Use a vent #150
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
| name: CI | |
| # Controls when the action will run. | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| max-parallel: 10 | |
| matrix: | |
| python-version: ['3.12', '3.11', '3.10', '3.9'] | |
| os: [ubuntu-latest, macos-latest] | |
| exclude: | |
| # mac os: exclude all but the last two (available) python releases | |
| - os: macos-latest | |
| python-version: 3.10 | |
| - os: macos-latest | |
| python-version: 3.9 | |
| steps: | |
| - name: checkout | |
| uses: actions/[email protected] | |
| with: | |
| persist-credentials: false | |
| fetch-depth: 0 | |
| - name: install macOS dependencies | |
| if: ${{ matrix.os == 'macos-latest' }} | |
| run: brew install -q samtools bcftools xz | |
| - name: setup python | |
| uses: actions/[email protected] | |
| with: | |
| python-version: ${{ matrix.python }} | |
| - name: set up virtual env | |
| run: python3 -m venv venv | |
| - name: upgrade pip | |
| run: python3 -m pip install --upgrade pip | |
| - name: pip install development dependencies | |
| run: | | |
| python3 -m pip install cython | |
| python3 -m pip install -r dev-requirements.txt | |
| - name: install pysam under Linux | |
| if: ${{ matrix.os == 'ubuntu-latest' }} | |
| run: python3 -m pip install pysam | |
| - name: install pyfaidx from current branch | |
| run: python3 -m pip install . | |
| - name: Cache test data | |
| uses: actions/[email protected] | |
| with: | |
| path: tests/data | |
| key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('tests/data/*') }} | |
| - name: download test data | |
| run: python3 tests/data/download_gene_fasta.py | |
| - name: run pyfaidx tests | |
| run: pytest --cov=pyfaidx --cov-report=xml tests | |
| - name: run acidbio tests | |
| run: | | |
| git clone https://github.com/mdshw5/acidbio.git | |
| cd acidbio/bed | |
| python3 -m pip install -r requirements.txt | |
| cp config_template.yaml config.yaml | |
| python3 bedrunall.py --tool pyfaidx BED03 ./ | |
| - name: Upload coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| continue-on-error: true | |
| with: | |
| fail_ci_if_error: true | |
| files: ./coverage.xml | |
| verbose: true |