Fixup pxd definitions for tbx_t struct #207
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: Build | |
| on: [push, pull_request] | |
| jobs: | |
| docker-build: | |
| name: Docker Run Test on ${{ matrix.platform }}-${{ matrix.python_tag_type }} | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| platform: | |
| - linux/amd64 | |
| - linux/arm64 | |
| python_tag_type: | |
| - slim | |
| - alpine | |
| exclude: | |
| # amd64 with glibc have full direct test | |
| - platform: linux/amd64 | |
| python_tag_type: slim | |
| # test alpine only on amd64 | |
| - platform: linux/arm64 | |
| python_tag_type: alpine | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Set up QEMU | |
| uses: docker/setup-qemu-action@v3 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Docker Build | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| file: ./ci/Dockerfile.${{ matrix.python_tag_type }}.test | |
| platforms: ${{ matrix.platform }} | |
| tags: cyvcf2:${{ matrix.python_tag_type }}-test | |
| push: false | |
| load: true | |
| build-args: | | |
| PYTHON_VERSION=${{ matrix.python_tag_type }} | |
| - name: Docker Run Tests | |
| run: | | |
| docker run --rm --platform ${{ matrix.platform }} cyvcf2:${{ matrix.python_tag_type }}-test pytest --cov cyvcf2 --cov-report term-missing | |
| build: | |
| name: Run tests on Python ${{ matrix.python-version }} ${{ matrix.os }} | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-22.04, macos-12] | |
| python-version: | |
| ["pypy3.10", "3.7", "3.8", "3.9", "3.10", "3.11", "3.12"] | |
| exclude: | |
| # Run only the latest versions on macOS and windows | |
| - os: macos-12 | |
| python-version: "pypy3.10" | |
| - os: macos-12 | |
| python-version: "3.7" | |
| - os: macos-12 | |
| python-version: "3.8" | |
| - os: macos-12 | |
| python-version: "3.9" | |
| - os: macos-12 | |
| python-version: "3.10" | |
| - os: macos-12 | |
| python-version: "3.11" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Set macOS env | |
| if: runner.os == 'macOS' | |
| run: | | |
| # building options | |
| echo "MACOSX_DEPLOYMENT_TARGET=10.9" >> "$GITHUB_ENV" | |
| echo "ARCHFLAGS=-arch x86_64" >> "$GITHUB_ENV" | |
| - name: Install Linux build prerequisites | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y --no-install-recommends libcurl4-openssl-dev zlib1g-dev libssl-dev liblzma-dev \ | |
| libbz2-dev libdeflate-dev | |
| - name: Install macOS build prerequisites | |
| if: runner.os == 'macOS' | |
| run: | | |
| brew install automake libdeflate | |
| - name: Install | |
| run: | | |
| pip install -r requirements.txt | |
| pip install pytest pytest-cov | |
| CYVCF2_HTSLIB_CONFIGURE_OPTIONS="--enable-libcurl --enable-s3 --enable-lzma --enable-bz2 --with-libdeflate" \ | |
| CYTHONIZE=1 python setup.py build_ext -i | |
| - name: Test | |
| run: | | |
| pytest --cov cyvcf2 --cov-report term-missing | |
| windows_build: | |
| name: Run tests on Python windows-2022 MSYS2 UCRT64 | |
| runs-on: windows-2022 | |
| defaults: | |
| run: | |
| shell: msys2 {0} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: "Setup MSYS2" | |
| uses: msys2/setup-msys2@v2 | |
| with: | |
| msystem: UCRT64 | |
| path-type: inherit | |
| install: >- | |
| mingw-w64-ucrt-x86_64-gcc | |
| mingw-w64-ucrt-x86_64-make | |
| mingw-w64-ucrt-x86_64-libdeflate | |
| mingw-w64-ucrt-x86_64-xz | |
| mingw-w64-ucrt-x86_64-curl | |
| mingw-w64-ucrt-x86_64-zlib | |
| mingw-w64-ucrt-x86_64-bzip2 | |
| mingw-w64-ucrt-x86_64-tools-git | |
| mingw-w64-ucrt-x86_64-python-pkgconfig | |
| mingw-w64-ucrt-x86_64-pkg-config | |
| mingw-w64-ucrt-x86_64-ninja | |
| mingw-w64-ucrt-x86_64-python | |
| mingw-w64-ucrt-x86_64-python-pip | |
| make | |
| automake | |
| autoconf | |
| git | |
| - name: Install Windows build prerequisites | |
| run: | | |
| cd htslib | |
| autoreconf -i | |
| ./configure --enable-libcurl --enable-s3 --enable-lzma --enable-bz2 --with-libdeflate | |
| make | |
| make install | |
| - name: Install | |
| run: | | |
| pip install -r requirements.txt | |
| pip install pytest pytest-cov | |
| CYTHONIZE=1 python setup.py build_ext -i | |
| - name: Test | |
| run: | | |
| pytest --cov cyvcf2 --cov-report term-missing | |
| sdist: | |
| runs-on: ubuntu-22.04 | |
| strategy: | |
| matrix: | |
| python-version: ["3.12"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| submodules: recursive | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install sdist prerequisites | |
| run: | | |
| pip install -r requirements.txt | |
| - name: Create source distribution | |
| run: CYTHONIZE=1 python setup.py sdist | |
| - name: Install Linux build prerequisites | |
| if: runner.os == 'Linux' | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y --no-install-recommends libcurl4-openssl-dev zlib1g-dev libssl-dev liblzma-dev \ | |
| libbz2-dev libdeflate-dev | |
| - name: Build (via sdist tarball) | |
| run: pip install --verbose --no-deps --no-binary='cyvcf2' cyvcf2-*.tar.gz | |
| working-directory: dist | |
| - name: Install test prerequisites | |
| run: | | |
| pip install pytest pytest-cov | |
| - name: Test | |
| run: | | |
| pytest --import-mode importlib --cov cyvcf2 --cov-report term-missing | |
| - name: Upload sdist tarball | |
| if: runner.os == 'Linux' | |
| uses: actions/upload-artifact@v3 | |
| with: | |
| name: sdist | |
| path: dist/cyvcf2-*.tar.gz | |
| retention-days: 7 |