test-spras.yml

name: Test SPRAS

on: [push, pull_request]

jobs:
  # Installs the conda environment but does not run tests because the tests require Linux Docker images
  conda-only:
    name: Test conda environment
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [macos-latest, windows-latest]
    steps:
    - name: Checkout repository
      uses: actions/checkout@v2
    - name: Install conda environment
      uses: conda-incubator/setup-miniconda@v2
      with:
        activate-environment: spras
        environment-file: environment.yml
        auto-activate-base: false
        miniconda-version: 'latest'
    # Log conda environment contents
    - name: Log conda environment
      shell: bash --login {0}
      run: conda list

  # Runs the test code and Snakemake workflow in the conda environment
  test:
    name: Run test cases and workflow
    # The Docker images will be pulled in both the docker job and this test job
    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: spras
        environment-file: environment.yml
        auto-activate-base: false
        miniconda-version: 'latest'
    # Log conda environment contents
    - name: Log conda environment
      shell: bash --login {0}
      run: conda list
    # Formerly used Singularity instead of Apptainer (see https://github.com/eWaterCycle/setup-singularity/issues/6)
    - name: Install Apptainer
      uses: eWaterCycle/setup-apptainer@v2
      with:
        # Choose version from https://github.com/apptainer/apptainer/releases
        apptainer-version: 1.2.2
    - name: Run tests
      shell: bash --login {0}
      # Verbose output and disable stdout and stderr capturing
      run: pytest -vs
    - name: Run Snakemake workflow
      shell: bash --login {0}
      run: snakemake --cores 2 --configfile config/config.yaml --show-failed-logs

  # Builds the Docker images
  docker:
    name: Build Docker images
    runs-on: ${{ matrix.os }}
    strategy:
      matrix:
        os: [ubuntu-latest]
    steps:
    - name: Checkout repository
      uses: actions/checkout@v2
      # Pull from Docker Hub to use the cache
      # https://medium.com/mobileforgood/coding-tips-patterns-for-continuous-integration-with-docker-on-travis-ci-9cedb8348a62
      # https://github.com/docker/build-push-action/issues/7
    - name: Pull Docker images
      run: |
        docker pull reedcompbio/omics-integrator-1:latest
        docker pull reedcompbio/omics-integrator-2:v2
        docker pull reedcompbio/pathlinker:v2
        docker pull reedcompbio/meo:latest
        docker pull reedcompbio/mincostflow:latest
        docker pull reedcompbio/allpairs:v2
        docker pull reedcompbio/domino:latest
        docker pull reedcompbio/py4cytoscape:v3
        docker pull reedcompbio/spras:v0.1.0
    - name: Build Omics Integrator 1 Docker image
      uses: docker/build-push-action@v1
      with:
        path: docker-wrappers/OmicsIntegrator1/.
        dockerfile: docker-wrappers/OmicsIntegrator1/Dockerfile
        repository: reedcompbio/omics-integrator-1
        tags: latest
        cache_froms: reedcompbio/omics-integrator-1:latest
        push: false
    - name: Remove Omics Integrator 1 Docker image
      # Remove the image to prevent the cache from being used. Here we use
      # `|| true` to prevent the job from failing if the image doesn't exist or
      # can't be removed for some reason
      run: docker rmi reedcompbio/omics-integrator-1:latest || true

    - name: Build Omics Integrator 2 Docker image
      uses: docker/build-push-action@v1
      with:
        path: docker-wrappers/OmicsIntegrator2/.
        dockerfile: docker-wrappers/OmicsIntegrator2/Dockerfile
        repository: reedcompbio/omics-integrator-2
        tags: v2
        cache_froms: reedcompbio/omics-integrator-2:latest
        push: false
    - name: Remove Omics Integrator 2 Docker image
      run: docker rmi reedcompbio/omics-integrator-2:latest || true

    - name: Build PathLinker Docker image
      uses: docker/build-push-action@v1
      with:
        path: docker-wrappers/PathLinker/.
        dockerfile: docker-wrappers/PathLinker/Dockerfile
        repository: reedcompbio/pathlinker
        tags: v2
        cache_froms: reedcompbio/pathlinker:latest
        push: false
    - name: Remove PathLinker Docker image
      run: docker rmi reedcompbio/pathlinker:latest || true

    - name: Build Maximum Edge Orientation Docker image
      uses: docker/build-push-action@v1
      with:
        path: docker-wrappers/MEO/.
        dockerfile: docker-wrappers/MEO/Dockerfile
        repository: reedcompbio/meo
        tags: latest
        cache_froms: reedcompbio/meo:latest
        push: false
    - name: Remove MEO Docker image
      run: docker rmi reedcompbio/meo:latest || true

    - name: Build MinCostFlow Docker image
      uses: docker/build-push-action@v1
      with:
        path: docker-wrappers/MinCostFlow/.
        dockerfile: docker-wrappers/MinCostFlow/Dockerfile
        repository: reedcompbio/mincostflow
        tags: latest
        cache_froms: reedcompbio/mincostflow:latest
        push: false
    - name: Remove MinCostFlow Docker image
      run: docker rmi reedcompbio/mincostflow:latest || true

    - name: Build All Pairs Shortest Paths Docker image
      uses: docker/build-push-action@v1
      with:
        path: docker-wrappers/AllPairs/.
        dockerfile: docker-wrappers/AllPairs/Dockerfile
        repository: reedcompbio/allpairs
        tags: v2
        cache_froms: reedcompbio/allpairs:latest
        push: false
    - name: Remove All Pairs Shortest Paths Docker image
      run: docker rmi reedcompbio/allpairs:latest || true

    - name: Build DOMINO Docker image
      uses: docker/build-push-action@v1
      with:
        path: docker-wrappers/DOMINO/.
        dockerfile: docker-wrappers/DOMINO/Dockerfile
        repository: reedcompbio/domino
        tags: latest
        cache_froms: reedcompbio/domino:latest
        push: false
    - name: Remove DOMINO Docker image
      run: docker rmi reedcompbio/domino:latest || true

    - name: Build Cytoscape Docker image
      uses: docker/build-push-action@v1
      with:
        path: docker-wrappers/Cytoscape/.
        dockerfile: docker-wrappers/Cytoscape/Dockerfile
        repository: reedcompbio/py4cytoscape
        tags: v3
        cache_froms: reedcompbio/py4cytoscape:v3
        push: false
    - name: Remove Cytoscape Docker image
      run: docker rmi reedcompbio/py4cytoscape:v3 || true

    - name: Build SPRAS Docker image
      uses: docker/build-push-action@v1
      with:
        path: .
        dockerfile: docker-wrappers/SPRAS/Dockerfile
        repository: reedcompbio/spras
        tags: v0.2.0
        cache_froms: reedcompbio/spras:v0.2.0
        push: false
    - name: Remove SPRAS Docker image
      run: docker rmi reedcompbio/spras:v0.2.0 || true

  # Run pre-commit checks on source files
  pre-commit:
    name: Run pre-commit checks
    runs-on: ubuntu-latest
    steps:
    - name: Checkout repository
      uses: actions/checkout@v3
    - name: Setup Python
      uses: actions/setup-python@v4
      with:
        python-version: '3.11' # Match this to the version specified in environment.yml
    - name: Run pre-commit checks
      uses: pre-commit/action@v3.0.0