anndata-mcp-workshop

anndata-mcp-workshop

 [![Tests][badge-tests]][tests] [![Documentation][badge-docs]][documentation]

[badge-tests]: https://img.shields.io/github/actions/workflow/status/dschaub95/anndata-mcp-workshop/test.yaml?branch=main [badge-docs]: https://img.shields.io/readthedocs/anndata-mcp-workshop

A very interesting piece of code

Getting started

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

You can also find the project on BioContextAI, the community-hub for biomedical MCP servers: anndata-mcp-workshop on BioContextAI.

Installation

You need to have Python 3.10 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-workshop:

1. Use uvx to run it immediately

After publication to PyPI: ``bash uvx anndata_mcp_workshop ``

Or from a Git repository:

uvx git+https://github.com/dschaub95/anndata-mcp-workshop.git@main

2. Include it in one of various clients that supports the mcp.json standard

If your MCP server is published to PyPI, use the following configuration:

{
  "mcpServers": {
    "anndata-mcp-workshop": {
      "command": "uvx",
      "args": ["anndata_mcp_workshop"]
    }
  }
}

In case the MCP server is not yet published to PyPI, use this configuration:

{
  "mcpServers": {
    "anndata-mcp-workshop": {
      "command": "uvx",
      "args": ["git+https://github.com/dschaub95/anndata-mcp-workshop.git@main"]
    }
  }
}

For purely local development (e.g., in Cursor or VS Code), use the following configuration:

{
  "mcpServers": {
    "anndata-mcp-workshop": {
      "command": "uvx",
      "args": [
        "--refresh",
        "--from",
        "path/to/repository",
        "anndata_mcp_workshop"
      ]
    }
  }
}

If you want to reuse and existing environment for local development, use the following configuration:

{
  "mcpServers": {
    "anndata-mcp-workshop": {
      "command": "uv",
      "args": ["run", "--directory", "path/to/repository", "anndata_mcp_workshop"]
    }
  }
}

3. Install it through pip:

pip install --user anndata_mcp_workshop

4. Install the latest development version:

pip install git+https://github.com/dschaub95/anndata-mcp-workshop.git@main

Contact

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

Citation

t.b.a

[uv]: https://github.com/astral-sh/uv [issue tracker]: https://github.com/dschaub95/anndata-mcp-workshop/issues [tests]: https://github.com/dschaub95/anndata-mcp-workshop/actions/workflows/test.yaml [documentation]: https://anndata-mcp-workshop.readthedocs.io [changelog]: https://anndata-mcp-workshop.readthedocs.io/en/latest/changelog.html [api documentation]: https://anndata-mcp-workshop.readthedocs.io/en/latest/api.html [pypi]: https://pypi.org/project/anndata-mcp-workshop