Implement WsiAnnotations in C++ #1649
Workflow file for this run
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| name: CodeCov | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Install build dependencies | |
| run: | | |
| sudo apt update | |
| sudo apt install -y meson libgl1-mesa-glx libcairo2-dev libgdk-pixbuf2.0-dev libglib2.0-dev libjpeg-dev libpng-dev libtiff5-dev libxml2-dev libopenjp2-7-dev libsqlite3-dev zlib1g-dev libzstd-dev | |
| sudo apt install -y libfftw3-dev libexpat1-dev libgsf-1-dev liborc-0.4-dev libtiff5-dev ninja-build libboost-all-dev libopencv-dev | |
| - name: Install Rust for pyhaloxml | |
| run: | | |
| curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y | |
| echo "Rust and Cargo installed in:" | |
| echo $HOME/.cargo/bin | |
| ls $HOME/.cargo/bin | |
| export PATH="$HOME/.cargo/bin:$PATH" | |
| - name: Build and install OpenSlide | |
| run: | | |
| export PATH="$HOME/.cargo/bin:$PATH" | |
| git clone https://github.com/openslide/openslide.git | |
| cd openslide | |
| meson setup builddir | |
| meson compile -C builddir | |
| sudo meson install -C builddir | |
| cd .. | |
| - name: Build and install libvips | |
| run: | | |
| export PATH="$HOME/.cargo/bin:$PATH" | |
| git clone https://github.com/libvips/libvips.git | |
| cd libvips | |
| meson setup builddir --prefix=/usr/local | |
| meson compile -C builddir | |
| sudo meson install -C builddir | |
| sudo ldconfig | |
| cd .. | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.11 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install environment | |
| run: | | |
| export PATH="$HOME/.cargo/bin:$PATH" | |
| python -m pip install --upgrade pip | |
| python -m pip install ninja meson meson-python>=0.15.0 numpy==1.26.4 Cython>=0.29 spin pybind11 | |
| python -m pip install tifffile>=2024.7.2 pyvips>=2.2.3 tqdm>=2.66.4 pillow>=10.3.0 openslide-python>=1.3.1 spin | |
| python -m pip install opencv-python-headless>=4.9.0.80 shapely>=2.0.4 pybind11>=2.8.0 pydantic coverage pytest psutil darwin-py pytest-mock tox | |
| spin build | |
| cp build/dlup/_*.so dlup/ | |
| cp build/src/_*.so dlup/ | |
| python -m pip install . | |
| - name: Run coverage | |
| run: | | |
| coverage run -m pytest || true | |
| - name: Upload Coverage to Codecov | |
| uses: codecov/codecov-action@v4 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} |