"""
A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""

# Always prefer setuptools over distutils
from setuptools import setup, find_packages
# To use a consistent encoding
from codecs import open
from os import path

here = path.abspath(path.dirname(__file__))

# Get the long description from the README file
with open(path.join(here, 'README.md'), encoding='utf-8') as f:
    long_description = f.read()

setup(
    name='hominid',

    # Versions should comply with PEP440.  For a discussion on single-sourcing
    # the version across setup.py and the project code, see
    # https://packaging.python.org/en/latest/single_source_version.html
    version='1.0.0',

    description='Python MPI program using LASSO regression to find associations between host genetics and microbiome.',
    long_description=long_description,

    # The project's main homepage.
    url='https://github.com/blekhmanlab/hominid',

    # Author details
    author='Joshua Lynch',
    author_email='lynch197@umn.edu',

    # Choose your license
    license='MIT',

    # See https://pypi.python.org/pypi?%3Aaction=list_classifiers
    classifiers=[
        # How mature is this project? Common values are
        #   3 - Alpha
        #   4 - Beta
        #   5 - Production/Stable
        'Development Status :: 5 - Production/Stable',

        # Indicate who your project is intended for
        'Intended Audience :: Science/Research',
        'Topic:: Scientific / Engineering:: Bio - Informatics',

        # Pick your license as you wish (should match "license" above)
        'License :: OSI Approved :: MIT License',

        # Specify the Python versions you support here. In particular, ensure
        # that you indicate whether you support Python 2, Python 3 or both.
        'Programming Language :: Python :: 2',
        'Programming Language :: Python :: 2.7',
        'Programming Language :: Python :: 3',
        'Programming Language :: Python :: 3.5',
    ],

    # What does your project relate to?
    keywords='host genetics, microbiome',

    # You can just specify the packages manually here if your project is
    # simple. Or you can use find_packages().
    packages=find_packages(exclude=['contrib', 'docs', 'tests']),

    # Alternatively, if you want to distribute just a my_module.py, uncomment
    # this:
    #   py_modules=["my_module"],

    # List run-time dependencies here.  These will be installed by pip when
    # your project is installed. For an analysis of "install_requires" vs pip's
    # requirements files see:
    # https://packaging.python.org/en/latest/requirements.html
    install_requires=[
        'numpy',
        'pandas',
        'scipy',
        'scikit-learn',
        'scikits.bootstrap',
        'statsmodels',
        'mpi4py'
    ],

    # List additional groups of dependencies here (e.g. development
    # dependencies). You can install these using the following syntax,
    # for example:
    # $ pip install -e .[plot,test]
    extras_require={
        'plot': ['rpy2'],
        'test': ['pytest'],
    },

    # To provide executable scripts, use entry points in preference to the
    # "scripts" keyword. Entry points provide cross-platform support and allow
    # pip to create the appropriate form of executable for the target platform.
    entry_points={
        'console_scripts': [
            'hominid=hominid.hominid:main',
            'hominid_sort_results=hominid.sort_results:main',
            'hominid_stability_selection=hominid.stability_selection:main',
            'hominid_box_bar_plot=hominid.box_bar_plot:main'
        ],
    },
)
@@ -487,16 +487,89 @@
 read()%0A%0A
+with open('requirements.txt') as f:%0A    requirements = f.read().split()%0A%0A
 setup(%0A 
@@ -814,17 +814,17 @@
 sion='1.
-0
+1
 .0',%0A%0A  
@@ -1136,26 +1136,12 @@
 ail=
-'lynch197@umn.edu'
+None
 ,%0A%0A 
@@ -1904,104 +1904,8 @@
 th.%0A
-        'Programming Language :: Python :: 2',%0A        'Programming Language :: Python :: 2.7',%0A
     
@@ -2672,160 +2672,20 @@
 res=
-%5B%0A        'numpy',%0A        'pandas',%0A        'scipy',%0A        'scikit-learn',%0A        'scikits.bootstrap',%0A        'statsmodels',%0A        'mpi4py'%0A    %5D
+requirements
 ,%0A%0A 

update version to 1.1.0