Implement WsiAnnotations in C++ (#252) #1650
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: 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 }} |