Use dynamic annotation reader and writers #1653
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 }} |