run-tests.yml

name: "Unit tests"

on: [push, pull_request]

jobs:
  build:
    runs-on: ubuntu-latest
    continue-on-error: ${{ matrix.experimental }} # Experimental builds may fail

    defaults:
      run:
        shell: bash -l -e -o pipefail {0}

    env:
      PYTHON_VERSION: "3.10"
      SINGULARITY_VERSION: "3.11.1"

    strategy:
      matrix:
        include:
          - irods: "4.2.7"
            client_image: "ghcr.io/wtsi-npg/ub-16.04-irods-clients-4.2.7:latest"
            server_image: "ghcr.io/wtsi-npg/ub-16.04-irods-4.2.7:latest"
            experimental: false
          - irods: "4.2.11"
            client_image: "ghcr.io/wtsi-npg/ub-18.04-irods-clients-4.2.11:latest"
            server_image: "ghcr.io/wtsi-npg/ub-18.04-irods-4.2.11:latest"
            experimental: false
          - irods: "4.2.12"
            client_image: "ghcr.io/wtsi-npg/ub-18.04-irods-clients-4.2.12:latest"
            server_image: "ghcr.io/wtsi-npg/ub-18.04-irods-4.2.12:latest"
            experimental: false
          - irods: "4.3.1"
            client_image: "ghcr.io/wtsi-npg/ub-22.04-irods-clients-4.3.1:latest"
            server_image: "ghcr.io/wtsi-npg/ub-22.04-irods-4.3.1:latest"
            experimental: false
          - irods: "4.3.0"
            client_image: "ghcr.io/wtsi-npg/ub-22.04-irods-clients-4.3-nightly:latest"
            server_image: "ghcr.io/wtsi-npg/ub-22.04-irods-4.3-nightly:latest"
            experimental: true

    services:
      mysql:
        image: "mysql:8.0"
        ports:
          - "3306:3306"
        options: >-
          --health-cmd "mysqladmin ping"
          --health-interval 10s
          --health-timeout 5s
          --health-retries 10
        env:
          MYSQL_RANDOM_ROOT_PASSWORD: yes
          MYSQL_TCP_PORT: 3306
          MYSQL_USER: "test"
          MYSQL_PASSWORD: "test"
          MYSQL_DATABASE: "mlwarehouse"
      irods-server:
        image: ${{ matrix.server_image }}
        ports:
          - "1247:1247"
          - "20000-20199:20000-20199"
        options: >-
          --health-cmd "nc -z -v localhost 1247"
          --health-start-period 30s
          --health-interval 10s
          --health-timeout 20s
          --health-retries 6

    steps:
    - name: "Set environmental variables based on other environmental variables"
      run: |
         echo "SINGULARITY_CACHEDIR=$HOME/.singularity-cache" >> $GITHUB_ENV
         # '~' in SINGULARITY_CACHEDIR value (from say a env: section in this YAML) is not expanded by
         # singularity so that paths used are misleading/unclear

    - uses: actions/checkout@v3

    - name: "Install Singularity"
      run: |
        pkg="singularity-ce_${SINGULARITY_VERSION}-$(lsb_release -sc)_amd64.deb"
        curl -sSL -O "https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/$pkg"
        curl -sSL -O "https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/sha256sums"
        grep "$os_release" sha256sums | sha256sum
        sudo apt-get install -q -y "./$pkg"
                
        # Avoid the runner's loop devices being exhausted
        sudo singularity config global --set "max loop devices" 128
        
        # Enable DBus for this user, so that rootless cgroups works and we can create
        # Singularity service instances. See https://github.com/containers/podman/issues/5443
        systemctl --user enable --now dbus.socket
        echo DBUS_SESSION_BUS_ADDRESS="unix:path=/run/user/$(id -u)/bus" >> $GITHUB_ENV

    - name: "Cache Singularity images"
      uses: actions/cache@v3
      with:
        path: ${{ env.SINGULARITY_CACHEDIR }}
        key: ${{ runner.os }}-singularity

    - name: "Install iRODS client wrappers"
      env:
        DOCKER_IMAGE: ${{ matrix.client_image }}
      run: |
        # Use -s option for the wrappers to enable re-usable service instances
        # Install is to HOME rather than workspace to avoid clashes with repo e.g. in bin/
        singularity exec docker://$DOCKER_IMAGE singularity-wrapper -s -p $HOME/.local install
        echo "$HOME/.local/bin" >> $GITHUB_PATH

    - name: "Configure iRODS clients"
      env:
        DOCKER_IMAGE: ${{ matrix.client_image }}
        PREFIX: ${{ github.workspace }}
      run: |
        mkdir -p "$HOME/.irods"
        cat <<'EOF' > "$HOME/.irods/irods_environment.json"
        {
            "irods_host": "localhost",
            "irods_port": 1247,
            "irods_user_name": "irods",
            "irods_zone_name": "testZone",
            "irods_home": "/testZone/home/irods",
            "irods_default_resource": "replResc",
            "irods_default_hash_scheme": "MD5"
        }
        EOF

        echo "irods" | script -q -c "iinit" /dev/null
        ienv
        ils
        ilsresc
        
        baton-do --version

    - uses: actions/setup-python@v4
      with:
        python-version: ${{ env.PYTHON_VERSION }}
        cache: "pip"

    - name: "Setup Python dependencies"
      run: |
        pip install -r requirements.txt
        pip install -r test-requirements.txt

    - name: "Check code formatting [Black]"
      run: |
        black --check --diff ./src ./tests ./scripts

    - name: "Run tests"
      run: |
        pip install .
        pytest --it

    - name: "Log on failure"
      if: ${{ failure() }}
      run: journalctl --no-pager