No implicit prior in Parameter.prior_dist

Author: dweindl

petab/v2/core.py

@@ -1026,13 +1026,17 @@ def _validate(self) -> Self:
         return self
 
     @property
-    def prior_dist(self) -> Distribution:
-        """Get the prior distribution of the parameter."""
-        if self.estimate is False:
+    def prior_dist(self) -> Distribution | None:
+        """Get the prior distribution of the parameter.
+
+        :return: The prior distribution of the parameter, or None if no prior
+            distribution is set.
+        """
+        if not self.estimate:
             raise ValueError(f"Parameter `{self.id}' is not estimated.")
 
         if self.prior_distribution is None:
-            return Uniform(self.lb, self.ub)
+            return None
 
         if not (cls := _prior_to_cls.get(self.prior_distribution)):
             raise ValueError(
@@ -1858,7 +1862,11 @@ def get_priors(self) -> dict[str, Distribution]:
 
         :returns: The prior distributions for the estimated parameters.
         """
-        return {p.id: p.prior_dist for p in self.parameters if p.estimate}
+        return {
+            p.id: p.prior_dist if p.prior_distribution else Uniform(p.lb, p.ub)
+            for p in self.parameters
+            if p.estimate
+        }
 
     def sample_parameter_startpoints(self, n_starts: int = 100, **kwargs):
         """Create 2D array with starting points for optimization"""

petab/v2/lint.py

@@ -843,7 +843,7 @@ def run(self, problem: Problem) -> ValidationIssue | None:
 
             # TODO: check distribution parameter domains more specifically
             try:
-                if parameter.estimate:
+                if parameter.estimate and parameter.prior_dist is not None:
                     # .prior_dist fails for non-estimated parameters
                     _ = parameter.prior_dist.sample(1)
             except Exception as e: