initial fix of linter

.github/workflows/ci.yml

@@ -22,7 +22,7 @@ jobs:
           path: ~/Library/Caches/pip
         - os: windows-latest
           path: ~\AppData\Local\pip\Cache
-        python-version: ['3.7', '3.10']
+        python-version: ['3.10', '3.11']
     runs-on: ${{ matrix.os }}
 
     steps:
@@ -86,6 +86,7 @@ jobs:
       matrix:
         python-version: ['3.10']
 
+
     steps:
     - name: Check out repository
       uses: actions/checkout@v2

.github/workflows/deploy.yml

@@ -14,7 +14,7 @@ jobs:
     - name: Set up python
       uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: '3.10'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

setup.cfg

@@ -33,10 +33,9 @@ classifiers =
     License :: OSI Approved :: MIT License
     Operating System :: OS Independent
     Programming Language :: Python
+    Programming Language :: Python :: 3.11
+    Programming Language :: Python :: 3.10
     Programming Language :: Python :: 3.9
-    Programming Language :: Python :: 3.8
-    Programming Language :: Python :: 3.7
-    Programming Language :: Python :: 3.6
 keywords = YAML, SBML, PEtab, ODE
 
 [options]
@@ -48,7 +47,7 @@ install_requires =
 
 zip_safe = False
 include_package_data = True
-python_requires = >=3.6
+python_requires = >=3.9
 
 # Where is my code
 packages = find:

tests/test_CLI.py

@@ -1,3 +1,4 @@
+"""Tests of Command-line Interface."""
 import os
 import shutil
 
@@ -53,8 +54,7 @@ def test_yaml2petab_cli(script_runner):
 
 
 def test_yaml2sbml_validate_cli(script_runner):
-    """Test the command line command ``yaml2sbml_validate`"""
-
+    """Test the command line command `yaml2sbml_validate`."""
     path = os.path.dirname(os.path.abspath(__file__))
     yaml_dir = os.path.join(path, 'test_yaml2sbml/ode_input1.yaml')
 

tests/test_YamlModel.py

@@ -1,3 +1,4 @@
+"""Tests of the yaml2sbml model editor."""
 import os
 import shutil
 
@@ -12,6 +13,7 @@ class TestYamlModel(unittest.TestCase):
     """TestCase class for testing YamlModel."""
 
     def setUp(self):
+        """Set Up of tests."""
         # input directory
         this_dir, _ = os.path.split(__file__)
         self.test_input_folder = os.path.join(this_dir, 'test_yaml2sbml')
@@ -20,13 +22,12 @@ def setUp(self):
         self.test_dir = tempfile.mkdtemp()
 
     def tearDown(self):
+        """Tear Down of tests."""
         # remove temporary directory
         shutil.rmtree(self.test_dir)
 
     def test_load_and_write(self):
-        """
-        Test loading and writing.
-        """
+        """Test loading and writing."""
         # read in yaml
         yaml_dir = os.path.join(self.test_input_folder, 'ode_input2.yaml')
         model = YamlModel.load_from_yaml(yaml_dir)
@@ -40,9 +41,7 @@ def test_load_and_write(self):
         self.assertDictEqual(model._yaml_model, reloaded_model._yaml_model)
 
     def test_time(self):
-        """
-        Test all functionality regarding the time keyword.
-        """
+        """Test all functionality regarding the time keyword."""
         model = YamlModel()
         time_var = 't'
 
@@ -57,9 +56,7 @@ def test_time(self):
         self.assertFalse(model.is_set_time())
 
     def test_parameter(self):
-        """
-        Test all functionality regarding the 'parameters' keyword.
-        """
+        """Test all functionality regarding the 'parameters' keyword."""
         model = YamlModel()
         parameter_id = 'p1'
         model.add_parameter(parameter_id,
@@ -87,9 +84,7 @@ def test_parameter(self):
         self.assertListEqual(model.get_parameter_ids(), [])
 
     def test_ode(self):
-        """
-        Test all functionality regarding the 'odes' keyword.
-        """
+        """Test all functionality regarding the 'odes' keyword."""
         model = YamlModel()
 
         state_id = 's1'
@@ -120,9 +115,7 @@ def test_ode(self):
         self.assertListEqual(model.get_ode_ids(), [])
 
     def test_assignment(self):
-        """
-        Test all functionality regarding the 'assignments' keyword.
-        """
+        """Test all functionality regarding the 'assignments' keyword."""
         model = YamlModel()
 
         assignment_id = 's1'
@@ -149,9 +142,7 @@ def test_assignment(self):
         self.assertListEqual(model.get_assignment_ids(), [])
 
     def test_function(self):
-        """
-        Test all functionality regarding the 'functions' keyword.
-        """
+        """Test all functionality regarding the 'functions' keyword."""
         model = YamlModel()
 
         function_id = 'f'
@@ -179,9 +170,7 @@ def test_function(self):
         self.assertListEqual(model.get_function_ids(), [])
 
     def test_observable(self):
-        """
-        Test all functionality regarding the 'observables' keyword.
-        """
+        """Test all functionality regarding the 'observables' keyword."""
         model = YamlModel()
 
         observable_id = 'obs'
@@ -220,9 +209,7 @@ def test_observable(self):
         self.assertListEqual(model.get_observable_ids(), [])
 
     def test_condition(self):
-        """
-        Test all functionality regarding the 'conditions' keyword.
-        """
+        """Test all functionality regarding the 'conditions' keyword."""
         model = YamlModel()
 
         condition_id = 'cond'

tests/test_yaml2petab.py

@@ -1,3 +1,4 @@
+"""Tests of the yaml2petab functionalities of yaml2sbml."""
 import os
 import shutil
 import unittest
@@ -6,23 +7,20 @@
 
 
 class TestYaml2PEtab(unittest.TestCase):
-    """
-    TestCase class for testing ODE import from a generic yaml file
-    and conversion to PEtab.
-    """
+    """This tests ODE import from yaml & conversion to PEtab."""
 
     def setUp(self):
+        """Set Up of tests."""
         this_dir, _ = os.path.split(__file__)
         self.input_folder = os.path.join(this_dir, 'test_yaml2sbml')
         self.output_folder = os.path.join(this_dir, 'test_yaml2sbml_output')
 
     def tearDown(self):
+        """Tear Down od tests."""
         shutil.rmtree(self.output_folder)
 
     def test_petab_export(self):
-        """
-        Test PEtab export
-        """
+        """Test PEtab export."""
         input_yaml_dir = os.path.join(self.input_folder, 'ode_input2.yaml')
 
         yaml2PEtab.yaml2petab(input_yaml_dir,

tests/test_yaml2sbml.py

@@ -1,23 +1,20 @@
+"""Tests of the yamls2bml function."""
 import os
 import unittest
 
 from yaml2sbml.yaml2sbml import yaml2sbml, _parse_yaml
 
 
 class TestYaml2SBML(unittest.TestCase):
-    """
-    TestCase class for testing ODE import from a generic yaml file
-    and conversion to SBML.
-    """
+    """Tests  ODE import yaml file and conversion to SBML."""
 
     def setUp(self):
+        """Set Up of tests."""
         this_dir, _ = os.path.split(__file__)
         self.test_folder = os.path.join(this_dir, 'test_yaml2sbml')
 
     def test_yaml_import(self):
-        """
-        Test yaml import/SBML generation...
-        """
+        """Test yaml import & SBML generation."""
         yaml_dir = os.path.join(self.test_folder, 'ode_input1.yaml')
         expected_result_file = os.path.join(self.test_folder,
                                             'true_sbml_output.xml')
@@ -43,9 +40,7 @@ def test_yaml_import(self):
         os.remove(sbml_test_dir)
 
     def test_yaml_import_observables(self):
-        """
-        Test yaml import/export for a model containing observables.
-        """
+        """Test yaml import/export for a model containing observables."""
         yaml_dir = os.path.join(self.test_folder, 'ode_input2.yaml')
 
         expected_result_file = \
@@ -77,19 +72,15 @@ def test_yaml_import_observables(self):
         os.remove(sbml_test_dir)
 
     def test_catch_invalid_sbml_identifier(self):
-        """
-        Check for invalid SBML identifiers.
-        """
+        """Check for invalid SBML identifiers."""
         yaml_dir = os.path.join(self.test_folder,
                                 'ode_input_invalid_SBML_identifier.yaml')
         with self.assertRaises(RuntimeError):
             _parse_yaml(yaml_dir,
                         'Test_Model')
 
     def test_catch_invalid_math(self):
-        """
-        Check for strings that parseL3Formula can not parse.
-        """
+        """Check for strings that parseL3Formula can not parse."""
         yaml_dir = os.path.join(self.test_folder,
                                 'ode_input_invalid_formula.yaml')
         with self.assertRaises(RuntimeError):

tests/test_yaml_validation.py

@@ -1,3 +1,4 @@
+"""Test for yaml-file validation."""
 import os
 import unittest
 
@@ -7,50 +8,52 @@
 
 
 class TestYamlValidation(unittest.TestCase):
+    """TestCase class for yaml model validation."""
 
     def setUp(self):
+        """Set Up of Tests."""
         this_dir, _ = os.path.split(__file__)
         self.test_folder = os.path.join(this_dir, 'test_yaml2sbml')
 
     def test_validate_yaml_valid_1(self):
-        # Test validation for a valid yaml model.
+        """Test validation for a valid yaml model."""
         file_in = os.path.join(self.test_folder, 'ode_input1.yaml')
         validate_yaml(file_in)
 
     def test_validate_yaml_valid_2(self):
-        # Test validation for a second valid yaml model.
+        """Test validation for a second valid yaml model."""
         file_in = os.path.join(self.test_folder, 'ode_input2.yaml')
         validate_yaml(file_in)
 
     def test_validate_yaml_typos(self):
-        # Test if Error is thrown due to typos.
+        """Test if Error is thrown due to typos."""
         file_in = os.path.join(self.test_folder, 'ode_input_typos.yaml')
         with self.assertRaises(ValidationError):
             validate_yaml(file_in)
 
     def test_validate_yaml_typos_required(self):
-        # Test if Error is thrown due to typos.
+        """Test if Error is thrown due to typos."""
         file_in = os.path.join(self.test_folder,
                                'ode_input_typos_required.yaml')
         with self.assertRaises(ValidationError):
             validate_yaml(file_in)
 
     def test_validate_yaml_empty_section(self):
-        # Test if Error is thrown due to empty observable section.
+        """Test if Error is thrown due to empty observable section."""
         file_in = os.path.join(self.test_folder,
                                'ode_input_empty_section.yaml')
         with self.assertRaises(ValidationError):
             validate_yaml(file_in)
 
     def test_catch_invalid_time_block_missing_variable_key(self):
-        # Test time block without kew word "variable".
+        """Test time block without kew word "variable"."""
         file_in = os.path.join(self.test_folder,
                                'ode_input_invalid_time_1.yaml')
         with self.assertRaises(ValidationError):
             validate_yaml(file_in)
 
     def test_catch_invalid_time_block_as_array(self):
-        # Test time block as array instead of single object.
+        """Test time block as array instead of single object."""
         file_in = os.path.join(self.test_folder,
                                'ode_input_invalid_time_2.yaml')
         with self.assertRaises(ValidationError):

tox.ini

@@ -51,7 +51,7 @@ deps =
     pep8-naming >= 0.11.1
     pydocstyle >= 5.1.1
 commands =
-    flake8 yaml2sbml tests setup.py
+    flake8 yaml2sbml tests
     pydocstyle yaml2sbml tests setup.py
 description =
     Run flake8 with various plugins, and pydocstyle

yaml2sbml/yaml2PEtab.py

@@ -8,6 +8,7 @@
 import petab
 import yaml
 from pathlib import Path
+from petab.models.sbml_model import SbmlModel
 
 
 from .yaml2sbml import _parse_yaml_dict, _load_yaml_file
@@ -97,7 +98,8 @@ def _yaml2petab(yaml_model_dict: dict,
 
         warnings.warn('Since no petab_yaml_file_name is specified, the '
                       'specified measurement_table_name will have no effect.',
-                      RuntimeWarning)
+                      RuntimeWarning,
+                      stacklevel=2)
 
     elif petab_yaml_name is not None:
         _create_petab_problem_yaml(yaml_model_dict,
@@ -284,15 +286,15 @@ def validate_petab_tables(sbml_dir: str,
         condition_df = pd.read_csv(condition_table_dir,
                                    sep='\t',
                                    index_col='conditionId')
-        petab.lint.check_condition_df(condition_df, model)
+        petab.lint.check_condition_df(condition_df, SbmlModel(model))
 
     # check parameter table
     parameter_df = pd.read_csv(parameter_file_dir,
                                sep='\t',
                                index_col='parameterId')
 
     petab.lint.check_parameter_df(parameter_df,
-                                  sbml_model=model,
+                                  model=SbmlModel(model),
                                   observable_df=observable_df)
 
 
@@ -319,7 +321,8 @@ def _create_petab_table(block_list: list,
     for col_name in petab_table.head():
         if not (col_name in mandatory_id_list or col_name in optional_id_list):
             warnings.warn(f'PEtab warning: {col_name} is not part of the '
-                          f'PEtab standard and hence might have noe effect.')
+                          f'PEtab standard and hence might have noe effect.',
+                          stacklevel=2)
     return petab_table
 
 
@@ -359,11 +362,11 @@ def main():
 
     args = parser.parse_args()
 
-    print(f'Path to yaml file: {args.yaml_file}')
-    print(f'Output directory: {args.output_dir}')
-    print(f'Path to sbml/petab files: {args.model_name}')
+    print(f'Path to yaml file: {args.yaml_file}')  # noqa:T201
+    print(f'Output directory: {args.output_dir}')  # noqa:T201
+    print(f'Path to sbml/petab files: {args.model_name}')  # noqa:T201
 
-    print('Converting...')
+    print('Converting...')  # noqa:T201
 
     yaml2petab(args.yaml_file,
                args.output_dir,