Installation =========== PySlyde can be installed from PyPI or from source. This guide covers all installation methods and requirements. Requirements ----------- PySlyde requires Python 3.8 or higher and the following dependencies: * `numpy `_ >= 1.20.0 * `opencv-python `_ >= 4.5.0 * `openslide-python `_ >= 1.1.0 * `pandas `_ >= 1.3.0 * `matplotlib `_ >= 3.3.0 * `seaborn `_ >= 0.11.0 * `scikit-image `_ >= 0.18.0 * `scipy `_ >= 1.7.0 * `lmdb `_ >= 1.2.0 * `einops `_ >= 0.4.0 * `h5py `_ >= 3.1.0 * `huggingface_hub `_ >= 0.10.0 * `tensorflow `_ >= 2.8.0 * `torch `_ >= 1.10.0 * `timm `_ >= 0.6.0 * `webdataset `_ >= 0.2.0 Installation from PyPI --------------------- The easiest way to install PySlyde is using pip: .. code-block:: bash pip install pyslyde This will install PySlyde and all its dependencies automatically. Installation from Source ----------------------- To install from source, clone the repository and install in development mode: .. code-block:: bash git clone https://github.com/gregoryverghese/PySlide.git cd PySlide pip install -e . Development Installation ------------------------ For development work, install with development dependencies: .. code-block:: bash git clone https://github.com/gregoryverghese/PySlide.git cd PySlide pip install -e ".[dev]" This includes additional tools for development: * `pytest `_ - Testing framework * `pytest-cov `_ - Coverage reporting * `black `_ - Code formatting * `flake8 `_ - Linting * `mypy `_ - Type checking * `pre-commit `_ - Git hooks System Dependencies ------------------ Some dependencies may require system-level libraries: Ubuntu/Debian: ^^^^^^^^^^^^^ .. code-block:: bash sudo apt-get update sudo apt-get install libopenslide-dev libgl1-mesa-glx libglib2.0-0 macOS: ^^^^^^ .. code-block:: bash brew install openslide Windows: ^^^^^^^^ For Windows, most dependencies are available as pre-compiled wheels. If you encounter issues with OpenSlide, you may need to install it manually from the `OpenSlide website `_. Verifying Installation --------------------- To verify that PySlyde is installed correctly, run: .. code-block:: python import pyslyde print(pyslyde.__version__) You should see the version number printed without any errors. Troubleshooting -------------- Common Installation Issues ^^^^^^^^^^^^^^^^^^^^^^^^^ 1. **OpenSlide not found**: Make sure you have the system-level OpenSlide library installed. 2. **CUDA issues**: If you're using GPU acceleration, ensure you have the correct CUDA version installed for your PyTorch/TensorFlow version. 3. **Memory issues**: PySlyde works with large images, so ensure you have sufficient RAM (8GB+ recommended). 4. **Permission errors**: On some systems, you may need to use `pip install --user` or install with sudo. Getting Help ----------- If you encounter installation issues: 1. Check the `GitHub issues `_ for similar problems 2. Create a new issue with your system details and error messages 3. Contact the maintainer at gregory.verghese@gmail.com