pr-checks.yaml

# Tests that run on every PR

name: Pull Request Checks

on: [push, pull_request]

jobs:
  black:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
        name: Checkout repository

      - uses: actions/setup-python@v2
        name: Setup Python
        with:
          python-version: 3.9

      - name: Install black
        run: |
          python -m pip install --upgrade pip
          pip install black
      - name: Run black
        run: |
          black . --check
  # This job is copied over from `deploy.yaml`
  run-tests:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      # See: https://github.com/marketplace/actions/setup-conda
      - uses: s-weigand/setup-conda@v1
        with:
          conda-channels: "conda-forge"

      - name: Build environment
        run: |
          conda env create -f environment.yml
          eval "$(conda shell.bash hook)"
          conda activate cellxgene-gateway
          pip install markupsafe==2.0.1 # temporary workaround for jinja2-2.11.3 calling soft_unicode in markupsafe
          python setup.py install

      - name: Run tests
        run: |
          eval "$(conda shell.bash hook)"
          conda activate cellxgene-gateway
          coverage run -m unittest discover tests

      - name: Check coverage
        run: |
          eval "$(conda shell.bash hook)"
          conda activate cellxgene-gateway
          coverage report --fail-under 41
          coverage xml -i

      - name: "Upload coverage to Codecov"
        uses: codecov/codecov-action@v1
        with:
          token: ${{ secrets.CODECOV_TOKEN }}
          files: ./coverage.xml
          flags: unittests
          env_vars: OS,PYTHON
          name: codecov-umbrella
          fail_ci_if_error: true
          path_to_write_report: ./codecov_report.txt
          verbose: true