Installation

1. Install aweSOM and required dependencies:

   git clone https://github.com/tvh0021/aweSOM.git
   cd aweSOM
   pip install .
   

2. Install JAX with CUDA support separately, otherwise JAX will not recognize the GPU:

   pip install --upgrade "jax[cuda12_pip]" -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
   

If your system does not support CUDA, you can skip this step. SCE will automatically fall back to the CPU. However, the CPU-only version can be significantly slower for large datasets (see the performance tests).

Experimental

Apple Silicon users can also use JAX with Metal support; follow the instructions in the JAX documentation to install the Metal backend.

3. Install Sphinx and other required packages for building the documentation (optional):

   pip install -r docs/requirements.txt
   

4. Build the documentation (optional):

   cd docs
   make html
   open build/html/index.html