Metadata-Version: 2.4
Name: geome
Version: 0.0.3
Summary: Geometric Learning for Genome Data
Project-URL: Documentation, https://geome.readthedocs.io/
Project-URL: Homepage, https://github.com/theislab/geome
Project-URL: Source, https://github.com/theislab/geome
Author: Marcella Toth
Maintainer-email: Marcella Toth <toth.marcella@gmail.com>, Selman Ozleyen <syozleyen@gmail.com>, Chelsea Bright <chels.alex.bright@gmail.com>
License: MIT License
        
        Copyright (c) 2023, Marcella Toth
        
        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
        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
        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 :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Requires-Python: >=3.9
Requires-Dist: anndata
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: pytorch-lightning
Requires-Dist: scipy
Requires-Dist: session-info
Requires-Dist: squidpy
Requires-Dist: torch
Requires-Dist: torch-cluster
Requires-Dist: torch-geometric
Requires-Dist: torch-scatter
Requires-Dist: torch-sparse
Description-Content-Type: text/markdown

# geome

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

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

The repo provides a set of tools for creating PyTorch Geometric (PyG) data objects from AnnData objects, which are commonly used for storing and manipulating single-cell genomics data. In addition, the repo includes functionality for creating PyTorch Lightning (PyTorch-Lightning) DataModule objects from the PyG data objects, which can be used to create graph neural network (GNN) data pipelines. The PyG data objects represent graphs, where the nodes represent cells and the edges represent relationships between the cells, and can be used to perform GNN tasks such as node classification, graph classification, and link prediction. The repo is written in Python and utilizes the PyTorch, PyTorch Geometric, and PyTorch-Lightning libraries.

## Getting started

Please refer to the [documentation][link-docs]. In particular, the

-   [API documentation][link-api].

## Installation

You need to have Python 3.9 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 geome:

<!--
1) Install the latest release of `geome` from `PyPI <https://pypi.org/project/geome/>`_:

```bash
pip install geome
```
-->

1. Install the latest development version:


Without GPU support:

```bash
mamba create -n geome  python=3.10
mamba activate geome
pip install torch==2.1.0
pip install torch-scatter torch-sparse torch-cluster
pip install git+https://github.com/theislab/geome.git@main
```

With GPU:

```bash
mamba create -n geome  python=3.10
mamba activate geome
mamba install pytorch==2.1.0 torchvision==0.16.0 torchaudio==2.1.0 pytorch-cuda=12.1 -c pytorch -c nvidia
pip install torch-scatter torch-sparse torch-cluster -f https://data.pyg.org/whl/torch-2.1.0+cu121.html
pip install git+https://github.com/theislab/geome.git@main
```

## Release notes

See the [changelog][changelog].

## Contact

For questions and help requests, you can reach out in the [scverse discourse][scverse-discourse].
If you found a bug, please use the [issue tracker][issue-tracker].

## Credits

Some of the data for `DatasetHartmann` is distributed in this package.
It was originally retrieved from: https://zenodo.org/record/3951613#.Y9flQS-B1qv

This project was generated from [@cjolowicz]'s [Hypermodern Python Cookiecutter] template.

[@cjolowicz]: https://github.com/cjolowicz
[pypi]: https://pypi.org/
[hypermodern python cookiecutter]: https://github.com/cjolowicz/cookiecutter-hypermodern-python
[file an issue]: https://github.com/theislab/geome/issues
[pip]: https://pip.pypa.io/

## Citation

> t.b.a

[scverse-discourse]: https://discourse.scverse.org/
[issue-tracker]: https://github.com/theislab/geome/issues
[changelog]: https://geome.readthedocs.io/changelog.html
[link-docs]: https://geome.readthedocs.io/
[link-api]: https://geome.readthedocs.io/en/latest/api.html
