setup.py

#!/usr/bin/env python
''' Installation script for dipy package '''

import os
import sys
from copy import deepcopy
from os.path import join as pjoin, dirname, exists
from glob import glob

# BEFORE importing distutils, remove MANIFEST. distutils doesn't properly
# update it when the contents of directories change.
if exists('MANIFEST'): os.remove('MANIFEST')

# force_setuptools can be set from the setup_egg.py script
if not 'force_setuptools' in globals():
    # For some commands, always use setuptools
    if len(set(('develop', 'bdist_egg', 'bdist_rpm', 'bdist', 'bdist_dumb',
                'bdist_mpkg', 'bdist_wheel', 'install_egg_info', 'egg_info',
                'easy_install')).intersection(sys.argv)) > 0:
        force_setuptools = True
    else:
        force_setuptools = False

if force_setuptools:
    import setuptools

# Import distutils _after_ potential setuptools import above, and after removing
# MANIFEST
from distutils.core import setup
from distutils.extension import Extension

from cythexts import cyproc_exts, get_pyx_sdist
from setup_helpers import (install_scripts_bat, add_flag_checking,
                           SetupDependency, read_vars_from,
                           make_np_ext_builder)
from version_helpers import get_comrec_build

# Get version and release info, which is all stored in dipy/info.py
info = read_vars_from(pjoin('dipy', 'info.py'))

# We may just have imported setuptools, or we may have been exec'd from a
# setuptools environment like pip
using_setuptools = 'setuptools' in sys.modules
extra_setuptools_args = {}
if using_setuptools:
    # Try to preempt setuptools monkeypatching of Extension handling when Pyrex
    # is missing.  Otherwise the monkeypatched Extension will change .pyx
    # filenames to .c filenames, and we probably don't have the .c files.
    sys.path.insert(0, pjoin(dirname(__file__), 'fake_pyrex'))
    # Set setuptools extra arguments
    extra_setuptools_args = dict(
        tests_require=['nose'],
        test_suite='nose.collector',
        zip_safe=False,
        extras_require = dict(
            doc=['Sphinx>=1.0'],
            test=['nose>=0.10.1']))

# Define extensions
EXTS = []

# We use some defs from npymath, but we don't want to link against npymath lib
ext_kwargs = {'include_dirs':['src']}  # We add np.get_include() later

for modulename, other_sources, language in (
    ('dipy.reconst.peak_direction_getter', [], 'c'),
    ('dipy.reconst.recspeed', [], 'c'),
    ('dipy.reconst.vec_val_sum', [], 'c'),
    ('dipy.reconst.quick_squash', [], 'c'),
    ('dipy.tracking.distances', [], 'c'),
    ('dipy.tracking.streamlinespeed', [], 'c'),
    ('dipy.tracking.local.localtrack', [], 'c'),
    ('dipy.tracking.local.direction_getter', [], 'c'),
    ('dipy.tracking.local.tissue_classifier', [], 'c'),
    ('dipy.tracking.local.interpolation', [], 'c'),
    ('dipy.tracking.vox2track', [], 'c'),
    ('dipy.tracking.propspeed', [], 'c'),
    ('dipy.tracking.fbcmeasures', [], 'c'),
    ('dipy.segment.cythonutils', [], 'c'),
    ('dipy.segment.featurespeed', [], 'c'),
    ('dipy.segment.metricspeed', [], 'c'),
    ('dipy.segment.clusteringspeed', [], 'c'),
    ('dipy.segment.clustering_algorithms', [], 'c'),
    ('dipy.segment.mrf', [], 'c'),
    ('dipy.denoise.denspeed', [], 'c'),
    ('dipy.denoise.nlmeans_block', [],'c'),
    ('dipy.denoise.enhancement_kernel', [], 'c'),
    ('dipy.denoise.shift_twist_convolution', [], 'c'),
    ('dipy.align.vector_fields', [], 'c'),
    ('dipy.align.sumsqdiff', [], 'c'),
    ('dipy.align.expectmax', [], 'c'),
    ('dipy.align.crosscorr', [], 'c'),
    ('dipy.align.bundlemin', [], 'c'),
    ('dipy.align.transforms', [], 'c'),
    ('dipy.align.parzenhist', [], 'c'),
    ('dipy.utils.omp', [], 'c')):

    pyx_src = pjoin(*modulename.split('.')) + '.pyx'
    EXTS.append(Extension(modulename, [pyx_src] + other_sources,
                          language=language,
                          **deepcopy(ext_kwargs)))  # deepcopy lists


# Do our own build and install time dependency checking. setup.py gets called in
# many different ways, and may be called just to collect information (egg_info).
# We need to set up tripwires to raise errors when actually doing things, like
# building, rather than unconditionally in the setup.py import or exec
# We may make tripwire versions of build_ext, build_py, install
need_cython = True
pybuilder = get_comrec_build('dipy')
# Cython is a dependency for building extensions, iff we don't have stamped
# up pyx and c files.
build_ext, need_cython = cyproc_exts(EXTS,
                                     info.CYTHON_MIN_VERSION,
                                     'pyx-stamps')
# Add openmp flags if they work
simple_test_c = """int main(int argc, char** argv) { return(0); }"""
omp_test_c = """#include <omp.h>
int main(int argc, char** argv) { return(0); }"""
extbuilder = add_flag_checking(
    build_ext, [
        [['/arch:SSE2'], [], simple_test_c, 'USING_VC_SSE2'],
        [['-msse2', '-mfpmath=sse'], [], simple_test_c, 'USING_GCC_SSE2'],
        [['-fopenmp'], ['-fopenmp'], omp_test_c, 'HAVE_OPENMP']], 'dipy')

# Use ext builder to add np.get_include() at build time, not during setup.py
# execution.
extbuilder = make_np_ext_builder(extbuilder)
if need_cython:
    SetupDependency('Cython', info.CYTHON_MIN_VERSION,
                    req_type='install_requires',
                    heavy=True).check_fill(extra_setuptools_args)
SetupDependency('numpy', info.NUMPY_MIN_VERSION,
                req_type='install_requires',
                heavy=True).check_fill(extra_setuptools_args)
SetupDependency('scipy', info.SCIPY_MIN_VERSION,
                req_type='install_requires',
                heavy=True).check_fill(extra_setuptools_args)
SetupDependency('nibabel', info.NIBABEL_MIN_VERSION,
                req_type='install_requires',
                heavy=False).check_fill(extra_setuptools_args)

cmdclass = dict(
    build_py=pybuilder,
    build_ext=extbuilder,
    install_scripts=install_scripts_bat,
    sdist=get_pyx_sdist(include_dirs=['src']))


def main(**extra_args):
    setup(name=info.NAME,
          maintainer=info.MAINTAINER,
          maintainer_email=info.MAINTAINER_EMAIL,
          description=info.DESCRIPTION,
          long_description=info.LONG_DESCRIPTION,
          url=info.URL,
          download_url=info.DOWNLOAD_URL,
          license=info.LICENSE,
          classifiers=info.CLASSIFIERS,
          author=info.AUTHOR,
          author_email=info.AUTHOR_EMAIL,
          platforms=info.PLATFORMS,
          version=info.VERSION,
          requires=info.REQUIRES,
          provides=info.PROVIDES,
          packages     = ['dipy',
                          'dipy.tests',
                          'dipy.align',
                          'dipy.align.tests',
                          'dipy.core',
                          'dipy.core.tests',
                          'dipy.direction',
                          'dipy.direction.tests',
                          'dipy.tracking',
                          'dipy.tracking.local',
                          'dipy.tracking.local.tests',
                          'dipy.tracking.tests',
                          'dipy.tracking.benchmarks',
                          'dipy.reconst',
                          'dipy.reconst.benchmarks',
                          'dipy.reconst.tests',
                          'dipy.io',
                          'dipy.io.tests',
                          'dipy.viz',
                          'dipy.viz.tests',
                          'dipy.testing',
                          'dipy.testing.tests',
                          'dipy.boots',
                          'dipy.data',
                          'dipy.utils',
                          'dipy.data.tests',
                          'dipy.utils.tests',
                          'dipy.fixes',
                          'dipy.external',
                          'dipy.external.tests',
                          'dipy.segment',
                          'dipy.segment.benchmarks',
                          'dipy.segment.tests',
                          'dipy.sims',
                          'dipy.sims.tests',
                          'dipy.denoise',
                          'dipy.denoise.tests',
                          'dipy.workflows',
                          'dipy.workflows.tests'],

          ext_modules = EXTS,
          # The package_data spec has no effect for me (on python 2.6) -- even
          # changing to data_files doesn't get this stuff included in the source
          # distribution -- not sure if it has something to do with the magic
          # above, but distutils is surely the worst piece of code in all of
          # python -- duplicating things into MANIFEST.in but this is admittedly
          # only a workaround to get things started -- not a solution
          package_data = {'dipy':
                          [pjoin('data', 'files', '*')
                          ]},
          data_files=[('share/doc/dipy/examples',
                       glob(pjoin('doc', 'examples','*.py')))],
          scripts      = [pjoin('bin', 'dipy_reconst_dti'),
                          pjoin('bin', 'dipy_reconst_dti_restore'),
                          pjoin('bin', 'dipy_mask'),
                          pjoin('bin', 'dipy_median_otsu'),
                          pjoin('bin', 'dipy_nlmeans'),
                          ],

          cmdclass = cmdclass,
          **extra_args
        )


#simple way to test what setup will do
#python setup.py install --prefix=/tmp
if __name__ == "__main__":
    main(**extra_setuptools_args)