Thank you very much for implementing CellCharter!
As I discussed in the past, @LLehner had to implement a simplified version of CellCharter to avoid adding new dependences.
The most important one is replacing scVI's dimensionality reduction with PCA.

In my experience developing CellCharter I noticed that using PCA can considerably decrease the quality of the niches, especially in spatial transcriptomics datasets, and is not as scalable for large datasets.
For this reason I would like to propose to change the name of the flavor parameter in the calculate_niche function from "cellcharter" to "cellcharter_simple".

This is to discourage people from using the squidpy's implementation for benchmarking CellCharter against other methods.

In addition, assuming that people using squidpy's implementation will have less familiarity with CellCharter, I would propose using a more good-enough distance=3 as a default value instead of the current distance=1 (the docs currently say that it's required but from the code it looks like 1 is set by default).

A PR is on the way!

Let me know what you think :)