test.yml

name: Test TPS
on:
- push
- pull_request
jobs:
  pcsf:
    name: Test PCSF
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest]
    steps:
      - name: Checkout repository
        uses: actions/checkout@v2
      - name: Install conda environment
        uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: pcsf
          environment-file: pcsf/environment.yml
          auto-activate-base: false
          auto-update-conda: false
          miniconda-version: 'latest'
      # Log conda environment contents
      - name: Log conda environment
        shell: bash --login {0}
        run: conda list
      # Run the PCSF tests in the pcsf conda environment
      - name: Test PCSF
        shell: bash --login {0}
        run: pytest pcsf/tests/
  docker:
    name: Build Docker images
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest]
    steps:
      - name: checkout repository
        uses: actions/checkout@v2
      - name: Build TPS Docker image
        uses: docker/build-push-action@v1
        with:
          path: .
          dockerfile: containers/tps/Dockerfile
          repository: ajshedivy/tps
          tags: latest
          cache_froms: ajshedivy/tps:latest
          push: false
      - name: Build Cytoscape Docker image
        uses: docker/build-push-action@v1
        with:
          path: .
          dockerfile: containers/cytoscape/Dockerfile
          repository: ajshedivy/cytoscape
          tags: latest
          cache_froms: ajshedivy/cytoscape:latest
          push: false
  workflow:
    name: Test TPS workflow
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest]
    steps:
      - name: Checkout repository
        uses: actions/checkout@v2
      - name: Install conda environment
        uses: conda-incubator/setup-miniconda@v2
        with:
          activate-environment: tps_workflow
          environment-file: workflow/minimal_env.yml
          auto-activate-base: false
          miniconda-version: 'latest'
      # Log conda environment contents
      - name: Log conda environment
        shell: bash --login {0}
        run: conda list
      # Run the workflow tests
      - name: Test workflow with pytest
        shell: bash --login {0}
        # Verbose output and disable stdout and stderr capturing
        run: pytest -vs workflow/tests/
      - name: Test workflow with script
        shell: bash --login {0}
        run: bash workflow.sh --config workflow/config/default_config.yaml --execute all