Add ci back. Remove blast tests.

.github/workflows/ci.yml

@@ -0,0 +1,49 @@
+name: Python CI
+
+on: [push, pull_request]
+
+jobs:
+ build:
+ runs-on: ubuntu-latest
+ strategy:
+ matrix:
+ python-version: [3.7]
+
+ steps:
+ - uses: actions/checkout@v2
+
+ - name: Set up Python ${{ matrix.python-version }}
+ uses: actions/setup-python@v2
+ with:
+ python-version: ${{ matrix.python-version }}
+
+ - name: Cache pip
+ uses: actions/cache@v2
+ with:
+ path: ~/.cache/pip
+ key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
+ restore-keys: |
+ ${{ runner.os }}-pip-
+
+ - name: Install dependencies
+ run: |
+ sudo apt-get install -qq phyml
+ pip install --upgrade pip setuptools wheel
+ pip install --only-binary=numpy,scipy numpy scipy
+ pip install matplotlib ipython jupyter sympy pytest codecov pytest-cov
+ pip install -r requirements.txt
+ pip install .
+
+ - name: Run tests
+ run: pytest --cov-report=xml --cov=OrthoEvol tests/
+
+ - name: Upload coverage to Codecov
+ uses: codecov/codecov-action@v2
+ with:
+ token: ${{ secrets.CODECOV_TOKEN }}
+ files: ./coverage.xml
+ fail_ci_if_error: true
+
+ - name: Notify failure
+ if: failure()
+ run: echo "Build failed"

tests/test_cookies.py

@@ -10,7 +10,6 @@ def test_init(self):
  cookbook = CookBook()
  self.assertTrue(hasattr(cookbook, 'CookieJar'))
  self.assertIsInstance(cookbook.CookieJar, Path)
- # Test other attributes similarly
 
  @patch('builtins.open', new_callable=MagicMock)
  def test_new_recipes(self, mock_open):

tests/test_orthologs.py

@@ -26,23 +26,23 @@ def delete_phyml_output(self):
  def delete_treeviz_output(self):
  os.remove('example.png')
 
- def test_baseblastn(self):
- """Test the BaseBlastN class."""
- # The with statement is for travisci where a BLASTDB variable
- # is not set.
- # TIP: Remove the with statement if testing with BLASTDB in your
- # environment variables.
- with self.assertRaises(EnvironmentError):
- gpcr_blastn = BaseBlastN(project=self.project, method=1,
- save_data=True, acc_file="gpcr.csv",
- copy_from_package=True,
- ref_species='Homo_sapiens',
- proj_mana=None,
- project_path=self.project_path)
- self.assertEqual(gpcr_blastn.proj_mana, None)
- self.assertEqual(gpcr_blastn.acc_file, "gpcr.csv")
- self.assertTrue(gpcr_blastn.copy_from_package)
- self.delete_project(project_path=self.project_path)
+ # def test_baseblastn(self):
+ #  """Test the BaseBlastN class."""
+ #  # The with statement is for travisci where a BLASTDB variable
+ #  # is not set.
+ #  # TIP: Remove the with statement if testing with BLASTDB in your
+ #  # environment variables.
+ #  with self.assertRaises(EnvironmentError):
+ #  gpcr_blastn = BaseBlastN(project=self.project, method=1,
+ #  save_data=True, acc_file="gpcr.csv",
+ #  copy_from_package=True,
+ #  ref_species='Homo_sapiens',
+ #  proj_mana=None,
+ #  project_path=self.project_path)
+ #  self.assertEqual(gpcr_blastn.proj_mana, None)
+ #  self.assertEqual(gpcr_blastn.acc_file, "gpcr.csv")
+ #  self.assertTrue(gpcr_blastn.copy_from_package)
+ #  self.delete_project(project_path=self.project_path)
 
  # def test_phyml(self):
  # """Test the PhyML class."""
@@ -61,15 +61,15 @@ def test_treeviz(self):
  self.assertIsNotNone('example.png')
  self.delete_treeviz_output()
 
- def test_orthoblastn(self):
- """Test the OrthoBlastN class."""
- with self.assertRaises(EnvironmentError):
- ortho_blastn = OrthoBlastN(project="orthology-project",
- method=1, save_data=True,
- acc_file="gpcr.csv",
- copy_from_package=True)
- self.assertEqual(ortho_blastn.ref_species, 'Homo_sapiens')
- self.assertTrue(ortho_blastn.copy_from_package)
+ # def test_orthoblastn(self):
+ #  """Test the OrthoBlastN class."""
+ #  with self.assertRaises(EnvironmentError):
+ #  ortho_blastn = OrthoBlastN(project="orthology-project",
+ #  method=1, save_data=True,
+ #  acc_file="gpcr.csv",
+ #  copy_from_package=True)
+ #  self.assertEqual(ortho_blastn.ref_species, 'Homo_sapiens')
+ #  self.assertTrue(ortho_blastn.copy_from_package)
 
 
 if __name__ == '__main__':