Merge pull request #332 from marrink-lab/GH_actions

Implement GH actions

.github/workflows/run_tests.yml

@@ -0,0 +1,112 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: test package
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+env:
+  VERMOUTH_TEST_DSSP: mkdssp
+  SKIP_GENERATE_AUTHORS: 1
+  SKIP_WRITE_GIT_CHANGELOG: 1
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+       py_version: ["3.6", "3.7", "3.8", "3.9", "3.6-dev", "3.7-dev", "3.8-dev", "3.9-dev"] 
+       include:
+         - py_version: "3.6"
+           WITH_CODECOV: true
+           WITH_SCIPY: true
+         - py_version: "3.7"
+           WITH_CODECOV: true
+           WITH_SCIPY: true
+         - py_version: "3.8"
+           WITH_CODECOV: true
+           WITH_SCIPY: true
+         - py_version: "3.9"
+           WITH_CODECOV: true
+           WITH_SCIPY: false
+         - py_version: "3.8-dev"
+           WITH_CODECOV: true
+           WITH_SCIPY: true
+         - py_version: "3.9-dev"
+           WITH_CODECOV: true
+           WITH_SCIPY: true
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.py_version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.py_version }}
+    - name: Install dependencies part I
+      run: |
+        sudo apt-get install dssp
+        pip install --upgrade setuptools pip
+    - if: ${{ matrix.WITH_SCIPY }}
+      name: Install scipy
+      run: |
+        pip install scipy
+    - name: Install package and requirements
+      run: |
+        pip install --upgrade .
+        pip install -r requirements-tests.txt
+        
+    - name: Run pytest with codecoverage
+      run: |
+        coverage run --source=vermouth $(which pytest) -vv vermouth --hypothesis-show-statistics
+        coverage report --omit='*/bin/pytest'
+        
+    - if: ${{ matrix.WITH_CODECOV }}
+      name: Report code coverage 
+      run: |
+        codecov
+        
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python 3.7
+      uses: actions/setup-python@v2
+      with:
+        python-version: 3.9
+    - name: Install dependencies
+      run: |
+        pip install --upgrade setuptools pip
+        pip install --upgrade .
+        pip install -r requirements-tests.txt
+    - name: Run pylint 
+      run: |
+         python run_pylint.py --disable=fixme --fail-under=8.0 vermouth
+         python run_pylint.py --disable=fixme --fail-under=9.5 bin/martinize2 
+         
+   
+  docs:
+      runs-on: ubuntu-latest
+
+      steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v2
+        with:
+           python-version: 3.9
+      - name: Install dependencies
+        run: |
+          pip install --upgrade setuptools pip
+          pip install --upgrade .
+          pip install -r requirements-docs.txt
+          
+      - name: Run docs
+        run: | 
+          mkdir -p doc/source/_static
+          sphinx-build -EnW -b html doc/source/ doc/build/html

vermouth/tests/test_logging.py

@@ -70,14 +70,6 @@ def handle(self, record):
         self.test(record)
 
 
-@pytest.fixture
-def logger(request):
-    """Sets up a logger at loglevel 1 and attaches a LogHandler."""
-    logger_ = logging.getLogger(request.function.__name__)
-    logger_.setLevel(1)
-    return logger_
-
-
 @pytest.fixture(scope='module')
 def handler():
     """Sets up a LogHandler"""
@@ -105,7 +97,7 @@ def test_get_logger(name):
         st.dictionaries(KWARG_ST, st.integers(), min_size=0, max_size=5)
     )
 )
-def test_type_adapter(logger, handler, args, type_, default_type, extra):
+def test_type_adapter(handler, args, type_, default_type, extra):
     """Make sure the TypeAdapter sets the correct type attr"""
     def test(record):
         """Make sure the type attribute is as expected"""
@@ -121,6 +113,8 @@ def test(record):
             for key, val in extra.items():
                 assert getattr(record, key, None) == val
 
+    logger = logging.getLogger('test_type_adapter')
+    logger.setLevel(1)
     logger.addHandler(handler)
     logger = TypeAdapter(logger, default_type=default_type, extra=extra)
     handler.set_test(test)
@@ -148,7 +142,7 @@ def test(record):
         st.dictionaries(KWARG_ST, st.integers(), min_size=0, max_size=5)
     )
 )
-def test_style_type_adapter(logger, handler, args, kwargs, type_, default_type, extra):
+def test_style_type_adapter(handler, args, kwargs, type_, default_type, extra):
     """Make sure that if you have both a TypeAdapter and a StyleAdapter the
     type you provide ends up in the right place, and that it doesn't interfere
     with keyword formatting."""
@@ -165,6 +159,8 @@ def test(record):
             for key, val in extra.items():
                 assert getattr(record, key, None) == val
 
+    logger = logging.getLogger('test_style_type_adapter')
+    logger.setLevel(1)
     logger.addHandler(handler)
     logger = TypeAdapter(logger, default_type=default_type)
     logger = StyleAdapter(logger, extra=extra)
@@ -189,7 +185,7 @@ def test(record):
     extra=st.one_of(st.none(),
                     st.dictionaries(KWARG_ST, st.integers(), min_size=0, max_size=5))
 )
-def test_style_adapter(logger, handler, args, kwargs, extra):
+def test_style_adapter(handler, args, kwargs, extra):
     """Make sure the StyleAdapter can do keyword formatting"""
     def test(record):
         """Make sure the formatting worked"""
@@ -198,6 +194,8 @@ def test(record):
             for key, val in extra.items():
                 assert getattr(record, key, None) == val
 
+    logger = logging.getLogger('test_style_adapter')
+    logger.setLevel(1)
     logger.addHandler(handler)
     logger = StyleAdapter(logger, extra=extra)
     handler.set_test(test)
@@ -213,12 +211,14 @@ def test(record):
     args=st.lists(st.text(), min_size=0, max_size=5),
     kwargs=st.dictionaries(KWARG_ST, st.text(), min_size=1, max_size=5),
 )
-def test_passing_adapter(logger, handler, args, kwargs):
+def test_passing_adapter(handler, args, kwargs):
     """Make sure the PassingLoggerAdapter does not allow keywords to be set for
     formatting."""
     def test(_):
         assert False
     handler.set_test(test)
+    logger = logging.getLogger('test_passing_adapter')
+    logger.setLevel(1)
     logger.addHandler(handler)
     logger = PassingLoggerAdapter(logger)
     fmt = ['%s']*len(args) + ['%(' + name + ')s' for name in kwargs]