Metadata-Version: 2.4
Name: rapids_singlecell
Version: 0.13.1
Summary: running single cell analysis on Nvidia GPUs
Project-URL: Documentation, https://rapids-singlecell.readthedocs.io
Project-URL: Source, https://github.com/scverse/rapids_singlecell
Author: Severin Dicks
License: MIT License
        
        Copyright (c) 2022, Severin Dicks
        Copyright (c) 2025, scverse®
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
        copies of the Software, and to permit persons to whom the Software is
        furnished to do so, subject to the following conditions:
        
        The above copyright notice and this permission notice shall be included in all
        copies or substantial portions of the Software.
        
        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
        SOFTWARE.
License-File: LICENSE
Requires-Python: <3.14,>=3.10
Requires-Dist: anndata>=0.10.0
Requires-Dist: docrep
Requires-Dist: matplotlib>=3.4
Requires-Dist: natsort
Requires-Dist: numpy>=1.17.0
Requires-Dist: pandas
Requires-Dist: scanpy>=1.10.0
Requires-Dist: scikit-image
Requires-Dist: scikit-misc>=0.1.3
Requires-Dist: scipy>=1.4
Requires-Dist: statsmodels>=0.12.0
Requires-Dist: tqdm
Provides-Extra: doc
Requires-Dist: dask; extra == 'doc'
Requires-Dist: myst-nb; extra == 'doc'
Requires-Dist: nbsphinx>=0.8.12; extra == 'doc'
Requires-Dist: pytest; extra == 'doc'
Requires-Dist: readthedocs-sphinx-ext; extra == 'doc'
Requires-Dist: scanpydoc[theme,typehints]>=0.9.4; extra == 'doc'
Requires-Dist: sphinx-copybutton; extra == 'doc'
Requires-Dist: sphinx-design; extra == 'doc'
Requires-Dist: sphinx>=4.5.0; extra == 'doc'
Provides-Extra: rapids11
Requires-Dist: cudf-cu11==25.04.*; extra == 'rapids11'
Requires-Dist: cugraph-cu11==25.04.*; extra == 'rapids11'
Requires-Dist: cuml-cu11==25.04.*; extra == 'rapids11'
Requires-Dist: cupy-cuda11x; extra == 'rapids11'
Provides-Extra: rapids12
Requires-Dist: cudf-cu12==25.04.*; extra == 'rapids12'
Requires-Dist: cugraph-cu12==25.04.*; extra == 'rapids12'
Requires-Dist: cuml-cu12==25.04.*; extra == 'rapids12'
Requires-Dist: cupy-cuda12x; extra == 'rapids12'
Provides-Extra: test
Requires-Dist: bbknn; extra == 'test'
Requires-Dist: decoupler; extra == 'test'
Requires-Dist: fast-array-utils; extra == 'test'
Requires-Dist: igraph; extra == 'test'
Requires-Dist: profimp; extra == 'test'
Requires-Dist: pytest; extra == 'test'
Requires-Dist: scanpy>=1.10.0; extra == 'test'
Provides-Extra: test-minimal
Requires-Dist: bbknn; extra == 'test-minimal'
Requires-Dist: decoupler; extra == 'test-minimal'
Requires-Dist: fast-array-utils; extra == 'test-minimal'
Requires-Dist: profimp; extra == 'test-minimal'
Requires-Dist: pytest; extra == 'test-minimal'
Requires-Dist: scanpy>=1.10.0; extra == 'test-minimal'
Description-Content-Type: text/markdown

[![Stars](https://img.shields.io/github/stars/scverse/rapids_singlecell?style=flat&logo=GitHub&color=blue)](https://github.com/scverse/rapids_singlecell/stargazers)
[![PyPI](https://img.shields.io/pypi/v/rapids-singlecell?logo=PyPI)](https://pypi.org/project/rapids-singlecell)
[![Downloads](https://static.pepy.tech/badge/rapids-singlecell)](https://pepy.tech/project/rapids-singlecell)
[![Documentation Status](https://readthedocs.org/projects/rapids-singlecell/badge/?version=latest)](https://rapids-singlecell.readthedocs.io/en/latest/?badge=latest)
[![Build and Test](https://github.com/scverse/rapids_singlecell/actions/workflows/test-gpu.yml/badge.svg)](https://github.com/scverse/rapids_singlecell/actions/workflows/test-gpu.yml)
[![Chat](https://img.shields.io/badge/zulip-join_chat-%2367b08f.svg)](https://scverse.zulipchat.com)

# rapids-singlecell: GPU-Accelerated Single-Cell Analysis within scverse®

rapids-singlecell provides GPU-accelerated single-cell analysis with an AnnData-first API. It is largely compatible with Scanpy and includes selected functionality from Squidpy and decoupler. Computations use CuPy and NVIDIA RAPIDS for performance on large datasets.

- **GPU acceleration**: Common single-cell workflows on `AnnData` run on the GPU.
- **Ecosystem compatibility**: Works with Scanpy APIs; includes pieces from Squidpy and decoupler.
- **Simple installation**: Available via Conda and PyPI.

## Documentation

For more information please have a look through the [documentation](https://rapids-singlecell.readthedocs.io/en/latest/)


## Citation

If you use this code, please cite: [![DOI](https://zenodo.org/badge/364573913.svg)](https://zenodo.org/badge/latestdoi/364573913)

Please also consider citing: [rapids-single-cell-examples](https://zenodo.org/badge/latestdoi/265649968) and  [scanpy](https://doi.org/10.1186/s13059-017-1382-0)

In addition to that please cite the methods' original research articles in the [scanpy documentation](https://scanpy.readthedocs.io/en/latest/references.html)

If you use the accelerated decoupler functions please cite [decoupler](https://doi.org/10.1093/bioadv/vbac016)

[//]: # (numfocus-fiscal-sponsor-attribution)

rapids-singlecell 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.

<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>
