targets
+
+
 # ---------------------------------------------------------------------------
 # Full-problem integration
 # ---------------------------------------------------------------------------

From a91d621a76dc0fbcf76e861c77e77cb6b21d437a Mon Sep 17 00:00:00 2001
From: Branwen Snelling <branwen.snelling@crick.ac.uk>
Date: Wed, 19 Aug 2026 15:08:25 +0100
Subject: [PATCH 2/2] reformat ruff

---
 tests/v2/test_sciml.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/v2/test_sciml.py b/tests/v2/test_sciml.py
index 74ed2737..a6cdf098 100644
--- a/tests/v2/test_sciml.py
+++ b/tests/v2/test_sciml.py
@@ -467,9 +467,9 @@ def test_genuinely_missing_output_parameter_still_reported():
 # Experiment -> SBML conversion
 # ---------------------------------------------------------------------------
 
+
 def test_convert_experiments_with_array_data_condition_ids():
-    """Conditions defined only in array files are skipped in every period.
-    """
+    """Conditions defined only in array files are skipped in every period."""
     from petab.v2.converters import ExperimentsToSbmlConverter
 
     problem = _get_test_problem()