python updates and security fixes #201
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| # run test suites | |
| name: Tests | |
| on: | |
| - pull_request | |
| - push | |
| - release | |
| - workflow_dispatch | |
| # cancel the current workflow if another commit was pushed on the same PR or reference | |
| # uses the GitHub workflow name to avoid collision with other workflows running on the same PR/reference | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| # see: https://github.com/fkirc/skip-duplicate-actions | |
| skip_duplicate: | |
| continue-on-error: true | |
| runs-on: ubuntu-latest | |
| outputs: | |
| should_skip: ${{ steps.skip_duplicate.outputs.should_skip && ! contains(github.ref, 'refs/tags') }} | |
| steps: | |
| - id: skip_check | |
| uses: fkirc/skip-duplicate-actions@master | |
| with: | |
| concurrent_skipping: "same_content" | |
| skip_after_successful_duplicate: "true" | |
| do_not_skip: '["pull_request", "workflow_dispatch", "schedule", "release"]' | |
| # see: https://github.com/actions/setup-python | |
| tests: | |
| needs: skip_duplicate | |
| if: ${{ needs.skip_duplicate.outputs.should_skip != 'true' }} | |
| runs-on: ${{ matrix.os }} | |
| continue-on-error: ${{ matrix.allow-failure }} | |
| env: | |
| # override make command to install directly in active python | |
| CONDA_CMD: "" | |
| services: | |
| # Label used to access the service container | |
| mongodb: | |
| image: mongo:3.4.23 # DockerHub | |
| ports: | |
| - "27017:27017" | |
| strategy: | |
| matrix: | |
| os: [ubuntu-latest] | |
| python-version: ["3.9", "3.10", "3.11", "3.12"] | |
| allow-failure: [false] | |
| test-case: [test-local] | |
| include: | |
| # linter tests | |
| - os: ubuntu-latest | |
| python-version: 3.11 | |
| allow-failure: false | |
| test-case: lint | |
| # coverage test | |
| - os: ubuntu-latest | |
| python-version: 3.11 | |
| allow-failure: false | |
| test-case: coverage | |
| # smoke test of Docker image | |
| - os: ubuntu-latest | |
| python-version: None # doesn't matter which one (in docker), but match default of repo | |
| allow-failure: false | |
| test-case: docker-test | |
| # deprecated versions | |
| - os: ubuntu-latest | |
| python-version: 3.8 # EOL 2024-10 | |
| allow-failure: false | |
| test-case: test-local | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: "0" | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| if: ${{ matrix.python-version != 'None' }} | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install Dependencies | |
| if: ${{ matrix.python-version != 'None' }} | |
| # install package and dependencies directly, | |
| # skip sys/conda setup to use active python | |
| run: make install develop | |
| - name: Display Packages | |
| if: ${{ matrix.python-version != 'None' }} | |
| run: pip freeze | |
| - name: Display Environment Variables | |
| run: | | |
| hash -r | |
| env | sort | |
| - name: Run Tests | |
| run: make --no-keep-going ${{ matrix.test-case }} | |
| - name: Stop Workers | |
| if: ${{ matrix.python-version == 'None' }} | |
| run: make docker-stop | |
| - name: Upload coverage report | |
| uses: codecov/codecov-action@v4.0.1 | |
| if: ${{ success() && matrix.test-case == 'coverage' }} | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| files: ./coverage/coverage.xml | |
| fail_ci_if_error: true | |
| verbose: true | |
| deploy_pypi: | |
| needs: tests | |
| # Don't match master branch for upload to avoid duplicate error, even if the tag is usually applied on master. | |
| if: ${{ success() && github.event_name == 'push' && contains(github.ref, 'refs/tags') }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| with: | |
| fetch-depth: "0" | |
| - name: Setup Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Build Distribution Package | |
| run: make develop dist | |
| - name: Push Package to PyPi | |
| uses: pypa/gh-action-pypi-publish@release/v1 | |
| with: | |
| user: __token__ | |
| password: ${{ secrets.PYPI_API_TOKEN }} | |
| verbose: true # For debugging 'twine upload' if a problem occurs. |