.. template taken from SciPy who took it from Pandas (keep the chain going)

.. module:: openfe

=====================================
Welcome to OpenFE's documentation!
=====================================

The **OpenFE** toolkit provides a free and open-source framework for alchemical free energy calculations.
Using this toolkit you can plan, execute, and analyze free energy calculations using a variety of methods.

**Useful Links**:
`OpenFE Website <https://openfree.energy/>`__ |
`Example Tutorial notebooks <https://github.com/OpenFreeEnergy/ExampleNotebooks/>`__ |
`Source Repository <https://github.com/OpenFreeEnergy/openfe/>`__ |
`Issues & Ideas <https://github.com/OpenFreeEnergy/openfe/issues/>`__

.. grid:: 1 2 2 4
    :gutter: 3

    .. grid-item-card:: :fas:`download` Install openfe
        :text-align: center
        :link: installation
        :link-type: doc

        Follow our installation guide to get **openfe** running on your machine!

    .. grid-item-card:: :fas:`laptop-code` CLI
        :text-align: center
        :link: reference/cli/index
        :link-type: doc

        Documentation for **openfe**\'s simple command line interface.

    .. grid-item-card:: :fas:`person-chalkboard` Tutorials
        :text-align: center
        :link: tutorials/index
        :link-type: doc

        Step-by-step examples showing how to use the OpenFE toolkit.

    .. grid-item-card:: :fas:`book-open-reader` User Guide
        :text-align: center
        :link: guide/index
        :link-type: doc

        Explanations of key concept underlying the OpenFE toolkit.

    .. grid-item-card:: :fas:`table-list` Cookbooks
        :text-align: center
        :link: cookbook/index
        :link-type: doc

        How-to guides for common tasks.

    .. grid-item-card:: :fas:`code` Python API
        :text-align: center
        :link: reference/api/index
        :link-type: doc

        Comprehensive details of the **openfe** Python API.

    .. grid-item-card:: :fas:`gears` Protocols
        :text-align: center
        :link: guide/protocols/index
        :link-type: doc

        Details of the specific Free Energy Protocols included in **openfe**.

    .. grid-item-card:: :fas:`clock-rotate-left` Changelog 
        :text-align: center
        :link: CHANGELOG
        :link-type: doc

        A history of **openfe** releases.

.. toctree::
   :maxdepth: 2
   :hidden:

   installation
   tutorials/index
   guide/index
   cookbook/index
   reference/index
   CHANGELOG

Other OpenFE Ecosystem Projects:
--------------------------------

**openfe** is Open Free Energy's user-facing software for performing alchemical free energy calculations.
Below are other software projects the Open Free Energy team maintains, many of which are used by **openfe** itself.

* `konnektor <https://github.com/OpenFreeEnergy/konnektor/>`_: free energy network planning, modification, and analysis
* `kartograf <https://github.com/OpenFreeEnergy/kartograf/>`_: atom mappings focusing on 3D geometries
* `Lomap <https://github.com/OpenFreeEnergy/Lomap/>`_: planning perturbation networks for free energy calculations
* `cinnabar <https://github.com/OpenFreeEnergy/cinnabar/>`_ (formerly arsenic): plotting free energy calculation results
* `gufe <https://gufe.openfree.energy/en/latest/>`_ : data structures and models underlying the OpenFE ecosystem

Community-Developed Projects:
-----------------------------

* `alchemiscale <https://docs.alchemiscale.org/en/stable/>`_: high-throughput alchemical free energy execution, developed by `Datryllic <https://datryllic.com/>`_.