add required params check to sciml validations

Author: BSnelling

petab/v2/core.py

@@ -1417,20 +1417,6 @@ def from_yaml(
             else None
         )
 
-        # sciml extension
-        # if config.extensions and config.extensions[C.SCIML]:
-        # try:
-        #     from petab_sciml import (
-        #         ArrayDataStandard,
-        #         NNModel,
-        #         NNModelStandard,
-        #     )
-        # except ImportError as e:
-        #     raise ImportError(
-        #         "To generate a PEtab SciML problem, (petab_sciml) must"
-        #         "be installed."
-        #     ) from e
-
         # Neural network classes are constructed via pytorch for now to get the
         # proper inputs
         neural_networks = (

petab/v2/lint.py

@@ -1128,6 +1128,11 @@ def append_overrides(overrides):
     }
     parameter_ids -= condition_targets
 
+    hybridization_targets = {hyb.target_id for hyb in problem.hybridizations}
+    parameter_ids -= hybridization_targets
+    hybridization_target_values = {str(hyb.target_value) for hyb in problem.hybridizations}
+    parameter_ids -= hybridization_target_values
+
     return parameter_ids
 
 
@@ -1199,7 +1204,7 @@ def get_placeholders(
     CheckExperimentConditionsExist(),
     CheckUndefinedExperiments(),
     CheckObservablesDoNotShadowModelEntities(),
-    # CheckAllParametersPresentInParameterTable(),
+    CheckAllParametersPresentInParameterTable(),
     CheckValidParameterInConditionOrParameterTable(),
     CheckUnusedExperiments(),
     CheckUnusedConditions(),

tests/v2/test_sciml.py

@@ -63,7 +63,7 @@ def _get_test_problem():
     )
     problem.add_hybridization("net1_input1", "A")
     problem.add_hybridization("net1_input2", "B")
-    problem.add_hybridization("gamma_", "net1_output_1")
+    problem.add_hybridization("gamma_", "net1_output1")
     problem.add_neural_network_from_dict(
         "net1",
         nn_dict={