Metadata-Version: 2.3
Name: shadows
Version: 0.1a1
Summary: Low-memory data interfaces for scverse
Project-URL: Documentation, https://scverse.github.io/shadows
Project-URL: Source, https://github.com/scverse/shadows
Project-URL: Home-page, https://github.com/scverse/shadows
Author: Danila Bredikhin
Maintainer-email: Danila Bredikhin <danila@stanford.edu>
License: BSD 3-Clause License
        
        Copyright (c) 2020, Danila Bredikhin
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Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.10
Provides-Extra: all
Requires-Dist: anndata>=0.8; extra == 'all'
Requires-Dist: mudata>=0.2; extra == 'all'
Requires-Dist: scipy; extra == 'all'
Provides-Extra: dev
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Provides-Extra: test
Requires-Dist: anndata; extra == 'test'
Requires-Dist: mudata; extra == 'test'
Requires-Dist: pqdata; extra == 'test'
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Requires-Dist: pytest-cov; extra == 'test'
Requires-Dist: scipy; extra == 'test'
Requires-Dist: zarr; extra == 'test'
Description-Content-Type: text/markdown

<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](https://github.com/scverse/anndata) and [MuData](https://github.com/scverse/mudata).

It is an experimental project.

[![PyPi version](https://img.shields.io/pypi/v/shadows)](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)

