Metadata-Version: 1.1
Name: moiety-modeling
Version: 1.0.2
Summary: Moiety Modeling Implementation
Home-page: https://github.com/MoseleyBioinformaticsLab/moiety_modeling.git
Author: Huan Jin
Author-email: hji236@g.uky.edu
License: The Clear BSD License
Description: 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
        ~~~~~~~~~~
        
        Using moiety_modeling to optimize parameters of moiety model.
        
        .. code:: bash
        
           python3 -m moiety_modeling modeling --models=<model_jsonfile> --datasets=<dataset_jsonfile> --optimizations=<optimizationSetting_json> --repetition=100 --split --multiprocess --energyFunction=logDifference
        
        Using moiety_modeling to analyze optimized results and select the optimal model.
        
        .. code:: bash
        
           python3 -m moiety_modeling analyze optimizations --a <optimizationPaths_txtfile>
           python3 -m moiety_modeling analyze rank <analysisPaths_txtfile> --rankCriteria=AICc
        
        Using moiety_modeling to visualize the optimzed results.
        
        .. code:: bash 
        
           python3 -m moiety_modeling plot moiety <analysisResults_jsonfile>
        
        .. 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
        ~~~~~~~
        
        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/
        
        
        
Keywords: moiety modeling model optimization model selection
Platform: any
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
