setup.py

#!/usr/bin/env python

"""Connectome Mapper
"""
from glob import glob
import os
import sys
if os.path.exists('MANIFEST'): os.remove('MANIFEST')

packages=["cmp",
          "cmp.stages",
          "cmp.stages.connectionmatrix",
          "cmp.stages.converter",
          "cmp.stages.preprocessing",
          "cmp.stages.postprocessing",
          "cmp.stages.segmentation",
          "cmp.stages.reconstruction",
          "cmp.stages.parcellation",
          "cmp.stages.registration",
          "cmp.stages.tractography",
          "cmp.stages.rsfmri",
          "cmp.stages.stats",
          "cmp.stages.template_module",
          "cmp.pipeline"]

package_data = {'cmp':
                ['data/colortable_and_gcs/*.txt',
                 'data/colortable_and_gcs/my_atlas_gcs/*.gcs',
                 'pipeline/pipeline.proto',
                 'binary/linux2/bit32/*',
                 'binary/linux2/bit32/*.*',
                 'binary/linux2/bit64/*.*',
                 'binary/linux2/bit64/*',
                 'data/diffusion/gradient_tables/*.txt',
                 'data/diffusion/odf_directions/*.*',
                 'data/parcellation/lausanne2008/*.*',
                 'data/parcellation/lausanne2008/resolution83/*.*',
                 'data/parcellation/lausanne2008/resolution150/*.*',
                 'data/parcellation/lausanne2008/resolution258/*.*',
                 'data/parcellation/lausanne2008/resolution500/*.*',
                 'data/parcellation/lausanne2008/resolution1015/*.*',
                 'data/parcellation/nativefreesurfer/freesurferaparc/*.*',
                 ]}

################################################################################
# For some commands, use setuptools

if len(set(('develop', 'bdist_egg', 'bdist_rpm', 'bdist', 'bdist_dumb', 
            'bdist_wininst', 'install_egg_info', 'egg_info', 'easy_install',
            )).intersection(sys.argv)) > 0:
    from setup_egg import extra_setuptools_args

# extra_setuptools_args can be defined from the line above, but it can
# also be defined here because setup.py has been exec'ed from
# setup_egg.py.
if not 'extra_setuptools_args' in globals():
    extra_setuptools_args = dict()
    

def main(**extra_args):
    from distutils.core import setup
    from cmp.info import __version__
    # regenerate protoc
    import subprocess
    protofname = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'cmp', 'pipeline', 'pipeline.proto')
    protoout = os.path.join(os.path.abspath(os.path.dirname(__file__)), 'cmp', 'pipeline')
    protopath = os.path.dirname(protofname)
    cmd = 'protoc %s --proto_path=%s --python_out=%s' % (protofname, protopath, protoout)
    print "Calling protoc to generate protobuf python file in current version:"
    print cmd
    process = subprocess.call( cmd, shell = True,
                                  stdout = subprocess.PIPE,
                                  stderr = subprocess.STDOUT )
    print "protoc return code:", process
    
    setup(name='Connectome Mapper',
          version=__version__,
          description="""Connectome Mapper implements a full diffusion MRI processing pipeline, from raw Diffusion/T1/T2 """ + \
          """data to multi-resolution connection matrices. It also offers support for resting state fMRI data processing and multi-resolution functional connection matrices creation. """ + \
          """The Connectome Mapper is part of the Connectome Mapping Toolkit.""",
          author='EPFL LTS5 Diffusion Group',
          author_email='info@connectomics.org',
          url='http://www.connectomics.org/',
          scripts = glob('scripts/*'),
          packages = packages,
          package_data = package_data,
          **extra_args
         )

if __name__ == "__main__":
    main(**extra_setuptools_args)