ci.yml

name: CI
on:
  push:
    branches:
      - main
  pull_request:
jobs:
  pylint:
    name: Pylint
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v3
      - name: Setup Python 3.11
        uses: actions/setup-python@v4
        with:
          python-version: 3.11
      - name: Use pip cache
        uses: actions/cache@v3
        with:
          path: ~/.cache/pip
          key: pip-${{ hashFiles('**/requirements*.txt') }}
          restore-keys: |
            pip-
      - name: Install dependencies
        run: |
          pip install wheel
          pip install -r requirements.txt
          pip install -r requirements-dev.txt
          curl -sSL https://broad.io/install-gcs-connector | python3 - --auth-type UNAUTHENTICATED
      - name: Check formatting
        run: black --check gnomad tests
      - name: Check imports
        run: isort --check-only gnomad tests
      - name: Check docstrings
        run: pydocstyle gnomad tests
      - name: Check comment formatting
        run: autopep8 --exit-code --diff gnomad
      - name: Run Pylint
        run: ./lint
      - name: Run tests
        run: python -m pytest
  docs:
    name: Build documentation
    runs-on: ubuntu-latest
    steps:
      - name: Checkout
        uses: actions/checkout@v3
      - name: Setup Python 3.11
        uses: actions/setup-python@v4
        with:
          python-version: 3.11
      - name: Use pip cache
        uses: actions/cache@v3
        with:
          path: ~/.cache/pip
          key: pip-${{ hashFiles('**/requirements*.txt') }}
          restore-keys: |
            pip-
      - name: Install dependencies
        run: |
          pip install wheel
          pip install -r requirements.txt
          pip install -r docs/requirements.docs.txt
      - name: Build docs
        run: ./docs/build.sh
      - name: Publish to GitHub Pages
        if: github.event_name == 'push'
        run: |
          # Create empty gh-pages branch
          git checkout --orphan gh-pages

          # Remove files other than docs
          git rm -rf .
          find . -name __pycache__ | xargs rm -r

          # Move docs to root
          mv docs/html/* ./
          rm -r docs

          # Tell GitHub not to treat this as a Jekyll site
          touch .nojekyll

          git config user.name "${GITHUB_ACTOR}"
          git config user.email "${GITHUB_ACTOR}@users.noreply.github.com"

          git add .
          git commit --allow-empty -m "Update docs"

          git push --force origin gh-pages

          # Restore the original working tree by checking out the
          # commit that triggered the workflow.
          # This restores requirements.txt so that @actions/cache
          # can use it for determining the cache key.
          git checkout ${GITHUB_SHA}
  gnomad_qc:
    name: gnomad_qc checks
    runs-on: ubuntu-latest
    steps:
      - name: Checkout gnomad_methods
        uses: actions/checkout@v3
        with:
          path: gnomad_methods
      - name: Checkout gnomad_qc
        uses: actions/checkout@v3
        with:
          submodules: recursive
          repository: broadinstitute/gnomad_qc
          path: gnomad_qc
      - name: Setup Python 3.11
        uses: actions/setup-python@v4
        with:
          python-version: 3.11
      - name: Use pip cache
        uses: actions/cache@v3
        with:
          path: ~/.cache/pip
          key: pip-${{ hashFiles('gnomad_methods/**/requirements*.txt') }}
          restore-keys: |
            pip-
      - name: Install dependencies
        run: |
          pip install wheel
          pip install ./gnomad_methods
          cat gnomad_qc/requirements.txt | grep -v gnomad_methods > gnomad_qc/requirements-edited.txt
          pip install -r gnomad_qc/requirements-edited.txt
          pip install -r gnomad_methods/requirements-dev.txt
      - name: Run Pylint
        run: pylint --disable=R,C,W gnomad_qc
        working-directory: ./gnomad_qc