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#!/usr/bin/env python
import os
import sys
from numpy.distutils.misc_util import get_numpy_include_dirs
try:
import configparser
except ImportError:
import ConfigParser as configparser
from setuptools import setup, Extension
from setuptools.command.install import install
from Cython.Build import cythonize
def set_default_filestore(prefix, optfile):
config = configparser.ConfigParser()
config.read(optfile)
config.set("basic", "filestore", os.path.join(prefix, "db"))
config.set("webgl", "colormaps", os.path.join(prefix, "colormaps"))
with open(optfile, 'w') as fp:
config.write(fp)
class my_install(install):
def run(self):
install.run(self)
optfile = [f for f in self.get_outputs() if 'defaults.cfg' in f]
prefix = os.path.join(self.install_data, "share", "pycortex")
set_default_filestore(prefix, optfile[0])
self.copy_tree('filestore', prefix)
for root, folders, files in os.walk(prefix):
for folder in folders:
os.chmod(os.path.join(root, folder), 511)
for fname in files:
os.chmod(os.path.join(root, fname), 438)
ctm = Extension('cortex.openctm', [
'cortex/openctm.pyx',
'OpenCTM-1.0.3/lib/openctm.c',
'OpenCTM-1.0.3/lib/stream.c',
'OpenCTM-1.0.3/lib/compressRAW.c',
'OpenCTM-1.0.3/lib/compressMG1.c',
'OpenCTM-1.0.3/lib/compressMG2.c',
'OpenCTM-1.0.3/lib/liblzma/Alloc.c',
'OpenCTM-1.0.3/lib/liblzma/LzFind.c',
'OpenCTM-1.0.3/lib/liblzma/LzmaDec.c',
'OpenCTM-1.0.3/lib/liblzma/LzmaEnc.c',
'OpenCTM-1.0.3/lib/liblzma/LzmaLib.c',],
libraries=['m'], include_dirs=[
'OpenCTM-1.0.3/lib/',
'OpenCTM-1.0.3/lib/liblzma/'] + get_numpy_include_dirs(),
define_macros=[
('LZMA_PREFIX_CTM', None),
('OPENCTM_BUILD', None),
#('__DEBUG_', None),
]
)
formats = Extension('cortex.formats', ['cortex/formats.pyx'],
include_dirs=get_numpy_include_dirs())
setup(name='pycortex',
version='1.0.2',
description='Python Cortical mapping software for fMRI data',
author='James Gao',
author_email='james@jamesgao.com',
packages=['cortex', 'cortex.webgl', 'cortex.mapper', 'cortex.dataset',
'cortex.blender', 'cortex.tests', 'cortex.quickflat', 'cortex.polyutils'],
ext_modules=cythonize([ctm, formats]),
package_data={
'cortex': [
'svgbase.xml',
'defaults.cfg',
'bbr.sch'
],
'cortex.webgl': [
'*.html',
'favicon.ico',
'resources/js/*.js',
'resources/js/ctm/*.js',
'resources/css/*.css',
'resources/css/images/*',
'resources/css/ui-lightness/*.css',
'resources/css/ui-lightness/images/*',
'resources/images/*'
]
},
install_requires=[
'future', 'numpy', 'scipy', 'tornado==4.3',
'shapely', 'lxml', 'html5lib', 'h5py', 'numexpr', 'cython',
'matplotlib', 'pillow', 'nibabel', 'networkx==2.1',
],
cmdclass=dict(install=my_install),
include_package_data=True,
test_suite='nose.collector'
)