Installation#

To begin using scdiffeq, we recommend installing from PyPI for the stable release, or from GitHub for the latest developer version.

Install via pip (recommended for stable release)#

pip install scdiffeq

GitHub (Developer version)#

To access the latest version of scdiffeq from GitHub, clone the repository and install the editable version. Installation generally only takes a few seconds.

Using uv (recommended)#

git clone https://github.com/scDiffEq/scDiffEq.git; cd ./scDiffEq;

# Install uv if you haven't already: curl -LsSf https://astral.sh/uv/install.sh | sh
uv sync

Using pip#

git clone https://github.com/scDiffEq/scDiffEq.git; cd ./scDiffEq;
pip install -e .

With documentation dependencies#

If you want to build the documentation locally:

# Using uv
uv sync --extra docs

# Using pip
pip install -e ".[docs]"

Optional dependency groups#

Extra	Contents
`optional`	Integrations imported lazily by the features that use them: `umap-learn` (UMAP during preprocessing), `pillow` (simulation GIFs), `ipython` (notebook progress bars), and `psutil` / `wandb` (the `MemoryMonitor` callback). Install these if you use those features.
`docs`	Sphinx and theme packages needed to build this documentation.
`test`	`pytest`, for running the test suite.
`dev`	Jupyter, `ipykernel`, and `pytest` for interactive development.

# run the test suite
uv sync --extra test
uv run pytest

Network-dependent tests are marked slow and excluded by default; run them with pytest -m slow. Note that they download multi-gigabyte datasets.

Troubleshooting#

The pykeops library creates a cache. Sometimes, when you switch devices though retain the same disc (common when using a VM, for example), this cache will no longer be compatible with the installed drivers for that device. To clear and rewrite this cached, we can perform the following:

import pykeops

pykeops.clean_pykeops()