moiety-modeling 1.0

Moiety Modeling Implementation

moiety_modeling
===============


.. image:: https://img.shields.io/pypi/v/moiety_modeling.svg
:target: https://pypi.org/project/moiety_modeling
:alt: Current library version

.. image:: https://img.shields.io/pypi/pyversions/moiety_modeling.svg
:target: https://pypi.org/project/moiety_modeling
:alt: Supported Python versions

.. image:: https://api.travis-ci.org/MoseleyBioinformaticsLab/moiety_modeling.svg?branch=master
:target: https://travis-ci.org/MoseleyBioinformaticsLab/moiety_modeling
:alt: Travis CI status


`moiety_modeling` package provides facilities for moiety model representation, model optimization and model selection.


Citation
~~~~~~~~

Please cite the GitHub repository until our manuscript is accepted for
publication: https://github.com/MoseleyBioinformaticsLab/moiety_modeling.git


Installation
~~~~~~~~~~~~

'moiety_modeling' runs under Python 3.6+ and is available through python3-pip.
Install via pip or clone the git repo and install the following depencies and
you are ready to go!


Install on Linux
~~~~~~~~~~~~~~~~

Pip installation
----------------

.. code:: bash

python3 -m pip install moiety_modeling

GitHub Package installation
---------------------------

Make sure you have git_ installed:

.. code:: bash

git clone https://github.com/MoseleyBioinformaticsLab/moiety_modeling.git


Dependencies
------------

'moiety_modeling' requires the following Python libraries:

* docopt_ for creating the command-line interface.
* JSONPickle_ for saving Python objects in a JSON serializable form and outputting to a file.
* numpy_ and matplotlib_ for visualization of optimized results.
* scipy_ for application of optimization methods.
* SAGA-optimize_ for parameters optimization.


Quickstart
~~~~~~~~~~

.. code:: python




.. note:: Read the User Guide and the ``moiety_modeling`` Tutorial on ReadTheDocs_ to learn more and to see code examples on using the ``moiety_modeling`` as a library and as a command-line tool.


License
~~~~~~~

.. include:: ../LICENSE

Made available under the terms of The modified Clear BSD License. See full license in LICENSE_.

Authors
~~~~~~~

* **Huan Jin**
* **Hunter N.B. Moseley**


.. _pip: https://pip.pypa.io/
.. _git: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git/
.. _docopt: https://github.com/docopt/docopt
.. _JSONPickle: https://github.com/jsonpickle/jsonpickle
.. _numpy: http://www.numpy.org/
.. _matplotlib: https://github.com/matplotlib/matplotlib
.. _scipy: https://github.com/scipy/scipy
.. _SAGA-optimize: https://pypi.org/project/SAGA-optimize/
.. _LICENSE: https://github.com/MoseleyBioinformaticsLab/moiety_modeling/blob/master/LICENSE
.. _ReadTheDocs: https://moiety-modeling.readthedocs.io/en/latest/