def configuration(parent_package="", top_path=None):
    config = Configuration("math", parent_package, top_path)
    config.add_subpackage("test")
    config.add_subpackage("fit")

    # =====================================
    # histogramnd
    # =====================================
    histo_dir = "histogramnd"
    histo_src = [os.path.join(histo_dir, srcf) for srcf in ["chistogramnd.pyx", "src/histogramnd_c.c"]]
    histo_inc = [os.path.join(histo_dir, "include"), numpy.get_include()]

    config.add_extension("chistogramnd", sources=histo_src, include_dirs=histo_inc, language="c")
    # =====================================
    # =====================================

    # =====================================
    # histogramnd_lut
    # =====================================
    histo_dir = "histogramnd"
    histo_src = [os.path.join(histo_dir, srcf) for srcf in ["chistogramnd_lut.pyx"]]
    histo_inc = [os.path.join(histo_dir, "include"), numpy.get_include()]

    config.add_extension("chistogramnd_lut", sources=histo_src, include_dirs=histo_inc, language="c")
    # =====================================
    # =====================================

    # marching cubes
    mc_dir = "marchingcubes"
    mc_src = [os.path.join(mc_dir, srcf) for srcf in ["marchingcubes.pyx", "mc_lut.cpp"]]
    config.add_extension("marchingcubes", sources=mc_src, include_dirs=[mc_dir, numpy.get_include()], language="c++")

    return config

 def initialize_options(self):
     from numpy import get_include
     _build_ext.initialize_options(self)
     if self.include_dirs is None:
         self.include_dirs = get_include()
     else:
         self.include_dirs += get_include()

def geometry_extensions():
    compiler_args = (compiler.compiler_args_sse2 + compiler.compiler_args_sse3 + compiler.compiler_args_sse41 +
                     compiler.compiler_args_opt + compiler.compiler_args_sse41)
    define_macros = compiler.define_macros_sse41

    return [
        Extension('mdtraj.geometry._geometry',
            sources=['MDTraj/geometry/src/geometry.c',
                     'MDTraj/geometry/src/sasa.c',
                     'MDTraj/geometry/src/dssp.cpp',
                     'MDTraj/geometry/src/_geometry.pyx'],
            include_dirs=['MDTraj/geometry/include',
                          'MDTraj/geometry/src/kernels',
                          numpy.get_include()],
            define_macros=define_macros,
            extra_compile_args=compiler_args,
            libraries=extra_cpp_libraries,
            language='c++'),
        Extension('mdtraj.geometry.drid',
            sources=["MDTraj/geometry/drid.pyx",
                     "MDTraj/geometry/src/dridkernels.c",
                     "MDTraj/geometry/src/cephes/cbrt.c",
                     "MDTraj/geometry/src/cephes/isnan.c",
                     "MDTraj/geometry/src/moments.c"],
            include_dirs=["MDTraj/geometry/include",
                          "MDTraj/geometry/include/cephes",
                          numpy.get_include()],
            define_macros=define_macros,
            extra_compile_args=compiler_args)
        ]

def configuration(parent_package='', top_path=None):
    import numpy
    from numpy.distutils.misc_util import Configuration

    config = Configuration('neighbors', parent_package, top_path)
    libraries = []
    if os.name == 'posix':
        libraries.append('m')

    config.add_extension('ball_tree',
                         sources=['ball_tree.c'],
                         include_dirs=[numpy.get_include()],
                         libraries=libraries)

    config.add_extension('kd_tree',
                         sources=['kd_tree.c'],
                         include_dirs=[numpy.get_include()],
                         libraries=libraries)

    config.add_extension('dist_metrics',
                         sources=['dist_metrics.c'],
                         include_dirs=[numpy.get_include(),
                                       os.path.join(numpy.get_include(),
                                                    'numpy')],
                         libraries=libraries)

    config.add_extension('typedefs',
                         sources=['typedefs.c'],
                         include_dirs=[numpy.get_include()],
                         libraries=libraries)

    config.add_subpackage('tests')

    return config

def configuration(parent_package="", top_path=None):
    config = Configuration("tree", parent_package, top_path)
    libraries = []
    if os.name == 'posix':
        libraries.append('m')
        
    # check for pre-compiled versions for the encountered sklearn version
    if not os.path.isdir("{}/headers/{}".format(os.path.dirname(os.path.realpath(__file__)), sklearn.__version__)) or \
       not os.path.isfile("{}/headers/{}/_tree.c".format(os.path.dirname(os.path.realpath(__file__)), sklearn.__version__)):
        raise Exception(\
"""sklearnef holds no pre-compiled _tree.c for your current scikit-learn version ({version}).
Please download the corresponding header file from \
https://raw.githubusercontent.com/scikit-learn/scikit-learn/{version}/sklearn/tree/_tree.pxd,
place it in sklearnef/tree/headers/sklearn/tree/ and compile _tree.pyx with cython using \
'cython _tree.pyx -o headers/{version}/_tree.c -I headers/'. Then re-run \
the installation of sklearnef.""".format(version=sklearn.__version__))

    config.add_extension("_diffentropy",
                         sources=["headers/_diffentropy.c"],
                         include_dirs=[numpy.get_include()],
                         libraries=libraries + ['lapack', 'blas'],
                         extra_compile_args=["-O3"])

    config.add_extension("_tree",
                         sources=["headers/{version}/_tree.c".format(version=sklearn.__version__)],
                         include_dirs=[numpy.get_include()],
                         libraries=libraries,
                         extra_compile_args=["-O3"])
    
    config.add_subpackage("tests")

    return config

def configuration(parent_package='', top_path=None):
    from numpy.distutils.misc_util import Configuration

    cblas_libs, blas_info = get_blas_info()

    libraries = []
    if os.name == 'posix':
        cblas_libs.append('m')
        libraries.append('m')

    config = Configuration('cluster', parent_package, top_path)
    config.add_extension('_hierarchical',
                         sources=['_hierarchical.c'],
                         include_dirs=[numpy.get_include()],
                         libraries=libraries)

    config.add_extension(
        '_k_means',
        libraries=cblas_libs,
        sources=['_k_means.c'],
        include_dirs=[join('..', 'src', 'cblas'),
                      numpy.get_include(),
                      blas_info.pop('include_dirs', [])],
        extra_compile_args=blas_info.pop('extra_compile_args', []),
        **blas_info
    )
    return config

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 configuration(parent_package='', top_path=None):
    import numpy
    from numpy.distutils.misc_util import Configuration

    config = Configuration('utils', parent_package, top_path)
    config.add_subpackage('sparsetools')

    cblas_libs, blas_info = get_blas_info()

    libraries = []
    if os.name == 'posix':
        libraries.append('m')
        cblas_libs.append('m')

    config.add_extension('arraybuilder', sources=['arraybuilder.c'])

    config.add_extension('sparsefuncs', sources=['sparsefuncs.c'],
                         libraries=libraries)

    config.add_extension('arrayfuncs',
                         sources=['arrayfuncs.c'],
                         depends=[join('src', 'cholesky_delete.h')],
                         libraries=cblas_libs,
                         include_dirs=[join('..', 'src', 'cblas'),
                                       numpy.get_include(),
                                       blas_info.pop('include_dirs', [])],
                         extra_compile_args=blas_info.pop('extra_compile_args',
                                                          []),
                         **blas_info
                         )

    config.add_extension(
        'murmurhash',
        sources=['murmurhash.c', join('src', 'MurmurHash3.cpp')],
        include_dirs=['src'])

    config.add_extension('lgamma',
                         sources=['lgamma.cpp', join('src', 'Gamma.cpp')],
                         include_dirs=['src'],
                         libraries=libraries)

    config.add_extension('graph_shortest_path',
                         sources=['graph_shortest_path.c'],
                         include_dirs=[numpy.get_include()])

    config.add_extension('seq_dataset',
                         sources=['seq_dataset.c'],
                         include_dirs=[numpy.get_include()])

    config.add_extension('weight_vector',
                         sources=['weight_vector.c'],
                         include_dirs=[numpy.get_include()],
                         libraries=libraries)

    config.add_extension("random",
                         sources=["random.c"],
                         include_dirs=[numpy.get_include()],
                         libraries=libraries)

    return config

def configuration(parent_package='', top_path=None):
    from numpy.distutils.misc_util import Configuration

    config = Configuration('linear_model', parent_package, top_path)

    cblas_libs, blas_info = get_blas_info()

    libraries = []
    if os.name == 'posix':
        cblas_libs.append('m')
        libraries.append('m')

    config.add_extension('cd_fast',
         sources=['cd_fast.c'],
         libraries=cblas_libs,
         include_dirs=[join('..', 'src', 'cblas'),
                       numpy.get_include(),
                       blas_info.pop('include_dirs', [])],
         extra_compile_args=blas_info.pop('extra_compile_args', []),
         **blas_info
         )

    config.add_extension('sgd_fast',
         sources=['sgd_fast.c'],
         include_dirs=[numpy.get_include()],
         libraries=libraries,
         )

    # add other directories
    config.add_subpackage('tests')

    return config

def configuration(parent_package='', top_path=None):
    from numpy.distutils.misc_util import Configuration
    from numpy.distutils.system_info import get_info, BlasNotFoundError
    config = Configuration('map', parent_package, top_path)
    config.add_data_dir('tests')
    libraries = []
    if os.name == 'posix':
        libraries.append('m')

    config.add_extension('ball_tree',
                         sources=['ball_tree.c'],
                         include_dirs=[numpy.get_include()],
                         libraries=libraries)

    config.add_extension('ckdtree',
                         sources=['ckdtree.c'],
                         include_dirs=[numpy.get_include()],
                         libraries=libraries)

    config.add_extension('_load_nn_field_data',
                         sources=['_load_nn_field_data.c'],
                         include_dirs=[numpy.get_include()])

    config.add_extension('_gate_to_grid_map',
                         sources=['_gate_to_grid_map.c'],
                         libraries=libraries)

    return config

def configuration(parent_package='', top_path=None):
    from numpy.distutils.misc_util import Configuration

    config = Configuration('lightning', parent_package, top_path)

    randomdir = os.path.join(top_path, "lightning", "random")

    config.add_extension('dataset_fast',
                         sources=['dataset_fast.cpp'],
                         include_dirs=[numpy.get_include(), randomdir])

    config.add_extension('dual_cd_fast',
                         sources=['dual_cd_fast.cpp'],
                         include_dirs=[numpy.get_include(), randomdir])

    config.add_extension('loss_fast',
                         sources=['loss_fast.cpp'],
                         include_dirs=[numpy.get_include(), randomdir])

    config.add_extension('primal_cd_fast',
                         sources=['primal_cd_fast.cpp'],
                         include_dirs=[numpy.get_include(), randomdir])

    config.add_extension('sgd_fast',
                         sources=['sgd_fast.cpp'],
                         include_dirs=[numpy.get_include(), randomdir])

    config.add_subpackage('random')
    config.add_subpackage('tests')
    config.add_subpackage('datasets')

    return config

def make_extension_modules(mode="disable_threads", nfft_library_dirs=[], nfft_include_dirs=[]):

    ext_icosahedron = Extension(
        "condor.utils.icosahedron",
        sources=["src/utils/icosahedron/icosahedronmodule.c"],
        include_dirs=[numpy.get_include()],
    )

    _nfft_libraries = {
        "disable_threads": ["nfft3"],
        "enable_threads": ["nfft3_threads" ,"fftw3_threads" ,"fftw3"]
    }
    _nfft_macros = {
        "disable_threads" : [],
        "enable_threads" : [("ENABLE_THREADS", None)],
    }
    
    ext_nfft = Extension(
        "condor.utils.nfft",
        sources=["src/utils/nfft/nfftmodule.c"],
        library_dirs=nfft_library_dirs,
        libraries=_nfft_libraries[mode],
        include_dirs=[numpy.get_include()] + nfft_include_dirs,
        define_macros=_nfft_macros[mode],
        runtime_library_dirs = nfft_library_dirs,
        extra_link_args = [] if (nfft_library_dirs == []) else ['-Wl,-rpath,'+nfft_library_dirs[0]+',-L'+nfft_library_dirs[0]],
    )

    return [ext_icosahedron, ext_nfft]

def extensions():
    __builtins__.__NUMPY_SETUP__ = False
    import numpy as np
    ext_modules = [
        Extension(
            'pysas.world',
            ["pysas/world.pyx"] + glob("lib/world/*.cpp"),
            include_dirs=['lib/world', np.get_include()],
            extra_compile_args=["-O3"],
            language="c++",
        ),
        Extension(
            'pysas.mcep',
            ["pysas/mcep.pyx"],
            include_dirs=[np.get_include()],
            extra_compile_args=["-O3"],
            language="c++",
        ),
        Extension(
            'pysas.excite',
            ["pysas/excite.pyx"],
            include_dirs=[np.get_include()],
            extra_compile_args=["-O3"],
            language="c++",
        ),
        Extension(
            'pysas.synthesis.mlsa',
            ["pysas/synthesis/mlsa.pyx"],
            include_dirs=[np.get_include()],
            extra_compile_args=["-O3"],
            language="c++",
        )
    ]
    return ext_modules

def configuration(parent_package='', top_path=None):
    from numpy.distutils.misc_util import Configuration
    from numpy.distutils.system_info import get_info, BlasNotFoundError

    config = Configuration('pyLLE', parent_package, top_path)

    config.add_subpackage('python_only')

    config.add_extension('ball_tree',
                         language='c++',
                         sources=[join('wrappers', 'ball_tree.cpp')],
                         depends=[join('include', 'BallTree.h'),
                                  join('include', 'BallTreePoint.h')],
                         include_dirs=['include',numpy.get_include()])
    
    config.add_extension('LLE',
                         language='c++',
                         sources=[join('wrappers','LLE.cpp')]\
                             + MatVec_sources + LLE_sources,
                         libraries=['stdc++','blas','lapack','arpack'],
                         library_dirs = LIBS,
                         include_dirs=['include','lib/MatVec',
                                       numpy.get_include()] )
                         

    return config

def main():

    ext_modules = [

        Extension("lz4.lz4",
                  sources=["lz4/lz4.pyx", os.path.join(c_src_dir, 'lz4.c')],
                  include_dirs=[np.get_include(), c_src_dir],
                  define_macros=[],
                  extra_link_args=[],
                  extra_compile_args=['-mssse3', '-std=c99']),

        Extension("lz4.shuffle",
                  sources=["lz4/shuffle.pyx"],
                  include_dirs=[np.get_include()],
                  define_macros=[],
                  extra_link_args=[],
                  extra_compile_args=['-mssse3', '-std=c99']),

                  ]

    kwargs = dict(
        name = 'lz4',
        packages = ['lz4'],
        cmdclass = {'build_ext': build_ext},
        ext_modules = cythonize(ext_modules),
        )

    setup(**kwargs)

def main():
    packages = ['disvis', 'disvis.IO']
    requirements = ['numpy']

    ext = '.pyx' if CYTHON else '.c'
    ext_modules = [Extension("disvis.libdisvis",
                      [join("src", "libdisvis" + ext)],
                      include_dirs = [numpy.get_include()],
                  )]

    cmdclass = {}
    if CYTHON:
        ext_modules = cythonize(ext_modules)
        cmdclass = {'build_ext' : build_ext}

    package_data = {'disvis': [join('data', '*.npy'), 
                               join('kernels', '*.cl')]}

    scripts = [join('scripts', 'disvis')]

    setup(name="disvis",
          version='1.0.1',
          description='Quantifying and visualizing the interaction space of distance-constrainted macromolecular complexes',
          author='Gydo C.P. van Zundert',
          author_email='[email protected]',
          packages=packages,
          cmdclass=cmdclass,
          ext_modules=ext_modules,
          package_data=package_data,
          scripts=scripts,
          requires=requirements,
          include_dirs=[numpy.get_include()],
         )

def configuration(parent_package='', top_path=None):
    from numpy.distutils.misc_util import Configuration
    from numpy.distutils.system_info import get_info, BlasNotFoundError
    config = Configuration('io', parent_package, top_path)
    config.add_data_dir('tests')

    # determine and verify the at RSL location
    rsl_path = os.environ.get('RSL_PATH')
    if rsl_path is None:
        rsl_path = guess_rsl_path()
    rsl_lib_path = os.path.join(rsl_path, 'lib')
    rsl_include_path = os.path.join(rsl_path, 'include')

    # build the RSL interface if RSL is installed
    if check_rsl_path(rsl_lib_path, rsl_include_path):
        config.add_extension(
            '_rsl_interface',
            sources=['_rsl_interface.c'],
            libraries=['rsl'],
            library_dirs=[rsl_lib_path],
            include_dirs=[rsl_include_path] + [get_include()],
            runtime_library_dirs=[rsl_lib_path])
    else:
        import warnings
        warnings.warn(RSL_MISSING_WARNING % (rsl_path))

    config.add_extension('_sigmetfile',
                         sources=['_sigmetfile.c'],
                         include_dirs=[get_include()])

    config.add_extension('nexrad_interpolate',
                         sources=['nexrad_interpolate.c'],
                         include_dirs=[get_include()])

    return config

def configuration(parent_package='', top_path=None):
    from numpy.distutils.misc_util import Configuration

    config = Configuration('impl', parent_package, top_path)

    cblas_libs, blas_info = get_blas_info()

    config.add_extension('dataset_fast',
                         sources=['dataset_fast.c'],
                         include_dirs=[numpy.get_include()])

    config.add_extension('matrix_fact_fast',
                         sources=['matrix_fact_fast.c'],
                         include_dirs=[numpy.get_include()])

    config.add_extension('preprocessing_fast',
                         sources=['preprocessing_fast.c'],
                         include_dirs=[numpy.get_include()])

    config.add_extension('dict_fact_fast',
                         sources=['dict_fact_fast.c'],
                         include_dirs=[numpy.get_include()])

    config.add_extension('dict_fact_fast_partial',
                         sources=['dict_fact_fast_partial.c'],
                         include_dirs=[numpy.get_include()])

    config.add_subpackage('tests')

    return config

def main():
  setup(name             = 'glu',
        version          = get_version(),
        author           = 'Kevin Jacobs',
        author_email     = '[email protected]',
        maintainer       = 'Kevin Jacobs',
        maintainer_email = '[email protected]',
        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'],
                     } )

def configuration(parent_package='', top_path=None):
    from numpy.distutils.misc_util import Configuration

    libraries = []
    if os.name == 'posix':
        libraries.append('m')

    config = Configuration('cluster', parent_package, top_path)
    config.add_extension('_dbscan_inner',
                         sources=['_dbscan_inner.pyx'],
                         include_dirs=[numpy.get_include()],
                         language="c++")

    config.add_extension('_hierarchical',
                         sources=['_hierarchical.pyx'],
                         language="c++",
                         include_dirs=[numpy.get_include()],
                         libraries=libraries)

    config.add_extension('_k_means_elkan',
                         sources=['_k_means_elkan.pyx'],
                         include_dirs=[numpy.get_include()],
                         libraries=libraries)

    config.add_extension('_k_means',
                         sources=['_k_means.pyx'],
                         include_dirs=numpy.get_include(),
                         libraries=libraries)

    config.add_subpackage('tests')

    return config