.. figure:: https://github.com/brainets/frites/blob/master/docs/source/_static/logo_desc.png
:align: center
Frites
======
.. image:: https://github.com/brainets/frites/actions/workflows/test_doc.yml/badge.svg
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:target: https://github.com/brainets/frites/actions/workflows/flake.yml
.. image:: https://travis-ci.org/brainets/frites.svg?branch=master
:target: https://travis-ci.org/brainets/frites
.. image:: https://codecov.io/gh/brainets/frites/branch/master/graph/badge.svg
:target: https://codecov.io/gh/brainets/frites
.. image:: https://badge.fury.io/py/frites.svg
:target: https://badge.fury.io/py/frites
.. image:: https://pepy.tech/badge/frites
:target: https://pepy.tech/project/frites
.. image:: https://zenodo.org/badge/213869364.svg
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.. _Documentation: https://brainets.github.io/frites/
.. |Documentation| replace:: **Documentation**
.. _Installation: https://brainets.github.io/frites/install.html
.. |Installation| replace:: **Installation**
.. _Usage: https://brainets.github.io/frites/auto_examples/index.html
.. |Usage| replace:: **Usage example**
.. _API: https://brainets.github.io/frites/api/index.html
.. |API| replace:: **List of functions**
.. _Cite: https://brainets.github.io/frites/overview/ovw_cite.html
.. |Cite| replace:: **Cite Frites**
|Documentation|_ | |Installation|_ | |Usage|_ | |API|_ | |Cite|_
Description
===========
`Frites <https://brainets.github.io/frites/>`_ is a Python toolbox for assessing information-theorical measures on human and animal neurophysiological data (M/EEG, Intracranial). The aim of Frites is to extract task-related cognitive brain networks (i.e modulated by the task). The toolbox also includes directed and undirected connectivity metrics such as group-level statistics. Frites documentation is available online at https://brainets.github.io/frites/
.. figure:: https://github.com/brainets/frites/blob/master/docs/source/_static/network_framework.png
:align: center
Installation
============
Run the following command into your terminal to get the latest stable version :
.. code-block:: shell
pip install -U frites
You can also install the latest version of the software directly from Github :
.. code-block:: shell
pip install git+https://github.com/brainets/frites.git
For developers, you can install it in develop mode with the following commands :
.. code-block:: shell
git clone https://github.com/brainets/frites.git
cd frites
python setup.py develop
# or : pip install -e .
Dependencies
++++++++++++
The main dependencies of Frites are :
* `Numpy <https://numpy.org/>`_
* `Scipy <https://www.scipy.org/>`_
* `MNE Python <https://mne.tools/stable/index.html>`_
* `Xarray <http://xarray.pydata.org/en/stable/>`_
* `Joblib <https://joblib.readthedocs.io/en/latest/>`_
In addition to the main dependencies, here's the list of additional packages that you might need :
* `Numba <http://numba.pydata.org/>`_ : speed up the computations of some functions
* `Dcor <https://dcor.readthedocs.io/en/latest/>`_ for fast implementation of distance correlation
* `Matplotlib <https://matplotlib.org/>`_, `Seaborn <https://seaborn.pydata.org/>`_ and `Networkx <https://networkx.github.io/>`_ for plotting the examples
* Some example are using `scikit learn <https://scikit-learn.org/stable/index.html>`_ estimators
Acknowledgments
===============
See `acknowledgments <https://brainets.github.io/frites/overview/ovw_acknowledgments.html>`_
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