ci.yaml

name: Python tests
on: [push, pull_request]
jobs:
  test:
    runs-on: ubuntu-20.04
    steps:
      - name: checkout
        uses: actions/checkout@v3
        with:
          fetch-depth: 0
      - name: Install Python
        uses: actions/setup-python@v1
        with:
          python-version: 3.9
      - name: Install Poetry
        uses: snok/install-poetry@v1
        with:
          virtualenvs-create: false
          installer-parallel: true
          version: 1.2.2
      - name: Install dependencies
        run: |
          poetry install --no-dev
          sh install_local_depency.sh
      # Before running the test you have to download the tags!
      - name: Run tests
        run: |
            python get_data/get_fpbase_data.py allele_components/tags_fpbase.toml
            cd genestorian_module/test
            python -m unittest

 # Update docker image when committing to master branch if tests pass
  # push_to_registry:
  #   name: Push Docker image to Docker Hub
  #   runs-on: ubuntu-latest
  #   needs: test
  #   if: github.ref == 'refs/heads/master'
  #   steps:
  #     - name: Check out the repo
  #       uses: actions/checkout@v3

  #     - name: Log in to Docker Hub
  #       uses: docker/login-action@v2
  #       with:
  #         username: ${{ secrets.DOCKER_USERNAME }}
  #         password: ${{ secrets.DOCKER_PASSWORD }}

  #     - name: Extract metadata (tags, labels) for Docker
  #       id: meta
  #       uses: docker/metadata-action@v2
  #       with:
  #         images: genestorian_refinement_pipeline

  #     - name: Build and push Docker images
  #       uses: docker/build-push-action@v3.1.1

  #       with:
  #         context: .
  #         push: true
  #         tags: manulera/genestorian_refinement_pipeline:latest
  #         labels: ${{ steps.meta.outputs.labels }}