Better error message when there are fewer nodes than the number of dimensions in pmds layout #844
Workflow file for this run
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 | |
| 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: '0.23.4' | |
| - name: Install and configure Poetry | |
| uses: snok/install-poetry@v1 | |
| - name: Install tox | |
| run: python -m pip install tox-gh>=1.2 | |
| - name: Setup test suite | |
| run: tox -vv --notest | |
| - name: Run test suite | |
| run: tox --skip-pkg-install | |
| 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: Install and configure Poetry | |
| uses: snok/install-poetry@v1 | |
| - name: Install dependencies | |
| run: | | |
| poetry install --with dev | |
| - name: Run test suite | |
| run: | | |
| poetry 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 - ${{ matrix.case }} | |
| runs-on: ubuntu-latest | |
| needs: [ pre_job ] | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| case: | |
| - mpx_v1 | |
| - mpx_v2 | |
| if: needs.pre_job.outputs.should_skip == '{}' || !fromJSON(needs.pre_job.outputs.paths_result).python.should_skip | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python environment | |
| uses: ./.github/actions/setup-python | |
| with: | |
| python-version: "3.11" | |
| - uses: supplypike/setup-bin@v3 | |
| with: | |
| uri: 'https://opengene.org/fastp/fastp' | |
| name: 'fastp' | |
| version: '0.23.2' | |
| - name: Install and configure Poetry | |
| uses: snok/install-poetry@v1 | |
| - name: Install dependencies | |
| run: | | |
| poetry install --with dev | |
| - name: Run workflow tests | |
| run: | | |
| poetry run pytest -s -m "workflow_test" --basetemp=/tmp/pytest-results tests/integration/test_small_${{ matrix.case }}.yaml --log-cli-level=DEBUG |