Added new sample metadata. #1438
Workflow file for this run
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| 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: "3.12" | |
| 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: "4.3.2" | |
| client_image: "ghcr.io/wtsi-npg/ub-22.04-irods-clients-4.3.2:latest" | |
| server_image: "ghcr.io/wtsi-npg/ub-22.04-irods-4.3.2:latest" | |
| experimental: true | |
| - irods: "4.3.3" | |
| client_image: "ghcr.io/wtsi-npg/ub-22.04-irods-clients-4.3.3:latest" | |
| server_image: "ghcr.io/wtsi-npg/ub-22.04-irods-4.3.3: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: ${{ matrix.server_image }} | |
| ports: | |
| - "1247:1247" | |
| - "20000-20199:20000-20199" | |
| volumes: | |
| - /dev/shm:/dev/shm | |
| options: >- | |
| --health-cmd "nc -z -v localhost 1247" | |
| --health-start-period 60s | |
| --health-interval 10s | |
| --health-timeout 20s | |
| --health-retries 6 | |
| steps: | |
| - name: "Set environmental variables based on other environmental variables" | |
| run: | | |
| echo "SINGULARITY_CACHEDIR=$HOME/.singularity-cache" >> $GITHUB_ENV | |
| # '~' in SINGULARITY_CACHEDIR value (from say a env: section in this YAML) is not expanded by | |
| # singularity so that paths used are misleading/unclear | |
| - uses: actions/checkout@v4 | |
| - name: "Install Singularity" | |
| run: | | |
| pkg="singularity-ce_${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@v4 | |
| 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@v5 | |
| 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 |