https://github.com/4ment/torchtree-scipy

Package providing extra functionalities from SciPy
https://github.com/4ment/torchtree-scipy

phylogenetics python pytorch scipy torchtree

Last synced: 25 days ago
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Package providing extra functionalities from SciPy

• Host: GitHub
• URL: https://github.com/4ment/torchtree-scipy
• Owner: 4ment
• License: gpl-3.0
• Created: 2022-09-01T06:17:23.000Z (about 2 years ago)
• Default Branch: main
• Last Pushed: 2023-11-22T06:59:44.000Z (12 months ago)
• Last Synced: 2024-03-23T09:42:52.699Z (8 months ago)
• Topics: phylogenetics, python, pytorch, scipy, torchtree
• Language: Python
• Homepage:
• Size: 21.5 KB
• Stars: 1
• Watchers: 2
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# torchtree-scipy 

[![Testing](https://github.com/4ment/torchtree-scipy/actions/workflows/python-package.yml/badge.svg)](https://github.com/4ment/torchtree-scipy/actions/workflows/python-package.yml)

[![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)

![PyPI](https://img.shields.io/pypi/v/torchtree-scipy)

![PyPI - Python Version](https://img.shields.io/pypi/pyversions/torchtree-scipy)

## About torchtree-scypi

`torchtree-scipy` is a package that enhances the functionalities of [torchtree] by incorporating additional features from [SciPy].

## Dependencies

 - [SciPy]

 - [torchtree]

## Installation

### Installing from source

```bash

git clone https://github.com/4ment/torchtree-scipy

pip install torchtree-scipy/

```

### Installing latest stable version

You can install `torchtree-scipy` and its dependencies from PyPI with:

```

pip install torchtree-scipy

```

## Check install

If the installation was succesfull, this command should print the version of the `torchtree_scipy` library

```bash

python -c "import torchtree_scipy;print(torchtree_scipy.__version__)"

```

## Command line arguments

The `torchtree-scipy` plugin adds these arguments to the torchtree CLI:

```bash

torchtree-cli advi --help

  ...

  --scipy_gamma_site    use the GammaSiteModel implemented with SciPy

```

## Features

### Discrete gamma site model

This model implements the discretized gamma distribution to model rate heterogeity accross sites. The gradient of this model with respect to the shape parameter is calculated numerically using finite differences.

The easiest way to use this model is to use the argument `--scipy_gamma_site`. This sets the type of the site model to `torchtree_scipy.GammaSiteModel` in the JSON configuration file. The default step size is `epsilon=1.0e-6` but it can be changed manually in the JSON file.

## License

Distributed under the GPLv3 License. See [LICENSE](LICENSE) for more information.

## Acknowledgements

torchtree-scipy makes use of the following libraries and tools, which are under their own respective licenses:

 - [PyTorch]

 - [SciPy]

 - [torchtree]

[PyTorch]: https://pytorch.org

[scipy]: https://github.com/scipy/scipy

[torchtree]: https://github.com/4ment/torchtree