Repository navigation
Expand file tree
/
Copy pathsetup.py
More file actions
155 lines (136 loc) · 4.8 KB
/
Copy pathsetup.py
File metadata and controls
155 lines (136 loc) · 4.8 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
FD1B
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
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',
'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',
# See https://github.com/scipy/scipy/pull/8082
# and https://github.com/pymanopt/pymanopt/issues/77
'scipy!=1.0.0,<1.3.0',
'statsmodels',
'pymanopt',
'theano>=1.0.4', # See https://github.com/Theano/Theano/pull/6671
'pybind11>=1.7',
'psutil',
'nibabel',
],
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,
)