Merge pull request #179 from oncokb/add-flake8

Add flake8 github action and fix all flake8 errors

.github/workflows/pytest.yml

@@ -10,7 +10,24 @@ on:
     branches: [ master, next-minor-release ]
 
 jobs:
-  build:
+  lint:
+    name: Linting using flake8
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: actions/setup-python@v2
+        with:
+          python-version: "3.9"
+      - name: Run flake8
+        uses: julianwachholz/flake8-action@v2
+        with:
+          checkName: "Python Lint"
+          path: .
+          config: flake8.ini
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  pytest:
+    needs: lint
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
@@ -27,15 +44,9 @@ jobs:
         PYTHON_VERSION: ${{ matrix.python-version }}
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest
+        pip install pytest
         if [[ $PYTHON_VERSION =~ ^2\.[0-9]$ ]]; then pip install -r requirements/common.txt -r requirements/pip2.7.txt; fi
         if [[ $PYTHON_VERSION =~ ^3\.[0-9]$ ]]; then pip install -r requirements/common.txt -r requirements/pip3.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 pytest
       env:
         ONCOKB_API_TOKEN: ${{ secrets.ONCOKB_BOT_API_TOKEN }}
@@ -58,7 +69,7 @@ jobs:
         PYTHON_VERSION: ${{ matrix.python-version }}
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest
+        pip install pytest
         if ( $env:PYTHON_VERSION -match '^2\.[0-9]$' )
         {
           pip install -r requirements/common.txt -r requirements/pip2.7.txt
@@ -67,12 +78,6 @@ jobs:
         {
           pip install -r requirements/common.txt -r requirements/pip3.txt
         }
-    - 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 pytest
       env:
         ONCOKB_API_TOKEN: ${{ secrets.ONCOKB_BOT_API_TOKEN }}

.version-level

@@ -1 +1 @@
-minor
+patch