allow for sciml problems setting cond ids in array files

Author: BSnelling

petab/v2/converters.py

@@ -249,11 +249,13 @@ def _convert_experiment(self, experiment: Experiment) -> None:
             #  single-period experiments.
             if i_period == 0:
                 exp_ind_id = self.get_experiment_indicator(experiment.id)
-                # If condition ids are set by array data, skip as importers handle this
-                if set(period.condition_ids).issubset(
-                    self._new_problem._get_array_data_condition_ids()
-                ):
-                    continue
+                # Skip if condition ids are set by array data
+                # importers handle this
+                if self._new_problem.extensions.sciml:
+                    if set(period.condition_ids).issubset(
+                        self._new_problem.extensions.sciml._get_array_data_condition_ids()
+                    ):
+                        continue
 
                 for change in self._new_problem.get_changes_for_period(period):
                     period0_assignments.setdefault(

petab/v2/core.py

@@ -2288,14 +2288,6 @@ def add_experiment(self, id_: str, *args):
             Experiment(id=id_, periods=periods)
         )
 
-    def _get_array_data_condition_ids(self) -> set[str]:
-        """Get the set of condition IDs that are referenced in the array data files."""
-        condition_ids = set()
-        for array_data in self.array_data_files:
-            for input in array_data.inputs.values():
-                condition_ids.update(input.keys())
-        return condition_ids
-
     def __iadd__(self, other):
         """Add Observable, Parameter, Measurement, Condition, or Experiment"""
         from .core import (

petab/v2/extensions/sciml.py

@@ -303,3 +303,12 @@ def from_config(
             hybridization_tables=hybridization_tables,
             array_data_files=array_data_files,
         )
+
+    def _get_array_data_condition_ids(self) -> set[str]:
+        """Get the set of condition IDs that are referenced in the array data
+        files."""
+        condition_ids = set()
+        for array_data in self.array_data_files:
+            for input in array_data.inputs.values():
+                condition_ids.update(input.keys())
+        return condition_ids

petab/v2/lint.py

@@ -532,10 +532,10 @@ class CheckExperimentConditionsExist(ValidationTask):
     def run(self, problem: Problem) -> ValidationIssue | None:
         messages = []
         available_conditions = {c.id for c in problem.conditions}
-        if problem.array_data_files:
+        if problem.extensions.sciml:
             available_conditions |= {
                 key
-                for array_data in problem.array_data_files
+                for array_data in problem.extensions.sciml.array_data_files
                 for input_array in array_data.inputs.values()
                 for key in input_array.keys()
             }