MinGW version of pysam #311
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
| name: CI | ||
| on: [push, pull_request] | ||
| jobs: | ||
| direct: | ||
| runs-on: ${{ matrix.os }}-latest | ||
| strategy: | ||
| matrix: | ||
| os: [ubuntu, macos, windows] | ||
| 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 | ||
| # MSYS2 installs Python with pacman | ||
| python-version: 3.7 | ||
| - os: windows | ||
| python-version: 3.8 | ||
| - os: windows | ||
| python-version: 3.9 | ||
| - os: windows | ||
| python-version: 3.10 | ||
| - os: windows | ||
| python-version: 3.11 | ||
| - os: windows | ||
| python-version: 3.12 | ||
| os: [windows] | ||
| - {msystem: UCRT64, arch: x86_64} | ||
| steps: | ||
| - name: Checkout pysam | ||
| uses: actions/checkout@v4 | ||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v4 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| exclude: | ||
| - os: windows | ||
| - name: Install prerequisite Python libraries | ||
| run: pip install cython pytest pytest-pep8 setuptools | ||
| exclude: | ||
| - os: windows | ||
| - name: Install Linux build prerequisites | ||
| if: runner.os == 'Linux' | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install -q --no-install-recommends --no-install-suggests libcurl4-openssl-dev | ||
| - name: Update macOS build prerequisites | ||
| if: runner.os == 'macOS' | ||
| run: | | ||
| brew unlink xz || true # Remove brewed liblzma as it is not multiarch | ||
| - name: Install MSYS2 build prerequisites | ||
| if: runner.os == 'Windows' | ||
| uses: msys2/setup-msys2@v2 | ||
| with: | ||
| msystem: ucrt64 | ||
| update: true | ||
| install: >- | ||
| mingw-w64-${{ matrix.config.arch }}-base-devel | ||
| mingw-w64-${{ matrix.config.arch }}-cython | ||
| mingw-w64-${{ matrix.config.arch }}-python | ||
| mingw-w64-${{ matrix.config.arch }}-pip | ||
| mingw-w64-${{ matrix.config.arch }}-setuptools | ||
| mingw-w64-${{ matrix.config.arch }}-curl | ||
| mingw-w64-${{ matrix.config.arch }}-libdeflate | ||
| mingw-w64-${{ matrix.config.arch }}-bzip2 | ||
| mingw-w64-${{ matrix.config.arch }}-zlib | ||
| mingw-w64-${{ matrix.config.arch }}-python-pytest | ||
| mingw-w64-${{ matrix.config.arch }}-xz | ||
| mingw-w64-${{ matrix.config.arch }}-openssl | ||
| mingw-w64-${{ matrix.config.arch }}-libtre-git | ||
| mingw-w64-${{ matrix.config.arch }}-libiconv | ||
| - name: Build (directly from checkout) | ||
| run: python setup.py build | ||
| - name: Install test prerequisites | ||
| run: | | ||
| case $RUNNER_OS in | ||
| Linux) | ||
| sudo apt-get install -q --no-install-recommends --no-install-suggests samtools bcftools tabix | ||
| ;; | ||
| macOS) | ||
| brew install -q samtools bcftools | ||
| ;; | ||
| Windows) | ||
| pacman -S --noconfirm mingw-w64-${{ matrix.config.arch }}-samtools mingw-w64-${{ matrix.config.arch }}-bcftools | ||
| ;; | ||
| esac | ||
| - name: Run tests | ||
| run: | | ||
| export PYTHONPATH=$(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@v4 | ||
| 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@v3 | ||
| 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: ['3.7'] | ||
| defaults: | ||
| run: | ||
| shell: bash -l {0} # needed for conda activation | ||
| env: | ||
| HTSLIB_CONFIGURE_OPTIONS: "--disable-libcurl" | ||
| steps: | ||
| - name: Checkout pysam | ||
| uses: actions/checkout@v4 | ||
| - uses: conda-incubator/setup-miniconda@v2 | ||
| with: | ||
| channel-priority: strict | ||
| activate-environment: testenv | ||
| auto-activate-base: false | ||
| use-only-tar-bz2: true | ||
| - name: Set up Conda and Python ${{ matrix.python-version }} | ||
| run: | | ||
| conda config --add channels bioconda --add channels conda-forge | ||
| conda install python=${{ matrix.python-version }} cython | ||
| - 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 | ||
