Fix ONT permissions updates to retain unmanaged access controls #524
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: | |
| WSI_CONDA_CHANNEL: "https://dnap.cog.sanger.ac.uk/npg/conda/devel/generic" | |
| CONDA_TEST_ENVIRONMENT: "testenv" | |
| PYTHON_VERSION: "3.10" | |
| strategy: | |
| matrix: | |
| include: | |
| # iRODS 4.2.11 clients vs 4.2.7 server | |
| - irods: "4.2.11" | |
| server_image: "ghcr.io/wtsi-npg/ub-16.04-irods-4.2.7:latest" | |
| baton: "4.0.0" | |
| experimental: false | |
| # iRODS 4.2.11 clients vs 4.2.11 server | |
| - irods: "4.2.11" | |
| server_image: "ghcr.io/wtsi-npg/ub-18.04-irods-4.2.11:latest" | |
| baton: "4.0.0" | |
| experimental: false | |
| 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: | |
| image: ${{ matrix.server_image }} | |
| ports: | |
| - 1247:1247 | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: "Initialize Miniconda" | |
| run: | | |
| echo 'source $CONDA/etc/profile.d/conda.sh' >> "$HOME/.bash_profile" | |
| - name: "Cache Miniconda" | |
| id: cache-miniconda | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| ~/conda/pkgs | |
| ~/conda/envs | |
| key: ${{ runner.os }}-miniconda | |
| - name: "Configure Miniconda" | |
| run: | | |
| conda config --prepend pkgs_dirs "$HOME/conda/pkgs" | |
| conda config --prepend envs_dirs "$HOME/conda/envs" | |
| conda config --set auto_update_conda False | |
| conda config --prepend channels "$WSI_CONDA_CHANNEL" | |
| conda info | |
| - name: "Install iRODS clients" | |
| run: | | |
| conda create -y -n "$CONDA_TEST_ENVIRONMENT" | |
| conda install -y -n "$CONDA_TEST_ENVIRONMENT" "irods-icommands=${{ matrix.irods }}" | |
| conda install -y -n "$CONDA_TEST_ENVIRONMENT" "baton=${{ matrix.baton }}" | |
| - name: "Configure iRODS clients" | |
| run: | | |
| conda activate "$CONDA_TEST_ENVIRONMENT" | |
| 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 | |
| ilsresc | |
| ils | |
| baton-do --version | |
| - name: "Setup Python" | |
| run: | | |
| conda activate "$CONDA_TEST_ENVIRONMENT" | |
| conda install -c defaults python="$PYTHON_VERSION" | |
| - name: "Setup Python dependencies" | |
| run: | | |
| conda activate "$CONDA_TEST_ENVIRONMENT" | |
| pip install -r requirements.txt | |
| pip install -r test-requirements.txt | |
| - name: "Check code formatting [Black]" | |
| run: | | |
| conda activate "$CONDA_TEST_ENVIRONMENT" | |
| black --check --diff --quiet . | |
| - name: "Run tests" | |
| run: | | |
| conda activate "$CONDA_TEST_ENVIRONMENT" | |
| pip install . | |
| pytest --it |