<img src="./docs/img/shadows_header.jpg" data-canonical-src="./docs/img/shadows_header.svg" width="100%"/>

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:

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

• [x] AnnDataShadow and MuDataShadow for Zarr files.

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

• [x] 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

shadows is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS. If you like scverse® and want to support our mission, please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

<div align="center"> <a href="https://numfocus.org/project/scverse"> <img src="https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png" width="200" > </a> </div>