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
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
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
|
#!/usr/bin/env python
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See COPYING file distributed along with the PyMVPA package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
"""Python distutils setup for PyMVPA"""
from numpy.distutils.core import setup, Extension
import fnmatch
import glob
import os
import sys
if sys.version_info[:2] < (2, 6):
raise RuntimeError("PyMVPA requires Python 2.6 or higher")
# some config settings
bind_libsvm = 'local' # choices: 'local', 'system', None
libsvmc_extra_sources = []
libsvmc_include_dirs = []
libsvmc_libraries = []
extra_link_args = []
libsvmc_library_dirs = []
# platform-specific settings
if sys.platform == "darwin":
extra_link_args.append("-bundle")
if sys.platform.startswith('linux'):
# need to look for numpy (header location changes with v1.3)
from numpy.distutils.misc_util import get_numpy_include_dirs
libsvmc_include_dirs += get_numpy_include_dirs()
# when libsvm is forced -- before it was used only in cases
# when libsvm was available at system level, hence we switch
# from local to system at this point
# TODO: Deprecate --with-libsvm for 0.5
for arg in ('--with-libsvm', '--with-system-libsvm'):
if not sys.argv.count(arg):
continue
# clean argv if necessary (or distutils will complain)
sys.argv.remove(arg)
# assure since default is 'auto' wouldn't fail if it is N/A
bind_libsvm = 'system'
# when no libsvm bindings are requested explicitly
if sys.argv.count('--no-libsvm'):
# clean argv if necessary (or distutils will complain)
sys.argv.remove('--no-libsvm')
bind_libsvm = None
# if requested:
if bind_libsvm == 'local':
# we will provide libsvm sources later on # if libsvm.a is available locally -- use it
#if os.path.exists(os.path.join('build', 'libsvm', 'libsvm.a')):
libsvm_3rd_path = os.path.join('3rd', 'libsvm')
libsvmc_include_dirs += [libsvm_3rd_path]
libsvmc_extra_sources = [os.path.join(libsvm_3rd_path, 'svm.cpp')]
elif bind_libsvm == 'system':
# look for libsvm in some places, when local one is not used
libsvmc_libraries += ['svm']
if not sys.platform.startswith('win'):
libsvmc_include_dirs += [
'/usr/include/libsvm-3.0/libsvm',
'/usr/include/libsvm-2.0/libsvm',
'/usr/include/libsvm',
'/usr/local/include/libsvm',
'/usr/local/include/libsvm-2.0/libsvm',
'/usr/local/include']
else:
# no clue on windows
pass
elif bind_libsvm is None:
pass
else:
raise ValueError("Shouldn't happen that we get bind_libsvm=%r"
% (bind_libsvm,))
# define the extension modules
libsvmc_ext = Extension(
'mvpa2.clfs.libsvmc._svmc',
sources=libsvmc_extra_sources + [os.path.join('mvpa2', 'clfs', 'libsvmc', 'svmc.i')],
include_dirs=libsvmc_include_dirs,
library_dirs=libsvmc_library_dirs,
libraries=libsvmc_libraries,
language='c++',
extra_link_args=extra_link_args,
swig_opts=['-I' + d for d in libsvmc_include_dirs])
smlrc_ext = Extension(
'mvpa2.clfs.libsmlrc.smlrc',
sources=[ os.path.join('mvpa2', 'clfs', 'libsmlrc', 'smlr.c') ],
#library_dirs = library_dirs,
libraries=['m'] if not sys.platform.startswith('win') else [],
# extra_compile_args = ['-O0'],
extra_link_args=extra_link_args,
language='c')
ext_modules = [smlrc_ext]
if bind_libsvm:
ext_modules.append(libsvmc_ext)
# Notes on the setup
# Version scheme is: major.minor.patch<suffix>
def get_full_dir(path):
path_split = path.split(os.path.sep) # so we could run setup.py on any platform
path_proper = os.path.join(*path_split)
return (path_proper,
[f for f in glob.glob(os.path.join(path_proper, '*'))
if os.path.isfile(f)])
# borrowed from https://wiki.python.org/moin/Distutils/Tutorial
## Code borrowed from wxPython's setup and config files
## Thanks to Robin Dunn for the suggestion.
## I am not 100% sure what's going on, but it works!
def opj(*args):
path = os.path.join(*args)
return os.path.normpath(path)
def find_data_files(srcdir, *wildcards, **kw):
# get a list of all files under the srcdir matching wildcards,
# returned in a format to be used for install_data
file_list = []
recursive = kw.get('recursive', True)
for d, dirs, files in os.walk(srcdir, topdown=True):
for wc in wildcards:
files_ = [opj(d, x) for x in fnmatch.filter(files, wc)]
if files_:
file_list.append((d, files_))
if not recursive:
break # one would be enough ;)
return file_list
# define the setup
def setup_package():
# Perform 2to3 if needed
local_path = os.path.dirname(os.path.abspath(sys.argv[0]))
src_path = local_path
if sys.version_info[0] == 3:
src_path = os.path.join(local_path, 'build', 'py3k')
import py3tool
print("Converting to Python3 via 2to3...")
py3tool.sync_2to3('mvpa2', os.path.join(src_path, 'mvpa2'))
py3tool.sync_2to3('3rd', os.path.join(src_path, '3rd'))
# Borrowed from NumPy before this code was deprecated (everyone
# else moved on from 2to3)
# Ugly hack to make pip work with Python 3, see NumPy #1857.
# Explanation: pip messes with __file__ which interacts badly with the
# change in directory due to the 2to3 conversion. Therefore we restore
# __file__ to what it would have been otherwise.
global __file__
__file__ = os.path.join(os.curdir, os.path.basename(__file__))
if '--egg-base' in sys.argv:
# Change pip-egg-info entry to absolute path, so pip can find it
# after changing directory.
idx = sys.argv.index('--egg-base')
if sys.argv[idx + 1] == 'pip-egg-info':
sys.argv[idx + 1] = os.path.join(local_path, 'pip-egg-info')
# Run build
os.chdir(src_path)
sys.path.insert(0, src_path)
setup(name='pymvpa2',
version='2.6.0',
author='Michael Hanke, Yaroslav Halchenko, Nikolaas N. Oosterhof',
author_email='pkg-exppsy-pymvpa@lists.alioth.debian.org',
license='MIT License',
url='http://www.pymvpa.org',
description='Multivariate pattern analysis',
long_description=
"PyMVPA is a Python module intended to ease pattern classification "
"analyses of large datasets. It provides high-level abstraction of "
"typical processing steps and a number of implementations of some "
"popular algorithms. While it is not limited to neuroimaging data "
"it is eminently suited for such datasets.\n"
"PyMVPA is truly free software (in every respect) and "
"additionally requires nothing but free-software to run.",
# please maintain alphanumeric order
packages=[ 'mvpa2',
'mvpa2.algorithms',
'mvpa2.atlases',
'mvpa2.base',
'mvpa2.clfs',
'mvpa2.clfs.libsmlrc',
'mvpa2.clfs.libsvmc',
'mvpa2.clfs.skl',
'mvpa2.clfs.sg',
'mvpa2.cmdline',
'mvpa2.datasets',
'mvpa2.datasets.sources',
'mvpa2.featsel',
'mvpa2.kernels',
'mvpa2.mappers',
'mvpa2.mappers.glm',
'mvpa2.generators',
'mvpa2.measures',
'mvpa2.misc',
'mvpa2.misc.bv',
'mvpa2.misc.fsl',
'mvpa2.misc.io',
'mvpa2.misc.plot',
'mvpa2.misc.surfing',
'mvpa2.sandbox',
'mvpa2.support',
'mvpa2.support.afni',
'mvpa2.support.bayes',
'mvpa2.support.nipy',
'mvpa2.support.ipython',
'mvpa2.support.nibabel',
'mvpa2.support.scipy',
'mvpa2.testing',
'mvpa2.tests',
'mvpa2.tests.badexternals',
'mvpa2.viz',
],
data_files=[('mvpa2', [os.path.join('mvpa2', 'COMMIT_HASH')])]
+ find_data_files(os.path.join('mvpa2', 'data'),
'*.txt', '*.nii.gz', '*.rtc', 'README', '*.bin',
'*.dat', '*.dat.gz', '*.mat', '*.fsf', '*.par'),
scripts=glob.glob(os.path.join('bin', '*')),
ext_modules=ext_modules
)
if __name__ == '__main__':
setup_package()
|
