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        "author": "Huan Jin",
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            "License :: OSI Approved :: BSD License",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
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        "description": "SAGA_optimize\n=============\n\n\n.. image:: https://img.shields.io/pypi/l/SAGA_optimize.svg\n   :target: https://choosealicense.com/licenses/bsd-3-clause-clear/\n   :alt: License information\n\n.. image:: https://img.shields.io/pypi/v/SAGA_optimize.svg\n   :target: https://pypi.org/project/SAGA_optimize\n   :alt: Current library version\n\n.. image:: https://img.shields.io/pypi/pyversions/SAGA_optimize.svg\n   :target: https://pypi.org/project/SAGA_optimize\n   :alt: Supported Python versions\n\n.. image:: https://api.travis-ci.org/MoseleyBioinformaticsLab/SAGA_optimize.svg?branch=master\n   :target: https://travis-ci.org/MoseleyBioinformaticsLab/SAGA_optimize\n   :alt: Travis CI status\n\n\n\n`SAGA_optimize` is a novel type of combined simulated annealing and genetic algorithm\nused to find the optimal solutions to a set of parameters based on a given energy\nfunction calculated using the set of parameters.\n\n\nCitation\n~~~~~~~~\n\nPlease cite the GitHub repository until our manuscript is accepted for\npublications: https://github.com/MoseleyBioinformaticsLab/SAGA_optimize.git\n\n\nInstallation\n~~~~~~~~~~~~\n\n`SAGA_optimize` runs under Python 3.6+ and is available through python3-pip.\nInstall via pip or clone the git repo and install the following dependencies\nand you are ready to go!\n\n\nInstall on Linux\n----------------\n\nPip installation\n................\n\n.. code:: bash\n\n    python3 -m pip install SAGA-optimize\n\n\nGitHub Package installation\n...........................\n\n\nMake sure you have git_ installed:\n\n.. code:: bash \n \n    git clone https://github.com/MoseleyBioinformaticsLab/SAGA_optimize.git\n\n\nDependecies \n...........\n\n`SAGA_optimize` requires the following Python libraries:\n    \n    * JSONPickle_ for saving Python objects in a JSON serializable form and outputting to a file.\n\n\nQuickstart\n~~~~~~~~~~\n\n.. code:: python\n\n   >>> import SAGA_optimize\n   >>> saga = SAGA_optimize.SAGA(stepNumber=100000, temperatureStepSize=100, startTemperature=0.5, \n                                 alpha=1, direction=-1, energyCalculation=energyCalculation, crossoverRate=0.5, \n                                 mutationRate=3, annealMutationRate=1, populationSize=20)                  # SAGA instance creation.\n   >>> saga.addElementDescriptions(SAGA_optimize.ElementDescription(low=0, high=10), \n\t\t\t\t   SAGA_optimize.ElementDescription(low=0, high=10), \n                                   SAGA_optimize.ElementDescription(low=0, high=10), \n                                   SAGA_optimize.ElementDescription(low=0, high=10), \n                                   SAGA_optimize.ElementDescription(low=0, high=10))        # Add optimized parameters.\n   >>> optimized_population = saga.optimize()              # the population returned after the opitimization.\n\n.. note:: Read the User Guide and the ``SAGA_optimize`` Tutorial on ReadTheDocs_ to learn more and to see code examples on using the ``SAGA_optimize`` as a library.\n\n\nLicense\n~~~~~~~\n\nMade available under the terms of The Clear BSD License. See full license in LICENSE_.\n\nAuthors\n~~~~~~~\n\n* **Huan Jin**\n* **Hunter N.B. Moseley**\n\n.. _ReadTheDocs: https://saga-optimize.readthedocs.io/en/latest/\n.. _jsonpickle: https://jsonpickle.github.io/\n.. _git: https://git-scm.com/book/en/v2/Getting-Started-Installing-Git/\n.. _LICENSE: https://choosealicense.com/licenses/bsd-3-clause-clear/",
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