forked from mdtraj/mdtraj
-
Notifications
You must be signed in to change notification settings - Fork 0
/
setup.py
300 lines (260 loc) · 12.1 KB
/
setup.py
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
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
"""MDTraj: A modern, open library for the analysis of molecular dynamics trajectories
MDTraj is a python library that allows users to manipulate molecular dynamics
(MD) trajectories and perform a variety of analyses, including fast RMSD,
solvent accessible surface area, hydrogen bonding, etc. A highlight of MDTraj
is the wide variety of molecular dynamics trajectory file formats which are
supported, including RCSB pdb, GROMACS xtc, tng, and trr, CHARMM / NAMD dcd, AMBER
binpos, AMBER NetCDF, AMBER mdcrd, TINKER arc and MDTraj HDF5.
"""
from __future__ import print_function, absolute_import
DOCLINES = __doc__.split("\n")
import os
import sys
from glob import glob
from setuptools import setup, Extension, find_packages
sys.path.insert(0, '.')
from basesetup import (write_version_py, build_ext,
StaticLibrary, CompilerDetection)
try:
import numpy
import Cython
if Cython.__version__ < '0.19':
raise ImportError
from Cython.Build import cythonize
except ImportError:
print('-'*80, file=sys.stderr)
print('''Error: building mdtraj requires numpy and cython>=0.19
Try running the command ``pip install numpy cython`` or
``conda install numpy cython``.
or see http://docs.scipy.org/doc/numpy/user/install.html and
http://cython.org/ for more information.
If you're feeling lost, we recommend downloading the (free) Anaconda python
distribution https://www.continuum.io/downloads, because it comes with
these components included.''', file=sys.stderr)
print('-'*80, file=sys.stderr)
sys.exit(1)
try:
# add an optional --disable-openmp to disable OpenMP support
sys.argv.remove('--disable-openmp')
disable_openmp = True
except ValueError:
disable_openmp = False
##########################
VERSION = "1.9.3"
ISRELEASED = False
__version__ = VERSION
##########################
CLASSIFIERS = """\
Development Status :: 5 - Production/Stable
Intended Audience :: Science/Research
Intended Audience :: Developers
License :: OSI Approved :: GNU Lesser General Public License v2 or later (LGPLv2+)
Programming Language :: C
Programming Language :: Python
Programming Language :: Python :: 3
Topic :: Scientific/Engineering :: Bio-Informatics
Topic :: Scientific/Engineering :: Chemistry
Operating System :: Microsoft :: Windows
Operating System :: POSIX
Operating System :: Unix
Operating System :: MacOS
"""
# Global info about compiler
compiler = CompilerDetection(disable_openmp)
compiler.initialize()
extra_cpp_libraries = []
if sys.platform == 'darwin':
extra_cpp_libraries.append('stdc++')
os.environ['CXX'] = 'clang++'
os.environ['CC'] = 'clang'
if sys.platform == 'win32':
extra_cpp_libraries.append('Ws2_32')
# For determining if a path is relative (for dtr)
extra_cpp_libraries.append('Shlwapi')
################################################################################
# Declaration of the compiled extension modules (cython + c)
################################################################################
def format_extensions():
compiler_args = compiler.compiler_args_warn
xtc = Extension('mdtraj.formats.xtc',
sources=['mdtraj/formats/xtc/src/xdrfile.c',
'mdtraj/formats/xtc/src/xdr_seek.c',
'mdtraj/formats/xtc/src/xdrfile_xtc.c',
'mdtraj/formats/xtc/xtc.pyx',
],
include_dirs=['mdtraj/formats/xtc/include/',
'mdtraj/formats/xtc/'],
extra_compile_args=compiler_args)
trr = Extension('mdtraj.formats.trr',
sources=['mdtraj/formats/xtc/src/xdrfile.c',
'mdtraj/formats/xtc/src/xdr_seek.c',
'mdtraj/formats/xtc/src/xdrfile_trr.c',
'mdtraj/formats/xtc/trr.pyx'],
include_dirs=['mdtraj/formats/xtc/include/',
'mdtraj/formats/xtc/'],
extra_compile_args=compiler_args)
zlib_include_dirs = []
zlib_library_dirs = []
if sys.platform == 'win32':
# Conda puts the zlib headers in ./Library/... on windows
# If you're not using conda, good luck!
zlib_include_dirs += ["{}/Library/include".format(sys.prefix)]
zlib_library_dirs += ["{}/Library/lib".format(sys.prefix)]
else:
# On linux (and mac(?)) these paths should work for a standard
# install of python+zlib or a conda install of python+zlib
zlib_include_dirs += ["{}/include".format(sys.prefix)]
zlib_library_dirs += ["{}/lib".format(sys.prefix)]
tng = Extension('mdtraj.formats.tng',
sources=glob('mdtraj/formats/tng/src/compression/*.c') +
['mdtraj/formats/tng/src/lib/tng_io.c',
'mdtraj/formats/tng/src/lib/md5.c',
'mdtraj/formats/tng/tng.pyx'],
include_dirs=['mdtraj/formats/tng/include']
+ zlib_include_dirs,
define_macros=[('USE_ZLIB', 1)],
library_dirs=zlib_library_dirs,
libraries=['z'],
)
dcd = Extension('mdtraj.formats.dcd',
sources=['mdtraj/formats/dcd/src/dcdplugin.c',
'mdtraj/formats/dcd/dcd.pyx'],
include_dirs=["mdtraj/formats/dcd/include/",
'mdtraj/formats/dcd/'],
extra_compile_args=compiler_args)
binpos = Extension('mdtraj.formats.binpos',
sources=['mdtraj/formats/binpos/src/binposplugin.c',
'mdtraj/formats/binpos/binpos.pyx'],
include_dirs=['mdtraj/formats/binpos/include/',
'mdtraj/formats/binpos/'],
extra_compile_args=compiler_args)
dtr = Extension('mdtraj.formats.dtr',
sources=['mdtraj/formats/dtr/src/dtrplugin.cxx',
'mdtraj/formats/dtr/dtr.pyx'],
include_dirs=['mdtraj/formats/dtr/include/',
'mdtraj/formats/dtr/'],
define_macros=[('DESRES_READ_TIMESTEP2', 1)],
language='c++',
extra_compile_args=compiler_args,
libraries=extra_cpp_libraries)
return [xtc, trr, tng, dcd, binpos, dtr]
def rmsd_extensions():
compiler_args = (compiler.compiler_args_openmp + compiler.compiler_args_sse2 +
compiler.compiler_args_sse3 + compiler.compiler_args_opt +
compiler.compiler_args_warn)
compiler_libraries = compiler.compiler_libraries_openmp
libtheobald = StaticLibrary(
'mdtraj.core.lib.libtheobald',
sources=[
'mdtraj/rmsd/src/theobald_rmsd.c',
'mdtraj/rmsd/src/center.c'],
include_dirs=[
'mdtraj/rmsd/include'],
export_include=['mdtraj/rmsd/include/theobald_rmsd.h',
'mdtraj/rmsd/include/center.h'],
# don't enable OpenMP
extra_compile_args=(compiler.compiler_args_sse2 +
compiler.compiler_args_sse3 +
compiler.compiler_args_opt))
rmsd = Extension('mdtraj._rmsd',
sources=[
'mdtraj/rmsd/src/theobald_rmsd.c',
'mdtraj/rmsd/src/rotation.c',
'mdtraj/rmsd/src/center.c',
'mdtraj/rmsd/_rmsd.pyx'],
include_dirs=['mdtraj/rmsd/include'],
extra_compile_args=compiler_args,
libraries=compiler_libraries)
lprmsd = Extension('mdtraj._lprmsd',
sources=[
'mdtraj/rmsd/src/theobald_rmsd.c',
'mdtraj/rmsd/src/rotation.c',
'mdtraj/rmsd/src/center.c',
'mdtraj/rmsd/src/fancy_index.cpp',
'mdtraj/rmsd/src/Munkres.cpp',
'mdtraj/rmsd/src/euclidean_permutation.cpp',
'mdtraj/rmsd/_lprmsd.pyx'],
language='c++',
include_dirs=['mdtraj/rmsd/include'],
extra_compile_args=compiler_args,
libraries=compiler_libraries + extra_cpp_libraries)
return rmsd, lprmsd, libtheobald
def geometry_extensions():
compiler.initialize()
compiler_args = (
compiler.compiler_args_openmp +
compiler.compiler_args_sse2 + compiler.compiler_args_sse3 +
compiler.compiler_args_opt + compiler.compiler_args_warn)
define_macros = None
compiler_libraries = compiler.compiler_libraries_openmp + extra_cpp_libraries
return [
Extension('mdtraj.geometry._geometry',
sources=['mdtraj/geometry/src/sasa.cpp',
'mdtraj/geometry/src/dssp.cpp',
'mdtraj/geometry/src/geometry.cpp',
'mdtraj/geometry/src/_geometry.pyx',],
include_dirs=['mdtraj/geometry/include',
'mdtraj/geometry/src/kernels'],
depends=['mdtraj/geometry/src/kernels/anglekernels.h',
'mdtraj/geometry/src/kernels/dihedralkernels.h',
'mdtraj/geometry/src/kernels/distancekernels.h'],
define_macros=define_macros,
extra_compile_args=compiler_args,
libraries=compiler_libraries,
language='c++'),
Extension('mdtraj.geometry.drid',
sources=["mdtraj/geometry/drid.pyx",
"mdtraj/geometry/src/dridkernels.cpp",
"mdtraj/geometry/src/moments.cpp"],
include_dirs=["mdtraj/geometry/include"],
define_macros=define_macros,
extra_compile_args=compiler_args,
libraries=compiler_libraries,
language='c++'),
Extension('mdtraj.geometry.neighbors',
sources=["mdtraj/geometry/neighbors.pyx",
"mdtraj/geometry/src/neighbors.cpp"],
include_dirs=["mdtraj/geometry/include",],
define_macros=define_macros,
extra_compile_args=compiler_args,
libraries=compiler_libraries,
language='c++'),
Extension('mdtraj.geometry.neighborlist',
sources=["mdtraj/geometry/neighborlist.pyx",
"mdtraj/geometry/src/neighborlist.cpp"],
include_dirs=["mdtraj/geometry/include",],
define_macros=define_macros,
extra_compile_args=compiler_args,
libraries=compiler_libraries,
language='c++'),
]
extensions = format_extensions()
extensions.extend(rmsd_extensions())
extensions.extend(geometry_extensions())
write_version_py(VERSION, ISRELEASED, 'mdtraj/version.py')
setup(name='mdtraj',
author='Robert McGibbon',
description=DOCLINES[0],
long_description="\n".join(DOCLINES[2:]),
version=__version__,
license='LGPLv2.1+',
url='http://mdtraj.org',
download_url = "https://github.com/rmcgibbo/mdtraj/releases/latest",
platforms=['Linux', 'Mac OS-X', 'Unix', 'Windows'],
classifiers=CLASSIFIERS.splitlines(),
packages=find_packages(),
cmdclass={'build_ext': build_ext},
ext_modules=cythonize(extensions),
# setup_requires really doesn't work sufficently well with `pip install`
# to use. See https://github.com/mdtraj/mdtraj/issues/984. Also
# setup_requires=['setuptools>=18', 'cython>=0.22', 'numpy>=1.6'],
# Also, install_requires is no better, especially with numpy.
# See http://article.gmane.org/gmane.comp.python.distutils.devel/24218
# install_requires=['numpy>=1.6'],
package_data={'mdtraj.formats.pdb': ['data/*'], },
zip_safe=False,
entry_points={'console_scripts':
['mdconvert = mdtraj.scripts.mdconvert:entry_point',
'mdinspect = mdtraj.scripts.mdinspect:entry_point']},
)