setup.py

#!/usr/bin/env python
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
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#
#   See COPYING file distributed along with the PyMVPA package for the
#   copyright and license terms.
#
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"""Python distutils setup for PyMVPA"""

from numpy.distutils.core import setup, Extension
import fnmatch
import glob
import os
import sys


if sys.version_info[:2] < (2, 6):
    raise RuntimeError("PyMVPA requires Python 2.6 or higher")

# some config settings
bind_libsvm = 'local' # choices: 'local', 'system', None

libsvmc_extra_sources = []
libsvmc_include_dirs = []
libsvmc_libraries = []

extra_link_args = []
libsvmc_library_dirs = []

requires = {
    'core': [
        'scipy',
        'nibabel'
    ]
}

# platform-specific settings
if sys.platform == "darwin":
    extra_link_args.append("-bundle")

if sys.platform.startswith('linux'):
    # need to look for numpy (header location changes with v1.3)
    from numpy.distutils.misc_util import get_numpy_include_dirs
    libsvmc_include_dirs += get_numpy_include_dirs()

# when libsvm is forced -- before it was used only in cases
# when libsvm was available at system level, hence we switch
# from local to system at this point
# TODO: Deprecate --with-libsvm for 0.5
for arg in ('--with-libsvm', '--with-system-libsvm'):
    if not sys.argv.count(arg):
        continue
    # clean argv if necessary (or distutils will complain)
    sys.argv.remove(arg)
    # assure since default is 'auto' wouldn't fail if it is N/A
    bind_libsvm = 'system'

# when no libsvm bindings are requested explicitly
if sys.argv.count('--no-libsvm'):
    # clean argv if necessary (or distutils will complain)
    sys.argv.remove('--no-libsvm')
    bind_libsvm = None

# if requested:
if bind_libsvm == 'local':
    # we will provide libsvm sources later on # if libsvm.a is available locally -- use it
    #if os.path.exists(os.path.join('build', 'libsvm', 'libsvm.a')):
    libsvm_3rd_path = os.path.join('3rd', 'libsvm')
    libsvmc_include_dirs += [libsvm_3rd_path]
    libsvmc_extra_sources = [os.path.join(libsvm_3rd_path, 'svm.cpp')]
elif bind_libsvm == 'system':
    # look for libsvm in some places, when local one is not used
    libsvmc_libraries += ['svm']
    if not sys.platform.startswith('win'):
        libsvmc_include_dirs += [
            '/usr/include/libsvm-3.0/libsvm',
            '/usr/include/libsvm-2.0/libsvm',
            '/usr/include/libsvm',
            '/usr/local/include/libsvm',
            '/usr/local/include/libsvm-2.0/libsvm',
            '/usr/local/include']
    else:
        # no clue on windows
        pass
elif bind_libsvm is None:
    pass
else:
    raise ValueError("Shouldn't happen that we get bind_libsvm=%r"
                     % (bind_libsvm,))


# define the extension modules
libsvmc_ext = Extension(
    'mvpa2.clfs.libsvmc._svmc',
    sources=libsvmc_extra_sources + [os.path.join('mvpa2', 'clfs', 'libsvmc', 'svmc.i')],
    include_dirs=libsvmc_include_dirs,
    library_dirs=libsvmc_library_dirs,
    libraries=libsvmc_libraries,
    language='c++',
    extra_link_args=extra_link_args,
    swig_opts=['-I' + d for d in libsvmc_include_dirs])

smlrc_ext = Extension(
    'mvpa2.clfs.libsmlrc.smlrc',
    sources=[ os.path.join('mvpa2', 'clfs', 'libsmlrc', 'smlr.c') ],
    #library_dirs = library_dirs,
    libraries=['m'] if not sys.platform.startswith('win') else [],
    # extra_compile_args = ['-O0'],
    extra_link_args=extra_link_args,
    language='c')

ext_modules = [smlrc_ext]

if bind_libsvm:
    ext_modules.append(libsvmc_ext)

# Notes on the setup
# Version scheme is: major.minor.patch<suffix>

def get_full_dir(path):
    path_split = path.split(os.path.sep) # so we could run setup.py on any platform
    path_proper = os.path.join(*path_split)
    return (path_proper,
            [f for f in glob.glob(os.path.join(path_proper, '*'))
             if os.path.isfile(f)])

# borrowed from https://wiki.python.org/moin/Distutils/Tutorial
## Code borrowed from wxPython's setup and config files
## Thanks to Robin Dunn for the suggestion.
## I am not 100% sure what's going on, but it works!
def opj(*args):
    path = os.path.join(*args)
    return os.path.normpath(path)

def find_data_files(srcdir, *wildcards, **kw):
    # get a list of all files under the srcdir matching wildcards,
    # returned in a format to be used for install_data
    file_list = []
    recursive = kw.get('recursive', True)
    for d, dirs, files in os.walk(srcdir, topdown=True):
        for wc in wildcards:
            files_ = [opj(d, x) for x in fnmatch.filter(files, wc)]
            if files_:
                file_list.append((d, files_))
        if not recursive:
            break # one would be enough ;)

    return file_list

# define the setup
def setup_package():
    # Perform 2to3 if needed
    local_path = os.path.dirname(os.path.abspath(sys.argv[0]))
    src_path = local_path
    if sys.version_info[0] == 3:
        src_path = os.path.join(local_path, 'build', 'py3k')
        import py3tool
        print("Converting to Python3 via 2to3...")
        py3tool.sync_2to3('mvpa2', os.path.join(src_path, 'mvpa2'))
        py3tool.sync_2to3('3rd', os.path.join(src_path, '3rd'))

        # Borrowed from NumPy before this code was deprecated (everyone
        # else moved on from 2to3)
        # Ugly hack to make pip work with Python 3, see NumPy #1857.
        # Explanation: pip messes with __file__ which interacts badly with the
        # change in directory due to the 2to3 conversion.  Therefore we restore
        # __file__ to what it would have been otherwise.
        global __file__
        __file__ = os.path.join(os.curdir, os.path.basename(__file__))
        if '--egg-base' in sys.argv:
            # Change pip-egg-info entry to absolute path, so pip can find it
            # after changing directory.
            idx = sys.argv.index('--egg-base')
            if sys.argv[idx + 1] == 'pip-egg-info':
                sys.argv[idx + 1] = os.path.join(local_path, 'pip-egg-info')

    # Run build
    os.chdir(src_path)
    sys.path.insert(0, src_path)

    setup(name='pymvpa2',
          version='2.6.5.dev1',
          author='Michael Hanke, Yaroslav Halchenko, Nikolaas N. Oosterhof',
          author_email='pkg-exppsy-pymvpa@lists.alioth.debian.org',
          license='MIT License',
          url='http://www.pymvpa.org',
          description='Multivariate pattern analysis',
          long_description=
              "PyMVPA is a Python module intended to ease pattern classification "
              "analyses of large datasets. It provides high-level abstraction of "
              "typical processing steps and a number of implementations of some "
              "popular algorithms. While it is not limited to neuroimaging data "
              "it is eminently suited for such datasets.\n"
              "PyMVPA is truly free software (in every respect) and "
              "additionally requires nothing but free-software to run.",
          setup_requires=['numpy'],
          # please maintain alphanumeric order
          packages=[ 'mvpa2',
                     'mvpa2.algorithms',
                     'mvpa2.algorithms.benchmarks',
                     'mvpa2.atlases',
                     'mvpa2.base',
                     'mvpa2.clfs',
                     'mvpa2.clfs.libsmlrc',
                     'mvpa2.clfs.libsvmc',
                     'mvpa2.clfs.skl',
                     'mvpa2.clfs.sg',
                     'mvpa2.cmdline',
                     'mvpa2.datasets',
                     'mvpa2.datasets.sources',
                     'mvpa2.featsel',
                     'mvpa2.kernels',
                     'mvpa2.mappers',
                     'mvpa2.mappers.glm',
                     'mvpa2.generators',
                     'mvpa2.measures',
                     'mvpa2.misc',
                     'mvpa2.misc.bv',
                     'mvpa2.misc.fsl',
                     'mvpa2.misc.io',
                     'mvpa2.misc.plot',
                     'mvpa2.misc.surfing',
                     'mvpa2.sandbox',
                     'mvpa2.support',
                     'mvpa2.support.afni',
                     'mvpa2.support.bayes',
                     'mvpa2.support.nipy',
                     'mvpa2.support.ipython',
                     'mvpa2.support.nibabel',
                     'mvpa2.support.scipy',
                     'mvpa2.testing',
                     'mvpa2.tests',
                     'mvpa2.tests.badexternals',
                     'mvpa2.viz',
                   ],
          install_requires=requires['core'],
          data_files=[('mvpa2', [os.path.join('mvpa2', 'COMMIT_HASH')])]
                     + find_data_files(os.path.join('mvpa2', 'data'),
                                       '*.txt', '*.nii.gz', '*.rtc', 'README', '*.bin',
                                       '*.dat', '*.dat.gz', '*.mat', '*.fsf', '*.par'),
          scripts=glob.glob(os.path.join('bin', '*')),
          ext_modules=ext_modules
          )


if __name__ == '__main__':
    setup_package()