lumen-anndata 0.0.2
Lumen for anndata and scanpy
License: BSD
Requires Python: >=3.11

# ✨ lumen-anndata

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https://github.com/user-attachments/assets/836f0699-6379-4314-a861-7e3729d66f48



## Overview

lumen-anndata is an extension to enable [Lumen](https://lumen.holoviz.org/) to interact with [anndata](https://anndata.readthedocs.io/) objects, a common format for single-cell genomics data. It aims to allow researchers to use natural language to explore, analyze, and visualize complex single-cell datasets through a chat interface.

## Features
lumen-anndata supports the following capabilities:

- Natural language querying of anndata objects
- Integration with select scanpy functions for running analysis and static plotting
- Interactive visualization of single-cell data (UMAP, DotMap, HeatMap, Dendrogram, etc.) with HoloViz

## Installation

Install it via `pip`:

```bash
pip install lumen-anndata
```

## Usage

To launch the Lumen app, run:

```bash
lumen-anndata
```

---
---

## Development

```bash
git clone https://github.com/holoviz-topics/lumen-anndata
cd lumen-anndata
```

For a simple setup use [`uv`](https://docs.astral.sh/uv/):

```bash
uv venv
source .venv/bin/activate # on linux. Similar commands for windows and osx
uv pip install -e .[dev]
uv pip install "git+https://github.com/holoviz/lumen@main#egg=lumen[ai-llama]"
pre-commit run
pytest tests
```

For the full Github Actions setup use [pixi](https://pixi.sh):

```bash
pixi run pre-commit-install
pixi run postinstall
pixi run test
```

This repository is adapted from [copier-template-panel-extension](https://github.com/panel-extensions/copier-template-panel-extension)

To update to the latest template version run:

```bash
pixi exec --spec copier --spec ruamel.yaml -- copier update --defaults --trust
```

Note: `copier` will show `Conflict` for files with manual changes during an update. This is normal. As long as there are no merge conflict markers, all patches applied cleanly.

To update the embeddings to use a new version of `scanpy`, increment the version in `scripts/embed_docs.py` and run:

```bash
python scripts/embed_docs.py
```

Ensure you have an OpenAI API key set in your environment variables. You can set it in your terminal session with:

```bash
export OPENAI_API_KEY="sk-..."
```

## ❤️ Contributing

Contributions are welcome! Please follow these steps to contribute:

1. Fork the repository.
2. Create a new branch: `git checkout -b feature/YourFeature`.
3. Make your changes and commit them: `git commit -m 'Add some feature'`.
4. Push to the branch: `git push origin feature/YourFeature`.
5. Open a pull request.

Please ensure your code adheres to the project's coding standards and passes all tests.