Installation

Basic Install

pip install flashscenic

This installs the core package with dependencies: numpy, torch, regdiffusion, and scipy.

GPU Support

flashscenic requires PyTorch with CUDA support for GPU acceleration. If you don’t already have a CUDA-enabled PyTorch installation:

# Install PyTorch with CUDA (check https://pytorch.org for your CUDA version)
pip install torch --index-url https://download.pytorch.org/whl/cu121
pip install flashscenic

CPU fallback is available by passing device='cpu' to all functions.

Optional Dependencies

For building documentation:

pip install flashscenic[docs]

For running validation tests against pySCENIC/ctxcore:

pip install pyscenic ctxcore scanpy pandas pyarrow

Development Install

git clone https://github.com/haozhu233/flashscenic.git
cd flashscenic
pip install -e .