ci.yml

# GitHub Actions configuration **EXAMPLE**,
# MODIFY IT ACCORDING TO YOUR NEEDS!
# Reference: https://docs.github.com/en/actions

name: tests

on:
  push:
    # Avoid using all the resources/limits available by checking only
    # relevant branches and tags. Other branches can be checked via PRs.
    branches: [main]
    tags: ['v[0-9]*', '[0-9]+.[0-9]+*']  # Match tags that resemble a version
  pull_request:  # Run in every PR
  workflow_dispatch:  # Allow manually triggering the workflow
  schedule:
    # Run roughly every 15 days at 00:00 UTC
    # (useful to check if updates on dependencies break the package)
    - cron: '0 0 1,16 * *'

concurrency:
  group: >-
    ${{ github.workflow }}-${{ github.ref_type }}-
    ${{ github.event.pull_request.number || github.sha }}
  cancel-in-progress: false

jobs:
  prepare:
    runs-on: ubuntu-latest
    outputs:
      wheel-path: ${{ steps.distribution-paths.outputs.wheel }}
      tarball-path: ${{ steps.distribution-paths.outputs.tarball }}
    steps:
      - uses: actions/checkout@v3
        with: {fetch-depth: 0}  # deep clone for setuptools-scm
      - uses: actions/setup-python@v4
        with: {python-version: "3.11"}
      - name: Run static analysis and format checkers
        run: pipx run pre-commit run --all-files --show-diff-on-failure
      - name: Build package distribution files
        run: pipx run --spec 'tox~=3.0' tox -e clean,build
      - name: Record the paths of wheel and source tarball distributions
        id: distribution-paths
        run: |
          echo "wheel=$(ls dist/*.whl)" >> $GITHUB_OUTPUT
          echo "tarball=$(ls dist/*.tar.gz)" >> $GITHUB_OUTPUT
      - name: Store the distribution files for use in other stages
        # `tests`, `pypi-publish`, and `docker-publish` will use the same
        # pre-built distributions, so we make sure to release the exact
        # same package that was tested
        uses: actions/upload-artifact@v3
        with:
          name: python-distribution-files
          path: dist/
          retention-days: 1
        # Prevent scheduled workflow from ever being paused
      - name: Keepalive Workflow
        uses: gautamkrishnar/keepalive-workflow@1.1.0
        
                    
  test:
    needs: prepare
    strategy:
      matrix:
        python:
        - "3.8"
        - "3.11"  # newest Python that is stable
        platform:
        - ubuntu-latest
        - macos-latest
    env:
      OS: ${{ matrix.platform }}
      PYTHON: ${{ matrix.python }}
    runs-on: ${{ matrix.platform }}
    steps:
      - uses: actions/checkout@v3
      - uses: actions/setup-python@v4
        with:
          python-version: ${{ matrix.python }}
      - uses: actions/download-artifact@v3
        with: {name: python-distribution-files, path: dist/}
      - name: Run tests
        env:
          # New variables should match a `passenv` pattern under `[testenv]` in tox.ini
          SEVENBRIDGES_CONNECTION_URI: ${{ secrets.SEVENBRIDGES_CONNECTION_URI }}
          NEXTFLOWTOWER_CONNECTION_URI: ${{ secrets.NEXTFLOWTOWER_CONNECTION_URI }}
          SYNAPSE_CONNECTION_URI: ${{ secrets.SYNAPSE_CONNECTION_URI }}
        run: >-
          pipx run --spec 'tox~=3.0' tox
          --installpkg '${{ needs.prepare.outputs.wheel-path }}'
          -- -rFEx --durations 10 --color yes
      - name: Upload coverage to Codecov
        uses: codecov/codecov-action@v3
        with:
          # CodeCov can be flaky, so this step is not required for success
          fail_ci_if_error: false
          files: coverage.xml
          # Using matrix pattern from `codecov/codecov-action` README:
          # https://github.com/codecov/codecov-action#example-workflowyml-with-codecov-action
          env_vars: OS,PYTHON
          verbose: true

  pypi-publish:
    needs: [prepare, test]
    if: ${{ github.event_name == 'push' && contains(github.ref, 'refs/tags/') }}
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - uses: actions/setup-python@v4
        with: {python-version: "3.11"}
      - uses: actions/download-artifact@v3
        with: {name: python-distribution-files, path: dist/}
      - name: Publish Python Package to PyPI
        env:
          TWINE_REPOSITORY: pypi
          TWINE_USERNAME: __token__
          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
        run: pipx run --spec 'tox!=3.0' tox -e publish

  docker-publish:
    needs: [prepare, test]
    if: ${{ github.event_name == 'push' }}
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - uses: actions/download-artifact@v3
        with: {name: python-distribution-files, path: dist/}
      - uses: docker/setup-qemu-action@v2
      - uses: docker/setup-buildx-action@v2
      - uses: docker/login-action@v2
        with:
          registry: ghcr.io
          username: ${{ github.actor }}
          password: ${{ secrets.GITHUB_TOKEN }}
      - id: meta
        uses: docker/metadata-action@v4
        with:
          images: |
            ghcr.io/${{ github.repository }}
          tags: |
            type=semver,pattern={{version}}
            type=semver,pattern={{major}}.{{minor}}
            type=semver,pattern={{major}}
            type=ref,event=branch
            type=sha
      - name: Publish Python Package to Docker Hub and GHCR
        uses: docker/build-push-action@v3
        with:
          platforms: linux/amd64,linux/arm64
          context: .
          file: src/docker/Dockerfile
          build-args: |
            TARBALL_PATH=${{ needs.prepare.outputs.tarball-path }}
          push: true
          tags: ${{ steps.meta.outputs.tags }}
          labels: ${{ steps.meta.outputs.labels }}