Update deprecated functions in tests (#181)

* Fix deprecated tight layout matplotlib

* update deprecated functions in tests

* add deprecation 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_deprecated.py

@@ -0,0 +1,58 @@
+"""Check that deprecated functionality raises but still works."""
+import pytest
+import tempfile
+from pathlib import Path
+
+import petab
+
+from .test_sbml import create_test_data, check_model
+from .test_petab import petab_problem  # noqa: F401
+
+
+def test_problem_with_sbml_model():
+    """Test that a problem can be correctly created from sbml model."""
+    # retrieve test data
+    ss_model, condition_df, observable_df, measurement_df, parameter_df = \
+        create_test_data()
+
+    with pytest.deprecated_call():
+        petab_problem = petab.Problem(  # noqa: F811
+            sbml_model=ss_model.model,
+            condition_df=condition_df,
+            measurement_df=measurement_df,
+            parameter_df=parameter_df,
+        )
+
+    _, condition_model = petab.get_model_for_condition(
+        petab_problem, "condition_1")
+
+    check_model(condition_model)
+
+
+def test_to_files_with_sbml_model(petab_problem):  # noqa: F811
+    """Test problem.to_files."""
+    with tempfile.TemporaryDirectory() as outdir:
+        # create target files
+        sbml_file = Path(outdir, "model.xml")
+        condition_file = Path(outdir, "conditions.tsv")
+        measurement_file = Path(outdir, "measurements.tsv")
+        parameter_file = Path(outdir, "parameters.tsv")
+        observable_file = Path(outdir, "observables.tsv")
+
+        # write contents to files
+        with pytest.deprecated_call():
+            petab_problem.to_files(
+                sbml_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,
+            )
+
+        # exemplarily load some
+        parameter_df = petab.get_parameter_df(parameter_file)
+        same_nans = parameter_df.isna() == petab_problem.parameter_df.isna()
+        assert ((parameter_df == petab_problem.parameter_df) | same_nans) \
+            .all().all()

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

@@ -5,7 +5,6 @@
 from io import StringIO
 from math import nan
 from pathlib import Path
-from tempfile import TemporaryDirectory
 
 import libsbml
 import numpy as np
@@ -78,12 +77,13 @@ def petab_problem():
         observable_file_name = Path(temp_dir, "observables.tsv")
         petab.write_observable_df(observable_df, observable_file_name)
 
-        yield petab.Problem.from_files(
-            sbml_file=sbml_file_name,
-            measurement_file=measurement_file_name,
-            condition_file=condition_file_name,
-            parameter_file=parameter_file_name,
-            observable_files=observable_file_name)
+        with pytest.deprecated_call():
+            yield petab.Problem.from_files(
+                sbml_file=sbml_file_name,
+                measurement_file=measurement_file_name,
+                condition_file=condition_file_name,
+                parameter_file=parameter_file_name,
+                observable_files=observable_file_name)
 
 
 @pytest.fixture
@@ -95,10 +95,13 @@ def fujita_model_scaling():
     measurement_file = path / 'Fujita_measurementData.tsv'
     parameter_file = path / 'Fujita_parameters_scaling.tsv'
 
-    return petab.Problem.from_files(sbml_file=sbml_file,
-                                    condition_file=condition_file,
-                                    measurement_file=measurement_file,
-                                    parameter_file=parameter_file)
+    with pytest.deprecated_call():
+        return petab.Problem.from_files(
+            sbml_file=sbml_file,
+            condition_file=condition_file,
+            measurement_file=measurement_file,
+            parameter_file=parameter_file,
+        )
 
 
 def test_split_parameter_replacement_list():
@@ -570,13 +573,14 @@ 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)
@@ -625,7 +629,7 @@ def test_problem_from_yaml_v1_multiple_files():
       sbml_files: []
     """
 
-    with TemporaryDirectory() as tmpdir:
+    with tempfile.TemporaryDirectory() as tmpdir:
         yaml_path = Path(tmpdir, "problem.yaml")
         with open(yaml_path, 'w') as f:
             f.write(yaml_config)

tests/test_sbml.py

@@ -7,10 +7,10 @@
 import petab  # noqa: E402
 
 
-def test_get_condition_specific_models():
-    """Test for petab.sbml.get_condition_specific_models"""
+def create_test_data():
     # Create test model and data files
     import simplesbml
+
     ss_model = simplesbml.SbmlModel()
     ss_model.addCompartment(comp_id="compartment_1", vol=1)
     for i in range(1, 4):
@@ -51,18 +51,10 @@ def test_get_condition_specific_models():
     })
     parameter_df.set_index([petab.PARAMETER_ID], inplace=True)
 
-    petab_problem = petab.Problem(
-        sbml_model=ss_model.model,
-        condition_df=condition_df,
-        observable_df=observable_df,
-        measurement_df=measurement_df,
-        parameter_df=parameter_df
-    )
+    return ss_model, condition_df, observable_df, measurement_df, parameter_df
 
-    # Actual test
-    condition_doc, condition_model = petab.get_model_for_condition(
-        petab_problem, "condition_1")
 
+def check_model(condition_model):
     assert condition_model.getSpecies(
         "species_1").getInitialConcentration() == 15
     assert condition_model.getSpecies(
@@ -75,3 +67,24 @@ def test_get_condition_specific_models():
     assert condition_model.getParameter("parameter_1").getValue() == 1.25
     assert condition_model.getParameter("parameter_2").getValue() == 2.25
     assert condition_model.getParameter("parameter_3").getValue() == 2.25
+
+
+def test_get_condition_specific_models():
+    """Test for petab.sbml.get_condition_specific_models"""
+    # retrieve test data
+    ss_model, condition_df, observable_df, measurement_df, parameter_df = \
+        create_test_data()
+
+    petab_problem = petab.Problem(
+        model=petab.models.sbml_model.SbmlModel(ss_model.model),
+        condition_df=condition_df,
+        observable_df=observable_df,
+        measurement_df=measurement_df,
+        parameter_df=parameter_df
+    )
+
+    # create SBML model for condition with parameters updated from problem
+    _, condition_model = petab.get_model_for_condition(
+        petab_problem, "condition_1")
+
+    check_model(condition_model)