from setuptools import setup, Extension
from Cython.Distutils import build_ext
from Cython.Build import cythonize


ext_modules = cythonize(Extension("ndmg.graph.zindex", # the extension name
                                  sources=["ndmg/graph/zindex.pyx"],
                                  include_dirs=['.'],
                                  language="c"))
VERSION="0.1.1"

setup(
    name='ndmg',
    ext_modules = ext_modules,
    packages=[
        'ndmg',
        'ndmg.preproc',
        'ndmg.register',
        'ndmg.track',
        'ndmg.graph',
        'ndmg.stats',
        'ndmg.utils',
        'ndmg.timeseries',
        'ndmg.nuis',
        'ndmg.scripts'
    ],
    version=VERSION,
    entry_points = {
        'console_scripts': [
            'ndmg_dwi_pipeline=ndmg.scripts.ndmg_dwi_pipeline:main',
            'ndmg_func_pipeline=ndmg.scripts.ndmg_func_pipeline:main',
            'ndmg_bids=ndmg.scripts.ndmg_bids:main',
            'ndmg_cloud=ndmg.scripts.ndmg_cloud:main'
    ]
    },
    description='Neuro Data MRI to Graphs Pipeline',
    author='Greg Kiar, Will Gray Roncal and Eric Bridgeford',
    author_email='gkiar@jhu.edu, wgr@jhu.edu, ebridge2@jhu.edu',
    url='https://github.com/neurodata/ndmg',
    download_url='https://github.com/neurodata/ndmg/tarball/' + VERSION,
    keywords=[
        'connectome',
        'mri',
        'pipeline'
    ],
    classifiers=[],
    install_requires=[  # We didnt put versions for numpy, scipy, b/c travis-ci
        'networkx',
        'nibabel',
        'nilearn',
        'sklearn',
        'numpy',  # We use nump v1.10.4
        'scipy>=0.13.3',  # We use 0.17.0
        'dipy',
        'boto3',
        'matplotlib',
        'plotly==1.12.1',
        'cython',
        'pybids==0.6.4',
	'duecredit'
    ]
)

@@ -163,16 +163,17 @@
 zindex%22,
+ 
  # the e
@@ -186,16 +186,16 @@
 on name%0A
-
         
@@ -365,17 +365,19 @@
 %0AVERSION
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+ = 
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@@ -416,19 +416,17 @@
 _modules
- = 
+=
 ext_modu
@@ -713,19 +713,17 @@
 y_points
- = 
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 %7B%0A      
@@ -992,22 +992,26 @@
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@@ -1772,9 +1772,16 @@
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format setup.py to black