.. pyrates documentation master file, created by
   sphinx-quickstart on Wed Oct  3 12:55:59 2018.
   You can adapt this file completely to your liking, but it should at least
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.. image:: ../../../pyrates_logo_large.png
   :width: 900

PyRates Documentation
=====================

Documentation of `PyRates <https://github.com/pyrates-neuroscience/PyRates>`_, an open-source Python toolbox for dynamical systems modeling.

Content
-------

:doc:`Overview`
   `PyRates` features, installation instructions, and other general information.

:doc:`Use Examples`
   Galleries containing fully documented use examples that can be downloaded as `Python` scripts or `jupyter notebook` files.

:doc:`API`
   Detailed API of all classes and functions available to the user.

.. Hidden TOCs

.. toctree::
   :caption: Overview
   :maxdepth: 2
   :hidden:

   basic_info
   installation
   simple_example
   math_syntax
   template_specification
   changelog

.. toctree::
    :maxdepth: 4
    :numbered:
    :caption: Use Examples
    :hidden:

    model_definition
    implemented_models
    model_analysis

.. toctree::
    :maxdepth: 5
    :numbered:
    :caption: API
    :hidden:

    pyrates
    model_templates
    tests

Reference
---------

If you use PyRates, please cite:

`Gast, R., Knösche, T. R. & Kennedy, A. (2023). PyRates - A Code-Generation Tool for Dynamical Systems Modeling. PLOS Computational Biology 19 (12), e1011761. <https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011761>`_

`Gast, R., Rose, D., Salomon, C., Möller, H. E., Weiskopf, N., & Knösche, T. R. (2019). PyRates-A Python framework for rate-based neural simulations. PloS one, 14(12), e0225900. <https://doi.org/10.1371/journal.pone.0225900>`_

Contact
-------

If you have questions, problems or suggestions regarding PyRates, please contact `Richard Gast <https://www.richardgast.me>`_.

Contribute
----------

PyRates is an open-source project that everyone is welcome to contribute to. Check out our `GitHub repository <https://github.com/pyrates-neuroscience/PyRates>`_
for all the source code, open issues etc. and send us a pull request, if you would like to contribute something to our software.