Merge pull request #222 from eroller/patch-3 #155
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| 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: ${{ matrix.python }} | |
| - name: set up virtual env | |
| run: | | |
| python3 -m venv venv | |
| source venv/bin/activate | |
| echo PATH=$PATH >> $GITHUB_ENV | |
| - 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 | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| with: | |
| fail_ci_if_error: true | |
| files: ./coverage.xml | |
| verbose: true |