Merge pull request #20 from JBEI/use-pre-commit-consistently

Use `pre-commit` consistently

.github/workflows/python-package.yml

@@ -25,14 +25,12 @@ jobs:
  - name: Install dependencies
  run: |
  python -m pip install --upgrade pip
- python -m pip install flake8 mock pytest
+ python -m pip install flake8 mock pre-commit pytest
  if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
- - name: Lint with flake8
+ - name: Lint with pre-commit
  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
+ # Use pre-commit so code quality tools are applied consistently @ commit time and in CI
+ pre-commit run --all-files
  - name: Test with pytest
  run: |
  pytest