<commit_before>#!/usr/bin/env python
""" Installation script for dipy package """

import os
import sys
import platform
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 'force_setuptools' not 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
    # We need nosetests for numpy.testing<=1.15
    extra_setuptools_args = dict(
        tests_require=['pytest', 'nose'],
        test_suite='nose.collector',
        zip_safe=False,
        extras_require=dict(
            doc=['Sphinx>=1.0'],
            test=['pytest', '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.direction.pmf', [], 'c'),
        ('dipy.direction.probabilistic_direction_getter', [], 'c'),
        ('dipy.direction.closest_peak_direction_getter', [], 'c'),
        ('dipy.direction.bootstrap_direction_getter', [], 'c'),
        ('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.pca_noise_estimate', [], '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'),<commit_msg>update setup.py<commit_after>#!/usr/bin/env python
""" Installation script for dipy package """

import os
import sys
import platform
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 'force_setuptools' not 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
    # We need nosetests for numpy.testing<=1.15
    extra_setuptools_args = dict(
        tests_require=['pytest', 'nose'],
        test_suite='nose.collector',
        zip_safe=False,
        extras_require=dict(
            doc=['Sphinx>=1.0'],
            test=['pytest', '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.core.interpolation', [], 'c'),
        ('dipy.direction.pmf', [], 'c'),
        ('dipy.direction.probabilistic_direction_getter', [], 'c'),
        ('dipy.direction.closest_peak_direction_getter', [], 'c'),
        ('dipy.direction.bootstrap_direction_getter', [], 'c'),
        ('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.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.pca_noise_estimate', [], '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'),
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