shadows 0.1a1

Low-memory data interfaces for scverse

Shadows

Shadows are on-disk interfaces for scverse data standards such as AnnData and MuData.

It is an experimental project.

Installation

pip install shadows
# or
pip install git+https://github.com/scverse/shadows

Features

The shadows library aims to implement the following features:

• Shadow objects: Read-only AnnDataShadow and MuDataShadow for HDF5 files.

• AnnDataShadow and MuDataShadow for Zarr files.

• AnnDataShadow and MuDataShadow for Parquet-based serialization (pqdata).

• Data shadows for .pqdata and .zarr files on S3 storage.

Shadow objects

Briefly, shadow objects simply work like this:

from shadows import *
ash = AnnDataShadow("pbmc3k.h5ad")
msh = MuDataShadow("pbmc5k_citeseq.h5mu")

All the various features are showcased in the following tutorials:

• Getting started with shadow objects

• Advanced features of shadow objects