Merge pull request #48 from yaml2sbml-dev/feature_tests

Improve tests (closes #18, #34)

.github/workflows/ci_push.yml

@@ -29,10 +29,18 @@ jobs:
         .github/workflows/install_deps.sh amici
         pip install .
 
+    - name: flake8
+      run: |
+        ./run_flake8.sh
+
     - name: Run tests
       timeout-minutes: 5
       run: |
-        python -m pytest --cov=yaml2sbml --cov-report=xml tests -s
+        python -m pytest --nbmake --cov=yaml2sbml --cov-report=xml tests -s
+
+    - name: Test CLI
+      run: |
+        ./tests/test_CLI.sh
 
     - name: Codecov
       uses: codecov/codecov-action@v1

.github/workflows/install_deps.sh

@@ -8,6 +8,9 @@ pip install wheel
 # required for tests
 pip install pytest pytest-cov
 
+pip install flake8
+pip install nbmake
+
 # iterate over optional dependencies
 for par in "$@"; do
   case $par in

MANIFEST.in

@@ -0,0 +1 @@
+include yaml2sbml/yaml_schema.yaml

run_flake8.sh

@@ -0,0 +1,5 @@
+#!/usr/bin/env bash
+
+python3 -m flake8 \
+    --exclude=build,doc,examples,source \
+    --per-file-ignores='*/__init__.py:F401 test/*:T001,S101'

setup.py

@@ -13,13 +13,20 @@
     version="0.1.1",
     author="Jakob Vanhoefer, Marta R. A. Matos",
     author_email="[email protected]",
-    description="A small package to convert ODEs specified in a yaml file to SBML/PEtab.",
+    description="A small package to convert ODEs specified in "
+                "a yaml file to SBML/PEtab.",
     url="https://github.com/martamatos/yaml2sbml",
     packages=setuptools.find_packages(),
     install_requires=["python-libsbml>=5.18.0",
                       "PyYAML>=5.1",
                       "pandas>=1.0.1",
                       "petab>=0.1.4"],
+    tests_require=["amici>=0.11.10",
+                   "pypesto>=0.2.2"
+                   "numpy>=1.19.4",
+                   "matplotlib>=3.1.0",
+                   "flake8>=3.7.2",
+                   "nbmake>=0.1.0", ],
     extras_require={'examples': ["amici>=0.11.10",
                                  "numpy>=1.19.4",
                                  "matplotlib>=3.1.0"]},
@@ -29,5 +36,6 @@
         "License :: OSI Approved :: MIT License",
         "Operating System :: Unix",
     ],
-    entry_points=ENTRY_POINTS
+    entry_points=ENTRY_POINTS,
+    include_package_data=True
 )

tests/test_CLI.sh

@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+
+mkdir test_output
+
+# test yaml2sbml
+yaml2sbml ./test_yaml2sbml/ode_input1.yaml test_output/test_sbml.xml
+
+# test yaml2petab for both versions of the petab yaml flag
+yaml2petab ./test_yaml2sbml/ode_input2.yaml test_output petab_test_sbml.xml -y test_yaml.yml
+yaml2petab ./test_yaml2sbml/ode_input2.yaml test_output petab_test_sbml.xml --petab_yaml test_yaml.yml
+
+# test validator
+yaml2sbml_validate ./test_yaml2sbml/ode_input1.yaml
+
+rm -r test_output
+

tests/test_yaml2petab.py

@@ -6,28 +6,32 @@
 
 class TestYaml2PEtab(unittest.TestCase):
     """
-    TestCase class for testing ODE import from a generic yaml file and conversion to SBML.
+    TestCase class for testing ODE import from a generic yaml file
+    and conversion to PEtab.
     """
 
     def setUp(self):
         this_dir, _ = os.path.split(__file__)
         self.test_folder = os.path.join(this_dir, 'test_yaml2sbml')
 
     def test_petab_export(self):
-            """
-            Test PEtab export
-            """
-            ode_file = os.path.join(self.test_folder, 'ode_input2.yaml')
-
-            yaml2PEtab.yaml2petab(ode_file,
-                                  self.test_folder,
-                                  'sbml_test.xml')
-
-            yaml2PEtab.validate_petab_tables(os.path.join(self.test_folder, 'sbml_test.xml'),
-                                             self.test_folder)
-
-            for file in ['observable_table.tsv', 'parameter_table.tsv', 'condition_table.tsv', 'sbml_test.xml']:
-                os.remove(os.path.join(self.test_folder, file))
+        """
+        Test PEtab export
+        """
+        ode_file = os.path.join(self.test_folder, 'ode_input2.yaml')
+
+        yaml2PEtab.yaml2petab(ode_file,
+                              self.test_folder,
+                              'sbml_test.xml')
+
+        yaml2PEtab.validate_petab_tables(
+            os.path.join(self.test_folder, 'sbml_test.xml'), self.test_folder)
+
+        for f in ['observable_table.tsv',
+                  'parameter_table.tsv',
+                  'condition_table.tsv',
+                  'sbml_test.xml']:
+            os.remove(os.path.join(self.test_folder, f))
 
 
 if __name__ == '__main__':

tests/test_yaml2sbml.py

@@ -6,7 +6,8 @@
 
 class TestYaml2SBML(unittest.TestCase):
     """
-    TestCase class for testing ODE import from a generic yaml file and conversion to SBML.
+    TestCase class for testing ODE import from a generic yaml file
+    and conversion to SBML.
     """
 
     def setUp(self):
@@ -17,36 +18,46 @@ def test_yaml_import(self):
         """
         Test yaml import/SBML generation...
         """
-        ode_file = os.path.join(self.test_folder, 'ode_input2.yaml')
-        expected_result_file = os.path.join(self.test_folder, 'true_sbml_output.xml')
+        ode_file = os.path.join(self.test_folder, 'ode_input1.yaml')
+        expected_result_file = os.path.join(self.test_folder,
+                                            'true_sbml_output.xml')
 
         sbml_contents = _parse_yaml(ode_file)
 
         with open(expected_result_file, 'r') as f_in:
             expected_sbml_contents = f_in.read()
 
-        with open(os.path.join(self.test_folder, 'sbml_test.xml'), 'w') as f_out:
+        sbml_test_dir = os.path.join(self.test_folder, 'sbml_test.xml')
+        with open(sbml_test_dir, 'w') as f_out:
             f_out.write(sbml_contents)
 
         self.assertEqual(expected_sbml_contents, sbml_contents)
 
-        os.remove(os.path.join(self.test_folder, 'sbml_test.xml'))
+        os.remove(sbml_test_dir)
 
     def test_yaml_import_observables(self):
+        """
+        Test yaml import/export for a model containing observables
+        (that are not translated).
+        """
         ode_file = os.path.join(self.test_folder, 'ode_input2.yaml')
-        expected_result_file = os.path.join(self.test_folder, 'true_sbml_output.xml')
+
+        expected_result_file = \
+            os.path.join(self.test_folder, 'true_sbml_output.xml')
+
+        test_sbml_dir = os.path.join(self.test_folder, 'sbml_test.xml')
 
         sbml_contents = _parse_yaml(ode_file)
 
         with open(expected_result_file, 'r') as f_in:
             expected_sbml_contents = f_in.read()
 
-        with open(os.path.join(self.test_folder, 'sbml_test.xml'), 'w') as f_out:
+        with open(test_sbml_dir, 'w') as f_out:
             f_out.write(sbml_contents)
 
         self.assertEqual(expected_sbml_contents, sbml_contents)
 
-        os.remove(os.path.join(self.test_folder, 'sbml_test.xml'))
+        os.remove(test_sbml_dir)
 
 
 if __name__ == '__main__':

tests/test_yaml_validation.py

@@ -13,38 +13,46 @@ def setUp(self):
         self.test_folder = os.path.join(this_dir, 'test_yaml2sbml')
 
     def test_validate_yaml_valid_1(self):
+        # 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.
         file_in = os.path.join(self.test_folder, 'ode_input2.yaml')
         validate_yaml(file_in)
 
-    # Should throw an error because of typos
     def test_validate_yaml_typos(self):
+        # 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):
-        file_in = os.path.join(self.test_folder, 'ode_input_typos_required.yaml')
+        # 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):
-        file_in = os.path.join(self.test_folder, 'ode_input_empty_section.yaml')
+        # 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):
-        # time block without kew word "variable"
-        file_in = os.path.join(self.test_folder, 'ode_input_invalid_time_1.yaml')
+        # 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):
-        # time block as array instead of single object
-        file_in = os.path.join(self.test_folder, 'ode_input_invalid_time_2.yaml')
+        # 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):
             validate_yaml(file_in)