Currently, FastTag relies on a connectivity matrix that is usually generated during the preprocessing pipeline.
To decouple FastTag from specific preprocessing workflows (e.g., scanpy pipelines), we should:
- Move connectivity calculation (e.g., sc.pp.neighbors) to an optional helper function.
- Have FastTag raise an error if
.obsp['connectivities'] is missing.
- Optionally provide a utility like
prepare_adata_for_fasttag() for beginners.
This will improve modularity, portability, and reduce unnecessary dependencies.