Merge branch 'main' into validate_initial_changes

Author: dweindl

petab/v2/core.py

@@ -1901,6 +1901,27 @@ def validate(
 
         return validation_results
 
+    def assert_valid(self, **kwargs) -> None:
+        """Assert that the PEtab problem is valid.
+
+        :param kwargs: Additional arguments passed to :meth:`Problem.validate`.
+
+        :raises AssertionError: If the PEtab problem is not valid.
+        """
+        from ..v2.lint import ValidationIssueSeverity
+
+        validation_results = self.validate(**kwargs)
+        errors = [
+            r
+            for r in validation_results
+            if r.level >= ValidationIssueSeverity.ERROR
+        ]
+        if errors:
+            raise AssertionError(
+                "PEtab problem is not valid:\n"
+                + "\n".join(e.message for e in errors)
+            )
+
     def add_condition(
         self, id_: str, name: str = None, **kwargs: Number | str | sp.Expr
     ):

tests/v2/test_core.py

@@ -58,6 +58,16 @@ def test_condition_table_round_trip():
         assert conditions == conditions2
 
 
+def test_assert_valid():
+    problem = petab1to2(example_dir_fujita / "Fujita.yaml")
+    problem.assert_valid()
+    problem.observable_tables[0] = ObservableTable()
+    with pytest.raises(
+        AssertionError, match="not defined in the observable table"
+    ):
+        problem.assert_valid()
+
+
 def test_experiment_add_periods():
     """Test operators for Experiment"""
     exp = Experiment(id="exp1")