test

Author: dweindl

petab/v2/__init__.py

@@ -37,6 +37,7 @@
     models,  # noqa: F401, E402
 )
 from .conditions import *  # noqa: F403, F401, E402
+from .core import *  # noqa: F401, E402
 from .experiments import (  # noqa: F401, E402
     get_experiment_df,
     write_experiment_df,

petab/v2/converters.py

@@ -40,9 +40,11 @@ class ExperimentsToEventsConverter:
     #: ID of the parameter that indicates whether the model is in
     #  the pre-equilibration phase (1) or not (0).
     PREEQ_INDICATOR = "_petab_preequilibration_indicator"
+
     #: The condition ID of the condition that sets the
     #: pre-equilibration indicator to 1.
     CONDITION_ID_PREEQ_ON = "_petab_preequilibration_on"
+
     #: The condition ID of the condition that sets the
     #: pre-equilibration indicator to 0.
     CONDITION_ID_PREEQ_OFF = "_petab_preequilibration_off"
@@ -69,7 +71,7 @@ def __init__(self, problem: Problem, default_priority: float = None):
         self._original_problem = problem
         self._new_problem = deepcopy(self._original_problem)
 
-        self._model = self._new_problem.model.sbml_model
+        self._model: libsbml.Model = self._new_problem.model.sbml_model
         self._preeq_indicator = self.PREEQ_INDICATOR
 
         # The maximum event priority that was found in the unprocessed model.
@@ -85,7 +87,7 @@ def _get_experiment_indicator_condition_id(
         """Get the condition ID for the experiment indicator parameter."""
         return f"_petab_experiment_condition_{experiment_id}"
 
-    def _preprocess(self):
+    def _preprocess(self) -> None:
         """Check whether we can handle the given problem and store some model
         information."""
         model = self._model
@@ -184,7 +186,7 @@ def convert(self) -> Problem:
 
         return self._new_problem
 
-    def _convert_experiment(self, experiment: Experiment):
+    def _convert_experiment(self, experiment: Experiment) -> None:
         """Convert a single experiment to SBML events."""
         model = self._model
         experiment.sort_periods()
@@ -323,7 +325,9 @@ def _create_event_assignments_for_period(
                 )
 
     @staticmethod
-    def _change_to_event_assignment(change: Change, event: libsbml.Event):
+    def _change_to_event_assignment(
+        change: Change, event: libsbml.Event
+    ) -> None:
         """Convert a PEtab ``Change``  to an SBML event assignment."""
         sbml_model = event.getModel()
 

petab/v2/problem.py

@@ -838,7 +838,7 @@ def validate(
         )
 
         validation_results = ValidationResultList()
-        if self.config.extensions:
+        if self.config and self.config.extensions:
             extensions = ",".join(self.config.extensions.keys())
             validation_results.append(
                 ValidationIssue(

tests/v2/test_converters.py

@@ -0,0 +1,76 @@
+from math import inf
+
+from petab.v2 import Change, Condition, Experiment, ExperimentPeriod, Problem
+from petab.v2.converters import ExperimentsToEventsConverter
+from petab.v2.models.sbml_model import SbmlModel
+
+
+def test_experiments_to_events_converter():
+    """Test the ExperimentsToEventsConverter."""
+    ant_model = """
+    species X = 0
+    X' = 1
+    """
+    problem = Problem()
+    problem.model = SbmlModel.from_antimony(ant_model)
+    problem.add_condition("c1", X=1)
+    problem.add_condition("c2", X=2)
+    problem.add_experiment("e1", -inf, "c1", 10, "c2")
+
+    converter = ExperimentsToEventsConverter(problem)
+    converted = converter.convert()
+    assert converted.validate().has_errors() is False
+
+    assert isinstance(converted.model, SbmlModel)
+    sbml_model = converted.model.sbml_model
+
+    assert sbml_model.getNumEvents() == 2
+    assert converted.condition_table.conditions == [
+        Condition(
+            id="_petab_preequilibration_on",
+            changes=[
+                Change(
+                    target_id="_petab_preequilibration_indicator",
+                    target_value=1,
+                )
+            ],
+        ),
+        Condition(
+            id="_petab_preequilibration_off",
+            changes=[
+                Change(
+                    target_id="_petab_preequilibration_indicator",
+                    target_value=0,
+                )
+            ],
+        ),
+        Condition(
+            id="_petab_experiment_condition_e1",
+            changes=[
+                Change(
+                    target_id="_petab_experiment_indicator_e1", target_value=1
+                )
+            ],
+        ),
+    ]
+    assert converted.experiment_table.experiments == [
+        Experiment(
+            id="e1",
+            periods=[
+                ExperimentPeriod(
+                    time=-inf,
+                    condition_ids=[
+                        "_petab_experiment_condition_e1",
+                        "_petab_preequilibration_on",
+                    ],
+                ),
+                ExperimentPeriod(
+                    time=10.0,
+                    condition_ids=[
+                        "_petab_experiment_condition_e1",
+                        "_petab_preequilibration_off",
+                    ],
+                ),
+            ],
+        ),
+    ]