codecov.yml

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 }}