https://github.com/scverse/shadows
Shadow objects for AnnData and MuData (experimental)
https://github.com/scverse/shadows
Last synced: 11 months ago
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Shadow objects for AnnData and MuData (experimental)
- Host: GitHub
- URL: https://github.com/scverse/shadows
- Owner: scverse
- License: bsd-3-clause
- Created: 2023-10-31T15:59:35.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2025-02-28T16:09:51.000Z (over 1 year ago)
- Last Synced: 2025-05-03T09:05:55.779Z (about 1 year ago)
- Language: Python
- Homepage: http://scverse.org/shadows/
- Size: 2.18 MB
- Stars: 12
- Watchers: 3
- Forks: 0
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Shadows
Shadows are on-disk interfaces for scverse data standards such as [AnnData](https://github.com/scverse/anndata) and [MuData](https://github.com/scverse/mudata).
It is an experimental project.
[](https://pypi.org/project/shadows)
## 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](https://github.com/gtca/pqdata)).
- [x] Data shadows for `.pqdata` and `.zarr` files on S3 storage.
### Shadow objects
Briefly, shadow objects simply work like this:
```py
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](/docs/examples/shadow-objects.ipynb)
- [Advanced features of shadow objects](/docs/examples/shadows-features.ipynb)
[//]: # (numfocus-fiscal-sponsor-attribution)
shadows is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.
