Metadata-Version: 2.4
Name: napari-relax
Version: 0.1.0
Summary: A plugin to visualise and manipulate cell lineage trees
Author: Giannis Liaskas, Jules Vanaret
Author-email: Léo Guignard <leo.guignard@univ-amu.fr>
License: 
        Copyright (c) 2025, Léo Guignard
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        * Redistributions of source code must retain the above copyright notice, this
          list of conditions and the following disclaimer.
        
        * Redistributions in binary form must reproduce the above copyright notice,
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        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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Project-URL: Bug Tracker, https://github.com/guignardlab/napari-relax/issues
Project-URL: Documentation, https://guignardlab.github.io/napari-relax/
Project-URL: Source Code, https://github.com/guignardlab/napari-relax
Project-URL: User Support, https://github.com/guignardlab/napari-relax/issues
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Framework :: napari
Classifier: Intended Audience :: Developers
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Image Processing
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy
Requires-Dist: matplotlib
Requires-Dist: lineagetree<=4.0.0
Provides-Extra: all
Requires-Dist: napari[all]; extra == "all"
Provides-Extra: testing
Requires-Dist: tox; extra == "testing"
Requires-Dist: pytest; extra == "testing"
Requires-Dist: pytest-cov; extra == "testing"
Requires-Dist: pytest-qt; extra == "testing"
Requires-Dist: napari[qt]; extra == "testing"
Provides-Extra: docs
Requires-Dist: mkdocs<2,>=1.6; extra == "docs"
Requires-Dist: mkdocs-material<10,>=9.7; extra == "docs"
Requires-Dist: mkdocstrings[python]>=1.0; extra == "docs"
Dynamic: license-file

# napari-relax

[![License BSD-3](https://img.shields.io/pypi/l/napari-relax.svg?color=green)](https://github.com/guignardlab/napari-relax/raw/main/LICENSE)
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[![napari hub](https://img.shields.io/endpoint?url=https://api.napari-hub.org/shields/napari-relax)](https://napari-hub.org/plugins/napari-relax)
[![npe2](https://img.shields.io/badge/plugin-npe2-blue?link=https://napari.org/stable/plugins/index.html)](https://napari.org/stable/plugins/index.html)
[![Copier](https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/copier-org/copier/master/img/badge/badge-grayscale-inverted-border-purple.json)](https://github.com/copier-org/copier)

**ReLAX** (Reconstructed Lineage Analysis & eXploration) is a [napari] plugin to visualise and compare cell lineage trees. It gives [LineageTree] datasets a graphical interface, so no programming is needed.

**Documentation: [guignardlab.github.io/napari-relax](https://guignardlab.github.io/napari-relax/)**

## Features

- **Explore** tracking datasets in the napari viewer and in an interactive Lineage Viewer, side by side.
- **Relabel** lineages and save them as `.lT` files.
- **Recolor** cells by clone or by any numeric attribute of the dataset.
- **Compare** lineages and sublineages with unordered tree edit distances, shown as an interactive clustermap.
- **Compare across datasets**, even with different time resolutions.

ReLAX opens `.lT`, MaMuT and ASTEC `.xml`, Mastodon and `.bmf` files, and comes with two demo datasets under **File > Open Sample > ReLAX**.

## Installation

ReLAX requires Python 3.10 or newer and napari 0.9 or newer. You can install `napari-relax` via [pip]:

```
pip install napari-relax
```

If napari is not already installed, you can install `napari-relax` with napari and Qt via:

```
pip install "napari-relax[all]"
```

To install the latest development version:

```
pip install git+https://github.com/guignardlab/napari-relax.git
```

Then open **Plugins > Lineage tree analysis** or **Plugins > Cross Lineagetree comparison** in napari. The [Quick Start](https://guignardlab.github.io/napari-relax/quick_start/q_start/) walks through a first session.

## Contributing

Contributions are very welcome. Tests can be run with [tox], please ensure
the coverage at least stays the same before you submit a pull request.

The documentation is built with [MkDocs] from the `docs/` folder and published automatically when `main` changes. To preview it locally:

```
pip install -e ".[docs]"
mkdocs serve
```

See the [developer documentation](https://guignardlab.github.io/napari-relax/developer/architecture/) for an overview of the code.

## License

Distributed under the terms of the [BSD-3] license,
"napari-relax" is free and open source software

## Issues

If you encounter any problems, please [file an issue] along with a detailed description.

----------------------------------

This [napari] plugin was generated with [copier] using the [napari-plugin-template].

[napari]: https://github.com/napari/napari
[LineageTree]: https://guignardlab.github.io/LineageTree/
[copier]: https://copier.readthedocs.io/en/stable/
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[napari-plugin-template]: https://github.com/napari/napari-plugin-template
[MkDocs]: https://www.mkdocs.org/
[file an issue]: https://github.com/guignardlab/napari-relax/issues
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
