Merge pull request #140 from PixelgenTechnologies/fix/jaccard-index-s… #585
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| #schema: https://github.com/softprops/github-actions-schemas/blob/master/workflow.json | |
| name: "Test" | |
| on: | |
| push: | |
| branches: [main, dev] | |
| pull_request: | |
| branches: [main, dev] | |
| workflow_dispatch: | |
| permissions: | |
| id-token: write | |
| actions: write | |
| contents: read | |
| packages: write | |
| env: | |
| ANNOY_COMPILER_ARGS: "-DANNOYLIB_MULTITHREADED_BUILD,-mno-avx512f" | |
| jobs: | |
| pre_job: | |
| continue-on-error: true | |
| runs-on: ubuntu-latest | |
| # Map a step output to a job output | |
| outputs: | |
| should_skip: ${{ steps.skip_check.outputs.should_skip }} | |
| paths_result: ${{ steps.skip_check.outputs.paths_result }} | |
| steps: | |
| - id: skip_check | |
| uses: fkirc/skip-duplicate-actions@v5 | |
| if: ${{ !github.event.act }} | |
| with: | |
| concurrent_skipping: "same_content_newer" | |
| skip_after_successful_duplicate: "true" | |
| do_not_skip: '["workflow_dispatch"]' | |
| paths_filter: | | |
| python: | |
| paths: | |
| - 'pyproject.toml' | |
| - 'poetry.lock' | |
| - 'src/pixelator/**' | |
| - 'tests/**' | |
| paths_ignore: | |
| - 'tests/**/*.md' | |
| test: | |
| name: Test - python ${{ matrix.py }} | |
| if: needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).python.should_skip | |
| runs-on: ubuntu-latest | |
| needs: [pre_job] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| py: | |
| - "3.11" | |
| - "3.10" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python environment - ${{ matrix.py }} | |
| uses: ./.github/actions/setup-python | |
| with: | |
| python-version: ${{ matrix.py }} | |
| - uses: supplypike/setup-bin@v3 | |
| with: | |
| uri: 'https://opengene.org/fastp/fastp' | |
| name: 'fastp' | |
| version: '0.23.2' | |
| - name: Generate tox env for python version | |
| uses: actions/github-script@v6 | |
| id: set_tox_env | |
| with: | |
| script: | | |
| const pythonVersion = "${{ matrix.py }}" | |
| const toxEnv = "py" + pythonVersion.replace(/\./g, '') | |
| core.setOutput("tox_env", toxEnv) | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --user pipx | |
| python -m pipx ensurepath | |
| pipx install poetry | |
| pip install tox | |
| poetry self add poetry-plugin-export | |
| poetry export --output dev_requirements.txt --quiet --no-interaction --no-ansi --without-hashes --with dev | |
| pip install -r dev_requirements.txt | |
| pip install -e . | |
| - name: Run test suite on local python version | |
| run: tox -e ${{ steps.set_tox_env.outputs.tox_env }} --current-env | |
| test-coverage: | |
| name: "Check the test coverage" | |
| runs-on: ubuntu-latest | |
| needs: | |
| - pre_job | |
| if: needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).python.should_skip | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| - name: Set up Python environment | |
| uses: ./.github/actions/setup-python | |
| with: | |
| python-version: "3.11" | |
| - name: Create dependencies file | |
| run: | | |
| pip install poetry | |
| poetry export --output requirements.txt --without-hashes --no-interaction --no-ansi --with dev | |
| pip install -r requirements.txt | |
| - name: Run test suite | |
| run: | | |
| pytest --cov=src/ | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v3 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| test-workflow: | |
| name: Test small workflow - ${{ matrix.case }} | |
| runs-on: ubuntu-latest | |
| needs: [ pre_job ] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| case: | |
| - D21 | |
| if: needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).python.should_skip | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python environment | |
| uses: ./.github/actions/setup-python | |
| with: | |
| python-version: "3.11" | |
| - uses: supplypike/setup-bin@v3 | |
| with: | |
| uri: 'https://opengene.org/fastp/fastp' | |
| name: 'fastp' | |
| version: '0.23.2' | |
| - name: Install dependencies | |
| run: | | |
| pip install poetry | |
| poetry export --output requirements.txt --without-hashes --no-interaction --no-ansi --with dev | |
| pip install -r requirements.txt | |
| - name: Run workflow tests | |
| run: | | |
| pytest -s -m "workflow_test" --basetemp=/tmp/pytest-results tests/integration/test_small_${{ matrix.case }}.yaml --log-cli-level=DEBUG |