Metadata-Version: 2.4
Name: anndata-mcp
Version: 0.2.7
Summary: Allows to retrieve information about an AnnData object via MCP
Project-URL: Documentation, https://anndata-mcp.readthedocs.io/
Project-URL: Homepage, https://github.com/biocontext-ai/anndata-mcp
Project-URL: Source, https://github.com/biocontext-ai/anndata-mcp
Author: Darius Schaub, Malte Kuehl
Maintainer-email: Darius Schaub <schaub.darius@gmail.com>, Malte Kuehl <malte.kuehl@clin.au.dk>
License: 
        MIT License
        
        Copyright (c) 2025, Darius Schaub
        
        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
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        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
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Python: >=3.11
Requires-Dist: aiohttp>=3.13.2
Requires-Dist: anndata>=0.12.6
Requires-Dist: click
Requires-Dist: dask>=2025.9.1
Requires-Dist: fastmcp
Requires-Dist: httpx<1
Requires-Dist: xarray>=2025.9
Provides-Extra: dev
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Requires-Dist: pre-commit; extra == 'dev'
Requires-Dist: scanpy; extra == 'dev'
Requires-Dist: session-info2; extra == 'dev'
Requires-Dist: twine>=4.0.2; extra == 'dev'
Provides-Extra: doc
Requires-Dist: docutils!=0.18.*,!=0.19.*,>=0.8; extra == 'doc'
Requires-Dist: ipykernel; extra == 'doc'
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Requires-Dist: myst-nb>=1.1; extra == 'doc'
Requires-Dist: pandas; extra == 'doc'
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Requires-Dist: sphinx-copybutton; extra == 'doc'
Requires-Dist: sphinx-tabs; extra == 'doc'
Requires-Dist: sphinx>=8.1; extra == 'doc'
Requires-Dist: sphinxext-opengraph; extra == 'doc'
Provides-Extra: test
Requires-Dist: coverage; extra == 'test'
Requires-Dist: pytest; extra == 'test'
Requires-Dist: pytest-asyncio; extra == 'test'
Description-Content-Type: text/markdown

# AnnData MCP

[![BioContextAI - Registry](https://img.shields.io/badge/Registry-package?style=flat&label=BioContextAI&labelColor=%23fff&color=%233555a1&link=https%3A%2F%2Fbiocontext.ai%2Fregistry)](https://biocontext.ai/registry)
[![Tests][badge-tests]][tests]
[![Documentation][badge-docs]][documentation]

[badge-tests]: https://img.shields.io/github/actions/workflow/status/biocontext-ai/anndata-mcp/test.yaml?branch=main
[badge-docs]: https://img.shields.io/readthedocs/anndata-mcp

Allows to retrieve information about an AnnData object via MCP using the `read_lazy` function from `anndata`.

## Getting started

Please refer to the [documentation][],
in particular, the [API documentation][].

You can also find the project on [BioContextAI](https://biocontext.ai), the community-hub for biomedical MCP servers: [anndata-mcp on BioContextAI](https://biocontext.ai/registry/biocontext-ai/anndata-mcp).

## Installation

You need to have Python 3.11 or newer installed on your system.
If you don't have Python installed, we recommend installing [uv][].

There are several alternative options to install anndata-mcp:

1. Use `uvx` to run it immediately:

```bash
uvx anndata-mcp
```

2. Include it in one of various clients that supports the `mcp.json` standard, please use:

```json
{
  "mcpServers": {
    "anndata-mcp": {
      "command": "uvx",
      "args": ["anndata-mcp"]
    }
  }
}
```

3. Install it through `pip`:

```bash
pip install --user anndata-mcp
```

4. Install the latest development version:

```bash
pip install git+https://github.com/biocontext-ai/anndata-mcp.git@main
```

## Contact

If you found a bug, please use the [issue tracker][].

## Citation

If this MCP server is useful to your research, please cite the `BioContextAI` and the `anndata` publications:

```bibtex
@article{BioContext_AI_Kuehl_Schaub_2025,
  title={BioContextAI is a community hub for agentic biomedical systems},
  url={http://dx.doi.org/10.1038/s41587-025-02900-9},
  urldate = {2025-11-06},
  doi={10.1038/s41587-025-02900-9},
  year = {2025},
  month = nov,
  journal={Nature Biotechnology},
  publisher={Springer Science and Business Media LLC},
  author={Kuehl, Malte and Schaub, Darius P. and Carli, Francesco and Heumos, Lukas and Hellmig, Malte and Fernández-Zapata, Camila and Kaiser, Nico and Schaul, Jonathan and Kulaga, Anton and Usanov, Nikolay and Koutrouli, Mikaela and Ergen, Can and Palla, Giovanni and Krebs, Christian F. and Panzer, Ulf and Bonn, Stefan and Lobentanzer, Sebastian and Saez-Rodriguez, Julio and Puelles, Victor G.},
  year={2025},
  month=nov,
  language={en},
}
```

```bibtex
@article{Virshup2024,
  title = {anndata: Access and store annotated data
matrices},
  volume = {9},
  ISSN = {2475-9066},
  url = {http://dx.doi.org/10.21105/joss.04371},
  DOI = {10.21105/joss.04371},
  number = {101},
  journal = {Journal of Open Source Software},
  publisher = {The Open Journal},
  author = {Virshup,  Isaac and Rybakov,  Sergei and Theis,  Fabian J. and Angerer,  Philipp and Wolf,  F. Alexander},
  year = {2024},
  month = sep,
  pages = {4371}
}
```

[uv]: https://github.com/astral-sh/uv
[issue tracker]: https://github.com/biocontext-ai/anndata-mcp/issues
[tests]: https://github.com/biocontext-ai/anndata-mcp/actions/workflows/test.yaml
[documentation]: https://anndata-mcp.readthedocs.io
[changelog]: https://anndata-mcp.readthedocs.io/en/latest/changelog.html
[api documentation]: https://anndata-mcp.readthedocs.io/en/latest/api.html
[pypi]: https://pypi.org/project/anndata-mcp
