Merge pull request #404 from ISA-tools/github-action-build

Create buildandtestpython.yml

.github/workflows/buildandtestpython.yml

@@ -0,0 +1,40 @@
+name: Python package
+
+on:
+  pull_request:
+  push:
+    branches: master
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: [3.7, 3.8, 3.9]
+
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Download Test Data
+        run: |
+          bash -x get_test_data.sh
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install flake8 pytest
+          if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+      - name: Test with python unittests
+        run: |
+          behave --no-capture --no-capture-stderr --format=progress features/isa-file-handler.feature
+          coverage run -m unittest discover -s tests/
+          coverage report -m

tests/test_isatab2w4m.py

@@ -8,8 +8,6 @@
 from isatools.convert import isatab2w4m
 from isatools.tests import utils
 
-from nose.tools import nottest
-
 # Test presence of data folder
 def setUpModule():
     if not os.path.exists(utils.DATA_DIR):
@@ -31,7 +29,6 @@ def setUp(self):
     def tearDown(self):
         shutil.rmtree(self._tmp_dir)
 
-    @nottest
     def plain_test(self, study, test_dir):
 
         # Convert
@@ -67,7 +64,6 @@ def test_MTBLS338(self):
         self.plain_test('MTBLS338', 'MTBLS338-w4m')
 
     # Test NA filtering
-    @nottest
     def na_filtering_test(self, study, test_dir, samp_na_filtering=None, 
                           var_na_filtering=None):