rename

Author: dweindl

petab/v2/converters.py

@@ -20,14 +20,14 @@
 from .models._sbml_utils import add_sbml_parameter, check
 from .models.sbml_model import SbmlModel
 
-__all__ = ["ExperimentsToEventsConverter"]
+__all__ = ["ExperimentsToSbmlConverter"]
 
 
-class ExperimentsToEventsConverter:
-    """Convert PEtab experiments to SBML events.
+class ExperimentsToSbmlConverter:
+    """Convert PEtab experiments to SBML.
 
     For an SBML-model-based PEtab problem, this class converts the PEtab
-    experiments to events as far as possible.
+    experiments to initial assignments and events as far as possible.
 
     If the model already contains events, PEtab events are added with a higher
     priority than the existing events to guarantee that PEtab condition changes
@@ -38,8 +38,8 @@ class ExperimentsToEventsConverter:
     The PEtab problem must not contain any identifiers starting with
     ``_petab``.
 
-    All periods and condition changes that are represented by events
-    will be removed from the condition table.
+    All periods and condition changes that are represented by initial
+    assignments or events will be removed from the condition table.
     Each experiment will have at most one period with a start time of ``-inf``
     and one period with a finite start time. The associated changes with
     these periods are only the pre-equilibration indicator
@@ -454,7 +454,7 @@ def _create_event_assignments_for_period(
         :param changes: The PEtab condition changes that are to be applied
             at the start of the period.
         """
-        _add_assignment = ExperimentsToEventsConverter._add_assignment
+        _add_assignment = ExperimentsToSbmlConverter._add_assignment
         sbml_model = event.getModel()
         # collect IDs of compartments that are changed in this period
         changed_compartments = {

tests/v2/test_converters.py

@@ -3,12 +3,12 @@
 import pandas as pd
 
 from petab.v2 import Change, Condition, Experiment, ExperimentPeriod, Problem
-from petab.v2.converters import ExperimentsToEventsConverter
+from petab.v2.converters import ExperimentsToSbmlConverter
 from petab.v2.models.sbml_model import SbmlModel
 
 
 def test_experiments_to_events_converter():
-    """Test the ExperimentsToEventsConverter."""
+    """Test the ExperimentsToSbmlConverter."""
     ant_model = """
     species X = 0
     X' = 1
@@ -19,7 +19,7 @@ def test_experiments_to_events_converter():
     problem.add_condition("c2", X=2)
     problem.add_experiment("e1", -inf, "c1", 10, "c2")
 
-    converter = ExperimentsToEventsConverter(problem)
+    converter = ExperimentsToSbmlConverter(problem)
     converted = converter.convert()
     assert converted.validate().has_errors() is False
 
@@ -204,7 +204,7 @@ def test_simulate_experiment_to_events():
     problem.assert_valid()
 
     # convert PEtab experiments to SBML events and simulate in BasiCO
-    converter = ExperimentsToEventsConverter(problem)
+    converter = ExperimentsToSbmlConverter(problem)
     converted = converter.convert()
     # set experiment indicator to simulate experiment "e1"
     converted.model.sbml_model.getParameter(