Release 0.18.0 #704
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
| #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 - ${{ matrix.case }} | |
| runs-on: ubuntu-latest | |
| needs: [ pre_job ] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| case: | |
| - mpx_v1 | |
| - mpx_v2 | |
| if: needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).python.should_skip | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python environment | |
| uses: ./.github/actions/setup-python | |
| with: | |
| python-version: "3.11" | |
| - uses: supplypike/setup-bin@v3 | |
| with: | |
| uri: 'https://opengene.org/fastp/fastp' | |
| name: 'fastp' | |
| version: '0.23.2' | |
| - name: Install dependencies | |
| run: | | |
| pip install poetry | |
| poetry export --output requirements.txt --without-hashes --no-interaction --no-ansi --with dev | |
| pip install -r requirements.txt | |
| - name: Run workflow tests | |
| run: | | |
| pytest -s -m "workflow_test" --basetemp=/tmp/pytest-results tests/integration/test_small_${{ matrix.case }}.yaml --log-cli-level=DEBUG |