setup.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# To use:
#       python setup.py install
#

import os
import sys

try:
  try:
    import setuptools

  except ImportError:
    import distribute_setup
    distribute_setup.use_setuptools()

except ImportError:
  import ez_setup
  ez_setup.use_setuptools()


# minimum versions required
requires = ['numpy>=1.3', 'scipy>=0.7', 'tables>=2.1.2', 'ply>=2.5']

min_python_version = (2,7)
min_cython_version = '1.4'
min_numpy_version  = '1.3'
min_scipy_version  = '0.7'
min_tables_version = '2.1.2'
min_h5py_version   = '1.2.1'
min_ply_version    = '2.5'
min_nose_version   = '1.0.0'


if sys.version_info < min_python_version:
  version_str = '.'.join( map(str,min_python_version) )
  sys.stderr.write('Python %s or newer to required to install and run GLU!\n' % version_str)
  sys.exit(1)


import numpy as np

from   setuptools           import find_packages, Extension
from   numpy.distutils.core import setup


def get_version():
  vfile = os.path.join(os.path.dirname(__file__), 'glu', 'VERSION')
  version = file(vfile).readline().strip()
  return version


classifiers = '''\
Development Status :: 5 - Production/Stable
Home-page: http://code.google.com/p/glu-genetics/
Intended Audience :: Developers
Intended Audience :: Information Technology
Intended Audience :: Science/Research
License :: OSI Approved :: BSD License
Programming Language :: Python :: 2.7
Programming Language :: C
Programming Language :: Fortran
Topic :: Scientific/Engineering
Topic :: Software Development
Topic :: Database
Topic :: Software Development :: Libraries :: Python Modules
Operating System :: Unix
Operating System :: POSIX
Operating System :: MacOS :: MacOS X
Operating System :: Microsoft :: Windows
'''

def glmnet_config():
  from numpy.distutils.misc_util import Configuration
  config = Configuration('glm', 'glu.lib')
  return config.add_extension('_glmnet', sources=['glu/lib/glm/glmnet.pyf','glu/lib/glm/GLMnet.f'])


def cython_modules():
  try:
    from Cython.Build import cythonize

    ext = [
            Extension('glu.lib._illumina',              sources = ['glu/lib/_illumina.pyx']),
            Extension('glu.lib.genolib.helpers',        sources = ['glu/lib/genolib/helpers.pyx'],
                                                   include_dirs = [np.get_include()]),
            Extension('glu.lib.seqlib._cigar',          sources = ['glu/lib/seqlib/_cigar.pyx']),
            Extension('glu.lib.seqlib._edits',          sources = ['glu/lib/seqlib/_edits.pyx']),
            Extension('glu.lib.seqlib.gc',              sources = ['glu/lib/seqlib/gc.pyx']),
            Extension('glu.lib.seqlib.intervaltree',    sources = ['glu/lib/seqlib/intervaltree.pyx']),
          ]

    ext = cythonize(ext)

  # Fall back to using pre-generated C files
  except ImportError:
    ext = [
            Extension('glu.lib._illumina',              sources = ['glu/lib/_illumina.c']),
            Extension('glu.lib.genolib.helpers',        sources = ['glu/lib/genolib/helpers.c'],
                                                   include_dirs = [np.get_include()]),
            Extension('glu.lib.seqlib._cigar',          sources = ['glu/lib/seqlib/_cigar.c']),
            Extension('glu.lib.seqlib._edits',          sources = ['glu/lib/seqlib/_edits.c']),
            Extension('glu.lib.seqlib.gc',              sources = ['glu/lib/seqlib/gc.c']),
            Extension('glu.lib.seqlib.intervaltree',    sources = ['glu/lib/seqlib/intervaltree.c']),
          ]

  return ext


def main():
  setup(name             = 'glu',
        version          = get_version(),
        author           = 'Kevin Jacobs',
        author_email     = 'jacobske@mail.nih.gov',
        maintainer       = 'Kevin Jacobs',
        maintainer_email = 'jacobske@mail.nih.gov',
        platforms        = ['any'],
        description      = 'Genotype Library and Utilities (GLU)',
        long_description = ('Genotype Library and Utilities (GLU): Tools for the management of large '
                            'amounts of SNP genotype data and programs to check its quality and to '
                            'test for association between SNP markers with continuous or discrete '
                            'trait phenotypes.'),
        classifiers      = filter(None, classifiers.split('\n')),
        install_requires = requires,
        packages         = find_packages(),
        include_package_data = True,
        scripts          = ['bin/glu'],
        zip_safe         = False,
        test_suite       = 'nose.collector',
        ext_modules = [
                        Extension('glu.lib.genolib.bitarrayc',      sources = ['glu/lib/genolib/bitarrayc.c']),
                        Extension('glu.lib.genolib._genoarray',     sources = ['glu/lib/genolib/_genoarray.c',
                                                                               'glu/lib/genolib/bitarrayc.c',
                                                                               'glu/lib/genolib/_ibs.c',
                                                                               'glu/lib/genolib/_ld.c'],
                                                               include_dirs = [np.get_include()]),
                        Extension('glu.modules.struct._admix',      sources = ['glu/modules/struct/_admix.c'],
                                                               include_dirs = [np.get_include()]),
                        Extension('glu.modules.ld.pqueue',          sources = ['glu/modules/ld/pqueue.c']),
                        glmnet_config(),
                      ] + cython_modules(),
        entry_points={ 'console_scripts'    : ['glu = glu.lib.glu_launcher:main'],
                     } )


if __name__ == '__main__':
  main()