update deprecated functions in tests

Author: yannikschaelte

petab/problem.py

@@ -411,7 +411,7 @@ def to_files(
         visualization tables, they will be merged and written to a single file.
 
         Arguments:
-            sbml_file: SBML model destination
+            sbml_file: SBML model destination (deprecated)
             model_file: Model destination
             condition_file: Condition table destination
             measurement_file: Measurement table destination

tests/test_parameter_mapping.py

@@ -351,7 +351,8 @@ def test_partial_override(condition_df_2_conditions):
         actual = petab.get_optimization_to_simulation_parameter_mapping(
             measurement_df=measurement_df,
             condition_df=condition_df,
-            sbml_model=ss_model.model, parameter_df=parameter_df
+            model=petab.models.sbml_model.SbmlModel(ss_model.model),
+            parameter_df=parameter_df
         )
 
         # Comparison with NaN containing expected results fails after pickling!
@@ -399,7 +400,7 @@ def test_parameterized_condition_table():
             measurement_df=measurement_df,
             condition_df=condition_df,
             parameter_df=parameter_df,
-            sbml_model=ss_model.model
+            model=petab.models.sbml_model.SbmlModel(ss_model.model),
         )
 
         expected = [({}, {'dynamicParameter1': 'dynamicOverride1_1'},
@@ -467,7 +468,7 @@ def test_parameterized_condition_table_changed_scale():
             measurement_df=measurement_df,
             condition_df=condition_df,
             parameter_df=parameter_df,
-            sbml_model=ss_model.model
+            model=petab.models.sbml_model.SbmlModel(ss_model.model)
         )
 
         expected = [
@@ -487,8 +488,8 @@ def test_parameterized_condition_table_changed_scale():
             measurement_df=measurement_df,
             condition_df=condition_df,
             parameter_df=parameter_df,
-            sbml_model=ss_model.model,
-            scaled_parameters=True
+            model=petab.models.sbml_model.SbmlModel(ss_model.model),
+            scaled_parameters=True,
         )
 
         expected = [
@@ -510,7 +511,8 @@ def test_parameterized_condition_table_changed_scale():
             measurement_df=measurement_df,
             condition_df=condition_df,
             parameter_df=parameter_df,
-            sbml_model=ss_model.model)
+            model=petab.models.sbml_model.SbmlModel(ss_model.model),
+        )
 
         expected = [
             ({overridee_id: 'dynamicOverrideLog10'},

tests/test_petab.py

@@ -570,13 +570,14 @@ def test_to_files(petab_problem):  # pylint: disable=W0621
 
         # write contents to files
         petab_problem.to_files(
-            sbml_file=sbml_file,
+            model_file=sbml_file,
             condition_file=condition_file,
             measurement_file=measurement_file,
             parameter_file=parameter_file,
             visualization_file=None,
             observable_file=observable_file,
-            yaml_file=None)
+            yaml_file=None,
+        )
 
         # exemplarily load some
         parameter_df = petab.get_parameter_df(parameter_file)

tests/test_sbml.py

@@ -52,7 +52,7 @@ def test_get_condition_specific_models():
     parameter_df.set_index([petab.PARAMETER_ID], inplace=True)
 
     petab_problem = petab.Problem(
-        sbml_model=ss_model.model,
+        model=petab.models.sbml_model.SbmlModel(ss_model.model),
         condition_df=condition_df,
         observable_df=observable_df,
         measurement_df=measurement_df,