Installation

pip install "spatial-smooth[all]"

Note

[all] pulls every optional backend. For a minimal install, drop the extra (pip install spatial-smooth) and add only the extras you need (see below). To install the development version straight from the repository: pip install "spatial-smooth[all] @ git+https://github.com/settylab/spatial-smooth".

Only numpy, scipy, pandas and anndata are hard requirements. Everything else is an extra, imported lazily, and reported with the exact pip install line when missing.

extra	brings	needed for
dm	kompot	the Gaussian-process step (KompotGP)
embedding	palantir	computing the diffusion map
plot	scanpy, matplotlib	plotting
squidpy	squidpy	the squidpy plotting backend
kde	KDEpy	the fine-grid FFT smoother (Kde)

Check where you stand at any time:

import spatial_smooth as ss
ss.check_dependencies()

spatial_smooth v0.1.0 -- dependency check
  numpy       2.4.6       ok
  pandas      2.3.3       ok
  scipy       1.18.0      ok
  anndata     0.12.17     ok
  kompot      -           missing: pip install "kompot>=0.7.0" (optional)
  ...

Every missing optional dependency raises where it is first needed, naming the package, what it is for, and how to install it – never a bare ModuleNotFoundError from deep in a call stack.

Reading a smoothed object needs none of the extras: a colleague can open your .h5ad and plot it with scanpy alone.