.. -- mode: rst --

|Black|_ |Codecov|_ |JOSS|_

.. |Black| image:: https://img.shields.io/badge/code%20style-black-000000.svg .. _Black: https://github.com/psf/black

.. |Codecov| image:: https://codecov.io/gh/brainets/hoi/graph/badge.svg?token=7PNM2VD994 .. _Codecov: https://codecov.io/gh/brainets/hoi

.. |JOSS| image:: https://joss.theoj.org/papers/10.21105/joss.07360/status.svg .. _JOSS: https://doi.org/10.21105/joss.07360

.. image:: https://github.com/brainets/hoi/blob/main/docs/_static/hoi-logo.png :target: https://brainets.github.io/hoi/

Description

HOI (Higher Order Interactions) is a Python package to go beyond pairwise interactions by quantifying the statistical dependencies between 2 or more units using information-theoretical metrics. The package is built on top of Jax <https://github.com/google/jax>_ allowing computations on CPU or GPU.

Installation

Dependencies ++++++++++++

HOI requires :

• Python (>= 3.8)
• numpy(>=1.22)
• scipy (>=1.9)
• jax
• pandas
• scikit-learn
• jax-tqdm
• tqdm

User installation +++++++++++++++++

To install Jax on GPU or CPU-only, please refer to Jax's documentation : https://jax.readthedocs.io/en/latest/installation.html

If you already have a working installation of NumPy, SciPy and Jax, the easiest way to install hoi is using pip:

.. code-block:: shell

pip install -U hoi

You can also install the latest version of the software directly from Github :

.. code-block:: shell

pip install git+https://github.com/brainets/hoi.git

For developers ++++++++++++++

For developers, you can install it in develop mode with the following commands :

.. code-block:: shell

git clone https://github.com/brainets/hoi.git
cd hoi
pip install -e .['full']

The full installation of HOI includes additional packages to test the software and build the documentation :

• pytest
• pytest-cov
• codecov
• xarray
• sphinx!=4.1.0
• sphinx-gallery
• pydata-sphinx-theme
• sphinxcontrib-bibtex
• numpydoc
• matplotlib
• flake8
• pep8-naming
• black

Help and Support

Documentation +++++++++++++

• Link to the documentation: https://brainets.github.io/hoi/
• Overview of the mathematical background : https://brainets.github.io/hoi/theory.html
• List of implemented HOI metrics : https://brainets.github.io/hoi/api/modules.html
• Examples : https://brainets.github.io/hoi/auto_examples/index.html

Communication +++++++++++++

For questions, please use the following link : https://github.com/brainets/hoi/discussions

Acknowledgments

HOI was mainly developed during the Google Summer of Code 2023 (https://summerofcode.withgoogle.com/archive/2023/projects/z6hGpvLS)