Treat observableParameter overrides as placeholders in noise formulae (#231)

Author: dilpath

petab/parameters.py

@@ -298,14 +298,27 @@ def append_overrides(overrides):
         )
 
     # Add output parameters except for placeholders
-    for kwargs in [
-        dict(observables=True, noise=False),
-        dict(observables=False, noise=True),
-    ]:
+    for formula_type, placeholder_sources in (
+        (
+            # Observable formulae
+            {'observables': True, 'noise': False},
+            # can only contain observable placeholders
+            {'noise': False, 'observables': True}
+        ),
+        (
+            # Noise formulae
+            {'observables': False, 'noise': True},
+            # can contain noise and observable placeholders
+            {'noise': True, 'observables': True}
+        ),
+    ):
         output_parameters = observables.get_output_parameters(
-            observable_df, model, mapping_df=mapping_df, **kwargs
+            observable_df, model, mapping_df=mapping_df, **formula_type,
+        )
+        placeholders = observables.get_placeholders(
+            observable_df,
+            **placeholder_sources,
         )
-        placeholders = observables.get_placeholders(observable_df, **kwargs)
         for p in output_parameters:
             if p not in placeholders:
                 parameter_ids[p] = None

tests/test_petab.py

@@ -68,10 +68,10 @@ def petab_problem():
 
     observable_df = pd.DataFrame(
         data={
-            OBSERVABLE_ID: ["observable_1"],
+            OBSERVABLE_ID: ["obs1"],
             OBSERVABLE_NAME: ["julius"],
-            OBSERVABLE_FORMULA: ["observable_1"],
-            NOISE_FORMULA: [1],
+            OBSERVABLE_FORMULA: ["observable_1 * observableParameter1_obs1"],
+            NOISE_FORMULA: ["0.1 * observable_1 * observableParameter1_obs1"],
         }
     ).set_index(OBSERVABLE_ID)
 
@@ -653,7 +653,7 @@ def test_concat_condition_df():
 
 def test_get_observable_ids(petab_problem):  # pylint: disable=W0621
     """Test if observable ids functions returns correct value."""
-    assert set(petab_problem.get_observable_ids()) == {"observable_1"}
+    assert set(petab_problem.get_observable_ids()) == {"obs1"}
 
 
 def test_parameter_properties(petab_problem):  # pylint: disable=W0621
@@ -823,3 +823,35 @@ def test_problem_from_yaml_v1_multiple_files():
     assert petab_problem.measurement_df.shape[0] == 2
     assert petab_problem.observable_df.shape[0] == 2
     assert petab_problem.condition_df.shape[0] == 2
+
+
+def test_get_required_parameters_for_parameter_table(petab_problem):
+    """Test identification of required parameter table parameters.
+
+    NB: currently, this test only checks that observable parameter placeholders
+    in noise formulae are correctly identified as not required in the parameter
+    table.
+    """
+    noise_placeholders = petab.observables.get_output_parameters(
+        petab_problem.observable_df,
+        petab_problem.model,
+        observables=False,
+        noise=True,
+    )
+    # The observable parameter (scaling) appears in the noise formula,
+    # as part of the proportional error model.
+    assert "observableParameter1_obs1" in noise_placeholders
+
+    required_parameters_for_parameter_table = \
+        petab.parameters.get_required_parameters_for_parameter_table(
+            model=petab_problem.model,
+            condition_df=petab_problem.condition_df,
+            observable_df=petab_problem.observable_df,
+            measurement_df=petab_problem.measurement_df,
+        )
+    # The observable parameter is correctly recognized as a placeholder,
+    # i.e. does not need to be in the parameter table.
+    assert (
+        "observableParameter1_obs1"
+        not in required_parameters_for_parameter_table
+    )