Add HTSFile.flush() for flushing output streams #341
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| name: CI | |
| on: [push, pull_request] | |
| jobs: | |
| direct: | |
| runs-on: ${{ matrix.os }}-latest | |
| strategy: | |
| matrix: | |
| os: [ubuntu, macos] | |
| python-version: ['3.7', '3.8', '3.9', '3.10', '3.11', '3.12'] | |
| exclude: | |
| # Run only the latest few 3.x versions on macOS | |
| - os: macos | |
| python-version: 3.7 | |
| - os: macos | |
| python-version: 3.8 | |
| - os: macos | |
| python-version: 3.9 | |
| steps: | |
| - name: Checkout pysam | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install prerequisite Python libraries | |
| run: pip install cython pytest pytest-pep8 setuptools | |
| - name: Install Linux build prerequisites | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -q --no-install-recommends --no-install-suggests libcurl4-openssl-dev | |
| - name: Update macOS build prerequisites | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew unlink xz || true # Remove brewed liblzma as it is not multiarch | |
| - name: Build (directly from checkout) | |
| run: python setup.py build | |
| - name: Install test prerequisites | |
| run: | | |
| case $RUNNER_OS in | |
| Linux) | |
| sudo apt-get install -q --no-install-recommends --no-install-suggests samtools bcftools tabix | |
| ;; | |
| macOS) | |
| brew install -q samtools bcftools | |
| ;; | |
| esac | |
| - name: Run tests | |
| run: | | |
| export PYTHONPATH=$(echo $GITHUB_WORKSPACE/build/lib.*) | |
| export REF_PATH=':' | |
| pytest | |
| sdist: | |
| runs-on: ${{ matrix.os }}-latest | |
| strategy: | |
| matrix: | |
| os: [ubuntu, macos] | |
| python-version: ['3.10'] | |
| steps: | |
| - name: Checkout pysam | |
| uses: actions/checkout@v4 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install prerequisite Python libraries | |
| run: pip install cython pytest pytest-pep8 | |
| - name: Install build prerequisites | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -q --no-install-recommends --no-install-suggests libcurl4-openssl-dev | |
| - name: Create source distribution | |
| run: python setup.py sdist --owner=root --group=root | |
| - name: Build (via sdist tarball) | |
| run: pip install --verbose --no-deps --no-binary=':all:' pysam-*.tar.gz | |
| working-directory: dist | |
| - name: Install test prerequisites | |
| run: | | |
| case $RUNNER_OS in | |
| Linux) | |
| sudo apt-get install -q --no-install-recommends --no-install-suggests samtools bcftools tabix | |
| ;; | |
| macOS) | |
| brew install -q samtools bcftools | |
| ;; | |
| esac | |
| - name: Run tests | |
| run: REF_PATH=':' pytest | |
| - name: Upload sdist tarball | |
| if: runner.os == 'Linux' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: sdist | |
| path: dist/pysam-*.tar.gz | |
| retention-days: 14 | |
| conda: | |
| timeout-minutes: 20 | |
| runs-on: ${{ matrix.os }}-latest | |
| strategy: | |
| matrix: | |
| os: [ubuntu] | |
| python-version: ['3.10'] | |
| defaults: | |
| run: | |
| shell: bash -el {0} # needed for conda activation | |
| env: | |
| HTSLIB_CONFIGURE_OPTIONS: "--disable-libcurl" | |
| steps: | |
| - name: Checkout pysam | |
| uses: actions/checkout@v4 | |
| - name: Set up Conda and Python ${{ matrix.python-version }} | |
| uses: conda-incubator/setup-miniconda@v3 | |
| with: | |
| channels: conda-forge,bioconda | |
| channel-priority: strict | |
| python-version: ${{ matrix.python-version }} | |
| environment-file: devtools/environment-dev.yaml | |
| auto-activate-base: false | |
| - name: Build (directly from checkout) | |
| run: python setup.py install | |
| - name: Install test prerequisites via Conda | |
| run: conda install "samtools>=1.11" "bcftools>=1.11" "htslib>=1.11" pytest | |
| - name: Run tests | |
| run: REF_PATH=':' pytest |