[pre-commit.ci] pre-commit autoupdate #721
Workflow file for this run
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| name: CI - Tests | |
| on: | |
| pull_request: | |
| push: | |
| branches: | |
| - 'main' | |
| - 'push-action/**' # Allow pushing to protected branches (using CasperWA/push-protected) | |
| jobs: | |
| basic-tests: | |
| name: External | |
| uses: SINTEF/ci-cd/.github/workflows/ci_tests.yml@v2.8.3 | |
| with: | |
| # General setup | |
| install_extras: "[dev]" | |
| # pre-commit | |
| run_pre-commit: false | |
| # pylint & safety | |
| python_version_pylint_safety: "3.10" | |
| run_pylint: false | |
| run_safety: true | |
| # ID: 70612 | |
| # Package: Jinja2 | |
| # Has been disputed by the maintainer and multiple third parties. | |
| # For more information see: https://github.com/advisories/GHSA-f6pv-j8mr-w6rr | |
| safety_options: | | |
| --ignore=70612 | |
| # Build dist | |
| python_version_package: "3.10" | |
| build_libs: flit | |
| build_cmd: flit build | |
| # Build documentation | |
| run_build_docs: false | |
| docker: | |
| name: Docker | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| docker_target: ["development", "production"] | |
| env: | |
| # "Regular" entities service configuration values | |
| ENTITIES_SERVICE_MONGO_URI: mongodb://localhost:27017 | |
| ENTITIES_SERVICE_X509_CERTIFICATE_FILE: docker_security/test-client.pem | |
| ENTITIES_SERVICE_CA_FILE: docker_security/test-ca.pem | |
| # These are used in the Dockerfile as well as in pytest | |
| ENTITIES_SERVICE_HOST: localhost | |
| ENTITIES_SERVICE_PORT: 7000 | |
| steps: | |
| - name: Checkout ${{ github.repository }} | |
| uses: actions/checkout@v4 | |
| - name: Setup Python 3.10 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Run MongoDB | |
| run: | | |
| # Create folder for certificates | |
| mkdir -p docker_security | |
| # Generate certificates | |
| cd docker_security && ${{ github.workspace }}/.github/docker_init/setup_mongo_security.sh | |
| cd ${{ github.workspace }} | |
| # Pull mongo:8 image and run it | |
| docker pull mongo:8 | |
| docker run --rm -d \ | |
| --name "mongo" \ | |
| --network "host" \ | |
| --volume "${{ github.workspace }}/.github/docker_init/create_x509_user.js:/docker-entrypoint-initdb.d/0_create_x509_user.js" \ | |
| --volume "${{ github.workspace }}/docker_security:/mongo_tls" \ | |
| mongo:8 \ | |
| --tlsMode allowTLS --tlsCertificateKeyFile /mongo_tls/test-server1.pem --tlsCAFile /mongo_tls/test-ca.pem | |
| # Health check | |
| tmp_file=.dockerPs | |
| while ! docker exec mongo mongosh --eval "db.runCommand('ping').ok" mongodb://root:root@localhost:27017/?authSource=admin --quiet ; do | |
| docker ps -a > $tmp_file | |
| grep -E "^.*mongo .* Exited .*$" $tmp_file && exited=yes && break | |
| sleep 3 | |
| done | |
| rm -f $tmp_file | |
| # Write logs | |
| docker logs mongo | |
| if [ -n "$exited" ]; then | |
| exit 1 | |
| fi | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Build Docker image | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| target: ${{ matrix.docker_target }} | |
| load: true | |
| tags: entities-service | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| provenance: false | |
| build-args: | | |
| CI=1 | |
| - name: Install test dependencies | |
| run: | | |
| python -m pip install -U pip | |
| pip install -U setuptools wheel | |
| pip install -U -e .[testing] | |
| - name: Run Docker container | |
| run: | | |
| # Create logging directory and file | |
| mkdir -p logs | |
| touch -a logs/entities_service.log | |
| # Run the service in the background | |
| docker run -d \ | |
| --env ENTITIES_SERVICE_MONGO_URI \ | |
| --env ENTITIES_SERVICE_X509_CERTIFICATE_FILE \ | |
| --env ENTITIES_SERVICE_CA_FILE \ | |
| --name "entities-service" \ | |
| --network "host" \ | |
| --volume "${PWD}:/app" \ | |
| --user "$(id -u):$(id -g)" \ | |
| --init \ | |
| --entrypoint "gunicorn" \ | |
| entities-service \ | |
| --bind="0.0.0.0:${ENTITIES_SERVICE_PORT}" --workers=1 --worker-class="uvicorn.workers.UvicornWorker" --log-level="debug" --pythonpath=".github/utils" run_with_coverage:APP | |
| # Install requirements for health check | |
| sudo apt-get update && sudo apt-get install -y --no-install-recommends -fqqy curl | |
| # Health check | |
| tmp_file=.dockerPs | |
| while ! curl -sf http://localhost:${ENTITIES_SERVICE_PORT}/openapi.json >> /dev/null ; do | |
| docker ps -a > $tmp_file | |
| grep -E "^.*entities-service .* Exited .*$" $tmp_file && exited=yes && break | |
| sleep 1 | |
| done | |
| rm -f $tmp_file | |
| # Write logs | |
| docker logs entities-service | |
| if [ -n "$exited" ]; then | |
| exit 1 | |
| fi | |
| - name: Run tests | |
| run: | | |
| { | |
| pytest -vv --live-backend --cov-report= --color=yes | |
| } || { | |
| echo "Failed! Here's the Docker logs for the service:" && | |
| docker logs entities-service && | |
| echo -e "\nAnd the service log:" && | |
| cat logs/entities_service.log && | |
| exit 1 | |
| } | |
| - name: Collect coverage | |
| run: | | |
| # We can stop the service via a SIGINT signal. | |
| # Since we map the current directory to /app in the container, the coverage file will be | |
| # available in the current working directory. | |
| docker kill --signal=SIGTERM entities-service | |
| # Wait for the coverage file to be written and the service to stop | |
| sleep 10 | |
| # Combine the coverage data from pytest and the service | |
| { | |
| mv .coverage .coverage.pytest && | |
| coverage combine --data-file=.coverage.final --rcfile=pyproject.toml .coverage.pytest .coverage.docker && | |
| coverage xml --data-file=.coverage.final --rcfile=pyproject.toml -o coverage.xml && | |
| coverage report --data-file=.coverage.final --rcfile=pyproject.toml --show-missing --skip-covered --skip-empty | |
| } || { | |
| echo "Failed to collect coverage data." && | |
| echo "Here's the Docker logs for the service:" && | |
| docker logs entities-service && | |
| echo -e "\nAnd the service log:" && | |
| cat logs/entities_service.log && | |
| exit 1 | |
| } | |
| - name: Upload coverage | |
| if: github.repository_owner == 'SINTEF' | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: coverage.xml | |
| fail_ci_if_error: true | |
| env_vars: OS,PYTHON | |
| flags: docker | |
| env: | |
| OS: ubuntu-latest | |
| PYTHON: '3.10' | |
| - name: Clean up Docker | |
| if: always() | |
| run: | | |
| docker stop entities-service ||: | |
| docker rm entities-service ||: | |
| docker stop mongo ||: | |
| docker rm mongo ||: | |
| pytest: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python_version: ["3.10", "3.11", "3.12"] | |
| steps: | |
| - name: Checkout ${{ github.repository }} | |
| uses: actions/checkout@v4 | |
| - name: Setup Python ${{ matrix.python_version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python_version }} | |
| - name: Install test dependencies | |
| run: | | |
| python -m pip install -U pip | |
| pip install -U setuptools wheel flit | |
| pip install -U -e .[testing] | |
| - name: Run pytest | |
| run: pytest -vv --cov-report=xml --color=yes | |
| - name: Upload coverage | |
| if: github.repository_owner == 'SINTEF' | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| fail_ci_if_error: true | |
| env_vars: OS,PYTHON | |
| flags: local | |
| env: | |
| OS: ubuntu-latest | |
| PYTHON: ${{ matrix.python_version }} | |
| pre-commit-hooks: | |
| name: Run custom pre-commit hooks | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.10", "3.11", "3.12"] | |
| os: ["ubuntu-latest", "windows-latest"] | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Python dependencies | |
| run: | | |
| python -m pip install -U pip | |
| pip install -U setuptools wheel | |
| pip install pre-commit | |
| - name: Update pre-commit config file with Python version | |
| run: sed -i "s/SET_PYTHON_VERSION/python${{ matrix.python-version }}/g" .github/utils/.pre-commit-config_testing.yaml | |
| # Note, shell defaults to bash in ubuntu and pwsh in windows | |
| - name: Run validate-entities | |
| run: python .github/utils/run_pre-commit_hooks.py default | |
| - name: Run invalid-entities | |
| run: python .github/utils/run_pre-commit_hooks.py invalid-entities | |
| - name: Run mixed-validity | |
| run: python .github/utils/run_pre-commit_hooks.py mixed-validity | |
| - name: Run quiet | |
| run: python .github/utils/run_pre-commit_hooks.py quiet | |
| - name: Run quiet-mixed-validity | |
| run: python .github/utils/run_pre-commit_hooks.py quiet-mixed-validity | |
| - name: Run fail-fast | |
| run: python .github/utils/run_pre-commit_hooks.py fail-fast | |
| - name: Run validate-entities (cmd) | |
| if: runner.os == 'Windows' | |
| run: python .github/utils/run_pre-commit_hooks.py default | |
| shell: cmd | |
| - name: Run invalid-entities (cmd) | |
| if: runner.os == 'Windows' | |
| run: python .github/utils/run_pre-commit_hooks.py invalid-entities | |
| shell: cmd | |
| - name: Run mixed-validity (cmd) | |
| if: runner.os == 'Windows' | |
| run: python .github/utils/run_pre-commit_hooks.py mixed-validity | |
| shell: cmd | |
| - name: Run quiet (cmd) | |
| if: runner.os == 'Windows' | |
| run: python .github/utils/run_pre-commit_hooks.py quiet | |
| shell: cmd | |
| - name: Run quiet-mixed-validity (cmd) | |
| if: runner.os == 'Windows' | |
| run: python .github/utils/run_pre-commit_hooks.py quiet-mixed-validity | |
| shell: cmd | |
| - name: Run fail-fast (cmd) | |
| if: runner.os == 'Windows' | |
| run: python .github/utils/run_pre-commit_hooks.py fail-fast | |
| shell: cmd | |
| build-cli-docs: | |
| name: Build CLI docs | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout ${{ github.repository }} | |
| uses: actions/checkout@v4 | |
| - name: Setup Python 3.10 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.10" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install -U pip | |
| pip install -U setuptools wheel | |
| pip install -U -e .[cli] | |
| - name: Typer version | |
| run: typer --version | |
| - name: Build CLI docs | |
| run: | | |
| # Build the CLI documentation | |
| # Run it twice, since the first run may create a doc only for the `config` sub-typer app. | |
| typer entities_service.cli.main utils docs --output /tmp/CLI.md > /dev/null | |
| typer entities_service.cli.main utils docs --output /tmp/CLI.md > /dev/null | |
| diff --suppress-common-lines /tmp/CLI.md docs/CLI.md 2>&1 > /tmp/CLI_diff.md && ERROR_CODE=0 || ERROR_CODE=$? | |
| ERROR_CODE=$? | |
| if [ ${ERROR_CODE} -eq 2 ]; then | |
| echo "diff encountered an error." | |
| exit 2 | |
| elif [ ${ERROR_CODE} -eq 1 ]; then | |
| echo "CLI documentation has changed. Please update the documentation." | |
| echo "Diff:" | |
| cat /tmp/CLI_diff.md | |
| exit 1 | |
| elif [ ${ERROR_CODE} -eq 0 ]; then | |
| echo "CLI documentation is up-to-date." | |
| else | |
| echo "Unknown error." | |
| exit 3 | |
| fi |