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from distutils import sysconfig
from setuptools import setup, Extension, find_packages
from setuptools.command.build_ext import build_ext
import os
import sys
import setuptools
from copy import deepcopy
assert sys.version_info >= (3, 5), (
"Please use Python version 3.5 or higher, "
"lower versions are not supported"
)
here = os.path.abspath(os.path.dirname(__file__))
# Get the long description from the README file
with open(os.path.join(here, 'README.rst'), encoding='utf-8') as f:
long_description = f.read()
ext_modules = [
Extension(
'brainiak.factoranalysis.tfa_extension',
['brainiak/factoranalysis/tfa_extension.cpp'],
),
Extension(
'brainiak.fcma.fcma_extension',
['brainiak/fcma/src/fcma_extension.cc'],
),
Extension(
'brainiak.fcma.cython_blas',
['brainiak/fcma/cython_blas.pyx'],
),
Extension(
'brainiak.eventseg._utils',
['brainiak/eventseg/_utils.pyx'],
),
]
# As of Python 3.6, CCompiler has a `has_flag` method.
# cf http://bugs.python.org/issue26689
def has_flag(compiler, flagname):
"""Return a boolean indicating whether a flag name is supported on
the specified compiler.
"""
import tempfile
with tempfile.NamedTemporaryFile('w', suffix='.cpp') as f:
f.write('int main (int argc, char **argv) { return 0; }')
try:
compiler.compile([f.name], extra_postargs=[flagname])
except setuptools.distutils.errors.CompileError:
return False
return True
def cpp_flag(compiler):
"""Return the -std=c++[11/14] compiler flag.
The c++14 is prefered over c++11 (when it is available).
"""
if has_flag(compiler, '-std=c++14'):
return '-std=c++14'
elif has_flag(compiler, '-std=c++11'):
return '-std=c++11'
else:
raise RuntimeError('Unsupported compiler -- at least C++11 support '
'is needed!')
class BuildExt(build_ext):
"""A custom build extension for adding compiler-specific options."""
c_opts = {
'unix': ['-g0', '-fopenmp'],
}
# FIXME Workaround for using the Intel compiler by setting the CC env var
# Other uses of ICC (e.g., cc binary linked to icc) are not supported
if (('CC' in os.environ and 'icc' in os.environ['CC'])
or 'icc' in sysconfig.get_config_var('CC')):
c_opts['unix'] += ['-lirc', '-lintlc']
if sys.platform == 'darwin':
c_opts['unix'] += ['-stdlib=libc++', '-mmacosx-version-min=10.9',
'-ftemplate-depth-1024']
def build_extensions(self):
ct = self.compiler.compiler_type
opts = self.c_opts.get(ct, [])
if ct == 'unix':
opts.append('-DVERSION_INFO="%s"' %
self.distribution.get_version())
for ext in self.extensions:
ext.extra_compile_args = deepcopy(opts)
ext.extra_link_args = deepcopy(opts)
lang = ext.language or self.compiler.detect_language(ext.sources)
if lang == 'c++':
ext.extra_compile_args.append(cpp_flag(self.compiler))
ext.extra_link_args.append(cpp_flag(self.compiler))
build_ext.build_extensions(self)
def finalize_options(self):
super().finalize_options()
import numpy
import pybind11
self.include_dirs.extend([
numpy.get_include(),
pybind11.get_include(user=True),
pybind11.get_include(),
])
setup(
name='brainiak',
use_scm_version=True,
setup_requires=[
'cython',
'numpy!=1.17.*',
'pybind11>=1.7',
'setuptools_scm',
],
install_requires=[
'cython',
# Previous versions fail of the Anaconda package fail on MacOS:
# https://travis-ci.org/brainiak/brainiak/jobs/545838666
'mpi4py>=3',
'nitime',
# https://github.com/numpy/numpy/issues/14189
'numpy!=1.17.*',
'scikit-learn[alldeps]>=0.18,<0.22',
# See https://github.com/scipy/scipy/pull/8082
'scipy!=1.0.0',
'statsmodels',
'pymanopt',
'theano>=1.0.4', # See https://github.com/Theano/Theano/pull/6671
'pybind11>=1.7',
'psutil',
'nibabel',
'joblib',
'wheel', # See https://github.com/astropy/astropy-helpers/issues/501
],
author='Princeton Neuroscience Institute and Intel Corporation',
author_email='mihai.capota@intel.com',
url='http://brainiak.org',
description='Brain Imaging Analysis Kit',
license='Apache 2',
keywords='neuroscience, algorithm, fMRI, distributed, scalable',
long_description=long_description,
ext_modules=ext_modules,
cmdclass={'build_ext': BuildExt},
packages=find_packages(),
package_data={'brainiak.utils': ['grey_matter_mask.npy']},
python_requires='>=3.5',
zip_safe=False,
)