..

Author: dweindl

petab/v2/converters.py

@@ -221,7 +221,7 @@ def _convert_experiment(self, experiment: Experiment) -> None:
         # Collect values for initial assignments for the different experiments.
         #  All expressions must be combined into a single initial assignment
         #  per target.
-        # target_id -> (experiment_indicator, target_value)
+        # target_id -> [(experiment_indicator, target_value), ...]
         period0_assignments: dict[str, list[tuple[str, sp.Basic]]] = {}
 
         for i_period, period in enumerate(experiment.sorted_periods):
@@ -330,7 +330,14 @@ def _convert_experiment(self, experiment: Experiment) -> None:
 
     @staticmethod
     def _initial_value_from_element(target: libsbml.SBase) -> sp.Basic:
-        # use the initial value of the target as default
+        """Get the initial value of an SBML element.
+
+        The value to the size attribute of compartments,
+        the initial concentration or amount of species (amount for
+        `hasOnlySubstanceUnits=true`, concentration otherwise), and
+        the value of parameters, not considering any initial assignment
+        constructs.
+        """
         if target is None:
             raise ValueError("`target` is None.")
 

tests/v2/test_converters.py

@@ -26,7 +26,8 @@ def test_experiments_to_events_converter():
     assert isinstance(converted.model, SbmlModel)
     sbml_model = converted.model.sbml_model
 
-    assert sbml_model.getNumEvents() == 2
+    # one event -- the initial period is handled via initial assignments
+    assert sbml_model.getNumEvents() == 1
     assert converted.conditions == [
         Condition(
             id="_petab_preequilibration_on",
@@ -211,7 +212,6 @@ def test_simulate_experiment_to_events():
         "_petab_experiment_indicator_e1"
     ).setValue(1)
     sbml_actual = converted.model.to_sbml_str()
-    print(converted.model.to_antimony())
     basico.load_model(sbml_actual)
     df_actual = basico.run_time_course(values=timepoints)