..

Author: dweindl

petab/v2/converters.py

@@ -8,7 +8,6 @@
 import libsbml
 from sbmlmath import sbml_math_to_sympy, set_math
 
-from .C import TIME_PREEQUILIBRATION
 from .core import Change, Condition, Experiment, ExperimentPeriod
 from .models._sbml_utils import add_sbml_parameter, check
 from .models.sbml_model import SbmlModel
@@ -165,16 +164,16 @@ def _convert_experiment(self, experiment: Experiment):
         """Convert a single experiment to SBML events."""
         model = self._model
         experiment.sort_periods()
-        has_preequilibration = (
-            len(experiment.periods)
-            and experiment.periods[0].time == TIME_PREEQUILIBRATION
-        )
+        has_preequilibration = experiment.has_preequilibration
 
         # add experiment indicator
         exp_ind_id = self.get_experiment_indicator(experiment.id)
         if model.getElementBySId(exp_ind_id) is not None:
-            raise AssertionError(
-                f"Entity with ID {exp_ind_id} exists already."
+            raise ValueError(
+                f"The model has entity with ID `{exp_ind_id}`. "
+                "IDs starting with `petab_` are reserved for "
+                f"{self.__class__.__name__} and should not be used in the "
+                "model."
             )
         add_sbml_parameter(model, id_=exp_ind_id, constant=False, value=0)
         kept_periods = []
@@ -192,7 +191,7 @@ def _convert_experiment(self, experiment: Experiment):
                     "This cannot be represented in SBML."
                 )
 
-            if period.time == TIME_PREEQUILIBRATION:
+            if period.is_preequilibration:
                 # pre-equilibration cannot be represented in SBML,
                 #  so we need to keep this period in the Problem.
                 kept_periods.append(period)
@@ -227,7 +226,7 @@ def _convert_experiment(self, experiment: Experiment):
             period.condition_ids = [
                 self._get_experiment_indicator_condition_id(experiment.id),
                 self.CONDITION_ID_PREEQ_ON
-                if period.time == TIME_PREEQUILIBRATION
+                if period.is_preequilibration
                 else self.CONDITION_ID_PREEQ_OFF,
             ]
 
@@ -253,7 +252,7 @@ def _create_period_start_event(
 
         exp_ind_id = self.get_experiment_indicator(experiment.id)
 
-        if period.time == TIME_PREEQUILIBRATION:
+        if period.is_preequilibration:
             trig_math = libsbml.parseL3Formula(
                 f"({exp_ind_id} == 1) && ({self._preeq_indicator} == 1)"
             )
@@ -324,7 +323,8 @@ def _change_to_event_assignment(change: Change, event: libsbml.Event):
                 sbml_model, id_=change.target_id, constant=False, value=0
             )
         else:
-            # TODO: can that break models??
+            # We can safely change the `constant` attribute of the target.
+            #  "Constant" does not imply "boundary condition" in SBML.
             target.setConstant(False)
 
         # the target value may depend on parameters that are only

petab/v2/core.py

@@ -521,6 +521,11 @@ def _validate_ids(cls, condition_ids):
                 raise ValueError(f"Invalid {C.CONDITION_ID}: `{condition_id}'")
         return condition_ids
 
+    @property
+    def is_preequilibration(self) -> bool:
+        """Check if this period is a preequilibration period."""
+        return self.time == C.TIME_PREEQUILIBRATION
+
 
 class Experiment(BaseModel):
     """An experiment or a timecourse defined by an ID and a set of different
@@ -555,9 +560,10 @@ def __iadd__(self, other: ExperimentPeriod) -> Experiment:
         self.periods.append(other)
         return self
 
+    @property
     def has_preequilibration(self) -> bool:
         """Check if the experiment has preequilibration enabled."""
-        return any(period.time == -np.inf for period in self.periods)
+        return any(period.is_preequilibration for period in self.periods)
 
     def sort_periods(self) -> None:
         """Sort the periods of the experiment by time."""

petab/v2/models/_sbml_utils.py

@@ -33,15 +33,14 @@ def check(res: int):
 
 def add_sbml_parameter(
     model: libsbml.Model,
-    id_: str = None,
+    id_: str,
     value: float = None,
     constant: bool = None,
 ) -> libsbml.Parameter:
     """Add a parameter to the SBML model."""
     param = model.createParameter()
 
-    if id_ is not None:
-        param.setId(id_)
+    param.setId(id_)
 
     if value is not None:
         param.setValue(value)