Allow Reader/Writer to be context managers #240
Workflow file for this run
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| 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 | |
| # make sure to keep this numpy version in sync with setup.py | |
| - name: Test with oldest numpy that we support | |
| if: contains(fromJson('["3.7"]'), matrix.python-version) | |
| run: | | |
| pip install --force-reinstall --no-cache-dir 'numpy==1.16.0' | |
| pytest --cov cyvcf2 --cov-report term-missing | |
| - name: Test with newest available numpy | |
| run: | | |
| pip install -U numpy | |
| 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 | |
| - name: Test with newest available numpy | |
| run: | | |
| pip install -U numpy | |
| 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 | |
| # pytest 8.2.0~8.2.1 changed the behaivour of --import-mode, can't ignore local cyvcf2 folder. | |
| # So we need to pin it before it breaks again. | |
| run: | | |
| pip install pytest==8.1.2 pytest-cov | |
| - name: Test | |
| run: | | |
| pytest --import-mode importlib --cov cyvcf2 --cov-report term-missing | |
| - name: Test with newest available numpy | |
| run: | | |
| pip install -U numpy | |
| pytest --import-mode importlib --cov cyvcf2 --cov-report term-missing | |
| - name: Upload sdist tarball | |
| if: runner.os == 'Linux' | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: sdist | |
| path: dist/cyvcf2-*.tar.gz | |
| retention-days: 7 |