scachepy

Caching extension for Scanpy and Scvelo. Useful when you want to make sure that your clustering, UMAP, etc. are always exactly the same, and enables you to share and load these attributes conveniently. Everything in an AnnData object can be cached using scachepy - if not implemented, we show in the tutorial notebook how you can easily set up your own caching function.

Installation

pip install git+https://github.com/theislab/scachepy

Usage

We recommend checking out the tutorial notebook. In essence, you can:

import scachepy
c = scachepy.Cache(<directory>, separate_dirs=True, compression='lzma')

# set verbosity level
c.verbose(False)
# set whether to recache
c.force(True)

# view available functions
print(list(c.pl))

c.pp.pca(adata)
# also display and save some plots
c.pl.pca(adata)

# remove cached files
c.pp.clear()

# create a copy
adata_copy = c.pp.neighbors(adata, ..., copy=True)

# easily cache fields specified at runtime
# and override global settings
c.tl.louvain(adata, key_added='foo', force=False)
c.tl.louvain(adata, key_added='bar', verbose=True)

# and if you forgot to call the caching version of possibly
# long running function, we got you covered!
scv.tl.velocity_graph(adata, ...)
c.tl.velocity_graph(adata, ..., call=False)
...