todo

Author: dweindl

petab/v2/core.py

@@ -837,6 +837,7 @@ class Parameter(BaseModel):
     #: Nominal value.
     nominal_value: float | None = Field(alias=C.NOMINAL_VALUE, default=None)
     #: Parameter scale.
+    # TODO: keep or remove?
     scale: ParameterScale = Field(
         alias=C.PARAMETER_SCALE, default=ParameterScale.LIN
     )
@@ -902,12 +903,19 @@ def _validate(self) -> Self:
                 "Estimated parameter must have lower and upper bounds set"
             )
 
-        if self.lb is not None and self.ub is not None and self.lb >= self.ub:
+        # TODO: also if not estimated?
+        if (
+            self.estimate
+            and self.lb is not None
+            and self.ub is not None
+            and self.lb >= self.ub
+        ):
             raise ValueError("Lower bound must be less than upper bound.")
 
         # TODO parameterScale?
 
         # TODO priorType, priorParameters
+
         return self
 
 

petab/v2/lint.py

@@ -400,6 +400,9 @@ class CheckUniquePrimaryKeys(ValidationTask):
     """Check that all primary keys are unique."""
 
     def run(self, problem: Problem) -> ValidationIssue | None:
+        # TODO: check that IDs are globally unique
+        #  -- replaces CheckObservablesDoNotShadowModelEntities
+
         # check for uniqueness of all primary keys
         counter = Counter(c.id for c in problem.conditions_table.conditions)
         duplicates = {id for id, count in counter.items() if count > 1}