Bump setuptools from 75.3.0 to 75.5.0 #1005
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 |