Metadata-Version: 2.4
Name: treedata
Version: 0.2.5
Summary: anndata with trees
Project-URL: Documentation, https://treedata.readthedocs.io/
Project-URL: Homepage, https://github.com/colganwi/treedata
Project-URL: Source, https://github.com/colganwi/treedata
Author: William Colgan
Maintainer-email: William Colgan <wcolgan@mit.edu>
License: BSD 3-Clause License
        
        Copyright (c) 2024, William Colgan
        All rights reserved.
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        1. Redistributions of source code must retain the above copyright notice, this
           list of conditions and the following disclaimer.
        
        2. Redistributions in binary form must reproduce the above copyright notice,
           this list of conditions and the following disclaimer in the documentation
           and/or other materials provided with the distribution.
        
        3. Neither the name of the copyright holder nor the names of its
           contributors may be used to endorse or promote products derived from
           this software without specific prior written permission.
        
        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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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
Classifier: Programming Language :: Python :: 3.14
Requires-Python: >=3.11
Requires-Dist: anndata>=0.11
Requires-Dist: h5py
Requires-Dist: networkx
Requires-Dist: numpy
Requires-Dist: packaging
Requires-Dist: pandas
Requires-Dist: pyarrow
Requires-Dist: session-info2
Requires-Dist: zarr>=2
Description-Content-Type: text/markdown

[![Tests][badge-tests]][link-tests]
[![Documentation][badge-docs]][link-docs]
[![PyPI](https://img.shields.io/pypi/v/treedata.svg)](https://pypi.org/project/treedata)
[![codecov](https://codecov.io/github/YosefLab/treedata/branch/main/graph/badge.svg?token=YPhuxlw4my)](https://codecov.io/github/YosefLab/treedata)
[![PyPI Downloads](https://static.pepy.tech/personalized-badge/treedata?period=total&units=INTERNATIONAL_SYSTEM&left_color=GREY&right_color=GREEN&left_text=downloads)](https://pepy.tech/projects/treedata)

[badge-tests]: https://img.shields.io/github/actions/workflow/status/YosefLab/treedata/test.yaml?branch=main
[link-tests]: https://github.com/YosefLab/treedata/actions/workflows/test.yaml
[badge-docs]: https://img.shields.io/readthedocs/treedata

<img
  src="https://raw.githubusercontent.com/YosefLab/treedata/main/docs/_static/img/treedata_schema.svg"
  class="dark-light" align="right" width="350" alt="image"
/>

# TreeData - AnnData with trees

TreeData is a lightweight wrapper around AnnData which adds two additional attributes, `obst` and `vart`, to store [nx.DiGraph] trees for observations and variables. TreeData has the same interface as AnnData and is fully compatible with [scverse] packages like [Scanpy].

To learn more about TreeData, please refer to the [documentation][link-docs] or checkout the [getting started guide][link-getting-started].

See the [Pycea documentation](https://pycea.readthedocs.io/) to learn how TreeData can be used to analyze single-cell lineage tracing data.

## Installation

You need to have Python 3.10 or newer installed on your system. If you don't have
Python installed, we recommend installing [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge).

There are several alternative options to install treedata:

1. Install the latest release of `treedata` from [PyPI](https://pypi.org/project/treedata):

```bash
pip install treedata
```

2. Install the latest development version:

```bash
pip install git+https://github.com/YosefLab/treedata.git@main
```

## Release notes

See the [changelog][changelog].

## Contact

For questions and bug reports please use the [issue tracker][issue-tracker].

## Citation

> t.b.a

[scverse]: https://scverse.org/
[Scanpy]: https://scanpy.readthedocs.io/
[nx.DiGraph]: https://networkx.org/documentation/stable/reference/classes/digraph.html
[scverse-discourse]: https://discourse.scverse.org/
[issue-tracker]: https://github.com/YosefLab/treedata/issues
[changelog]: https://treedata.readthedocs.io/en/latest/changelog.html
[link-docs]: https://treedata.readthedocs.io
[link-getting-started]: https://treedata.readthedocs.io/en/latest/notebooks/getting-started.html
[link-api]: https://treedata.readthedocs.io/latest/api.html
