Fix parameter check constant (#82)

* Remove .DS_Store

* More informative error message

* Fix linter error for constant parameters

* Don't abuse parameter const-ness

* Adapt tests

* Update doc

doc/documentation_data_format.md

@@ -235,15 +235,15 @@ numeric value or `inf` (lower-case) for steady-state measurements.
 
 A tab-separated value text file containing information on model parameters.
 
-This table must comprise the following parameters:
-- All parameters from the SBML model, except for:
-    - `constant` and/or `boundaryCondition` parameters (see SBML specs)
-    - placeholder parameters (see `observableParameters` and `noiseParameters`
-      above)
-    - parameters included as column names in the *condition table*
+This table must include the following parameters:
 - Named parameter overrides introduced in the *conditions table*
 - Named parameter overrides introduced in the *measurement table*
 
+and must not include 
+- placeholder parameters (see `observableParameters` and `noiseParameters`
+  above)
+- parameters included as column names in the *condition table*
+
 One row per parameter with arbitrary order of rows and columns:
 
 | parameterId | [parameterName] | parameterScale | lowerBound  |upperBound | nominalValue | estimate | [priorType] | [priorParameters] |

petab/lint.py

@@ -294,8 +294,9 @@ def assert_overrides_match_parameter_count(measurement_df, observables, noise):
             if not len(replacements) == 1 \
                     or not isinstance(replacements[0], numbers.Number):
                 raise AssertionError(
-                    f'No place holders specified in model for:\n{row}\n'
-                    f'But parameter name or multiple overrides provided.')
+                    f'No placeholders specified in noise model for:\n{row}\n'
+                    f'But parameter name or multiple overrides provided in '
+                    'noiseParameters column.')
 
 
 def lint_problem(problem: 'core.Problem'):
@@ -390,12 +391,10 @@ def assert_model_parameters_in_condition_or_parameter_table(
         sbml_model: libsbml.Model,
         condition_df: pd.DataFrame,
         parameter_df: pd.DataFrame):
-    """Model non-placeholder model parameters must be either specified in the
-    condition or parameter table, unless they are AssignmentRule target, in
-    which case they must not occur in either.
-    Check that.
-
-    NOTE: SBML local parameters are ignored here"""
+    """Model parameters that are targets of AssignmentRule must not be present
+    in parameter table or in condition table columns. Other parameters must
+    only be present in either in parameter table or condition table columns.
+    Check that."""
 
     for parameter in sbml_model.getListOfParameters():
         parameter_id = parameter.getId()
@@ -416,11 +415,6 @@ def assert_model_parameters_in_condition_or_parameter_table(
                                  "present in condition table or in parameter "
                                  "table.")
 
-        if not is_assignee and not in_parameter_df and not in_condition_df:
-            raise AssertionError(f"Model parameter '{parameter_id}' neither "
-                                 "present in condition table nor in parameter "
-                                 "table.")
-
         if in_parameter_df and in_condition_df:
             raise AssertionError(f"Model parameter '{parameter_id}' present "
                                  "in both condition table and parameter "

tests/test_lint.py

@@ -159,10 +159,6 @@ def test_assert_model_parameters_in_condition_or_parameter_table():
     sbml.add_global_parameter(model, 'noiseParameter1_')
     sbml.add_global_parameter(model, 'observableParameter1_')
 
-    with pytest.raises(AssertionError):
-        lint.assert_model_parameters_in_condition_or_parameter_table(
-            model, pd.DataFrame(), pd.DataFrame())
-
     lint.assert_model_parameters_in_condition_or_parameter_table(
             model, pd.DataFrame(columns=['parameter1']), pd.DataFrame()
     )
@@ -176,8 +172,7 @@ def test_assert_model_parameters_in_condition_or_parameter_table():
             pd.DataFrame(columns=['parameter1']),
             pd.DataFrame(index=['parameter1']))
 
-    with pytest.raises(AssertionError):
-        lint.assert_model_parameters_in_condition_or_parameter_table(
+    lint.assert_model_parameters_in_condition_or_parameter_table(
             model, pd.DataFrame(), pd.DataFrame())
 
     sbml.create_assigment_rule(model, assignee_id='parameter1',