-
Notifications
You must be signed in to change notification settings - Fork 86
/
setup.py
431 lines (356 loc) · 15.3 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
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
try:
# use setuptools if we can
from setuptools import setup, Command, Extension
from setuptools.command.build_ext import build_ext
using_setuptools = True
except ImportError:
from distutils.core import setup, Command, Extension
from distutils.command.build_ext import build_ext
using_setuptools = False
from distutils import sysconfig
from distutils.ccompiler import get_default_compiler
from pkg_resources import get_build_platform
import os
import sys
import shutil
import glob
with open("eqcorrscan/__init__.py", "r") as init_file:
version_line = [line for line in init_file
if '__version__' in line][0]
VERSION = version_line.split()[-1].split("'")[1]
# Check if we are on RTD and don't build extensions if we are.
READ_THE_DOCS = os.environ.get('READTHEDOCS', None) == 'True'
long_description = '''
EQcorrscan: repeating and near-repeating earthquake detection and analysis
in Python. Open-source routines for: systematic template
creation, matched-filter detection, subspace detection, brightness detection,
clustering of seismic events, magnitude calculation by singular value
decomposition, and more!
'''
# Get a list of all the scripts not to be installed
scriptfiles = glob.glob('eqcorrscan/tutorials/*.py')
scriptfiles += glob.glob('eqcorrscan/scripts/*.py')
if READ_THE_DOCS:
try:
environ = os.environb
except AttributeError:
environ = os.environ
environ[b"CC"] = b"x86_64-linux-gnu-gcc"
environ[b"LD"] = b"x86_64-linux-gnu-ld"
environ[b"AR"] = b"x86_64-linux-gnu-ar"
def get_package_data():
"""
Get the library files for appveyor - this shouldn't make any difference
for install with system libraries.
"""
from pkg_resources import get_build_platform
package_data = {}
if get_build_platform() in ('win32', 'win-amd64'):
package_data['eqcorrscan.utils.lib'] = [
'libfftw3-3.dll', 'libfftw3f-3.dll', 'libfftw3l-3.dll']
return package_data
def get_package_dir():
from pkg_resources import get_build_platform
package_dir = {}
if get_build_platform() in ('win32', 'win-amd64'):
package_dir['eqcorrscan.utils.lib'] = os.path.join(
'eqcorrscan', 'utils', 'lib')
return package_dir
def get_include_dirs():
import numpy
from pkg_resources import get_build_platform
include_dirs = [os.path.join(os.getcwd(), 'include'),
os.path.join(os.getcwd(), 'eqcorrscan', 'utils', 'src'),
numpy.get_include(),
os.path.join(sys.prefix, 'include')]
if get_build_platform() in ('win32', 'win-amd64'):
# Add the Library dir
include_dirs.append(os.path.join(sys.prefix, 'Library', 'include'))
if get_build_platform().startswith('freebsd'):
include_dirs.append('/usr/local/include')
return include_dirs
def get_library_dirs():
from pkg_resources import get_build_platform
library_dirs = []
if get_build_platform() in ('win32', 'win-amd64'):
library_dirs.append(os.path.join(os.getcwd(), 'eqcorrscan', 'utils',
'lib'))
library_dirs.append(os.path.join(sys.prefix, 'lib'))
library_dirs.append(os.path.join(sys.prefix, 'Library', 'lib'))
library_dirs.append(os.path.join(sys.prefix, 'lib'))
if get_build_platform().startswith('freebsd'):
library_dirs.append('/usr/local/lib')
return library_dirs
def get_mkl():
from pkg_resources import get_build_platform
mkl_found = False
# TODO: not sure about windows so ignoring for now
if not get_build_platform() in ('win32', 'win-amd64'):
# look for MKL
mklroot = os.getenv("MKLROOT")
if mklroot is not None and os.path.isdir(mklroot):
if os.path.isdir(os.path.join(mklroot, "mkl")):
mklroot = os.path.join(mklroot, "mkl")
# look for MKL lib
_libdir = os.path.join(mklroot, "lib")
if os.path.isdir(os.path.join(_libdir, "intel64")):
_libdir = os.path.join(_libdir, "intel64")
libs = glob.glob(os.path.join(_libdir, "libmkl_rt.*"))
if len(libs) == 1:
_lib = os.path.splitext(os.path.basename(libs[0]))[0][3:]
mkl_lib = [_lib]
mkl_libdir = [_libdir]
# look for include
if os.path.exists(os.path.join(mklroot, "include", "fftw",
"fftw3.h")):
mkl_inc = [os.path.join(mklroot, "include", "fftw")]
mkl_found = True
# check for conda installed MKL too (doesn't set MKLROOT)
# this assume we are in a conda env (not root)
if not mkl_found:
conda = os.getenv("CONDA_PREFIX")
print(conda)
if conda is not None:
# look for MKL lib
libs = glob.glob(os.path.join(conda, "lib", "libmkl_rt.*"))
if len(libs) == 1:
_lib = os.path.splitext(os.path.basename(libs[0]))[0][3:]
mkl_lib = [_lib]
mkl_libdir = [os.path.join(conda, "lib")]
# look for include too
if os.path.exists(os.path.join(conda, "include", "fftw",
"fftw3.h")):
mkl_inc = [os.path.join(conda, "include", "fftw")]
mkl_found = True
elif os.path.exists(os.path.join(conda, "include",
"fftw3.h")):
mkl_inc = [os.path.join(conda, "include")]
mkl_found = True
if mkl_found:
print("Found MKL:")
print(" MKL includes:", mkl_inc)
print(" MKL lib dirs:", mkl_libdir)
print(" MKL libs:", mkl_lib)
return mkl_inc, mkl_libdir, mkl_lib
else:
return None
def get_libraries():
from pkg_resources import get_build_platform
if get_build_platform() in ('win32', 'win-amd64'):
# libraries = ['libfftw3-3', 'libfftw3f-3']
libraries = ['fftw3', 'fftw3f']
else:
libraries = ['fftw3', 'fftw3_threads', 'fftw3f', 'fftw3f_threads']
return libraries
def export_symbols(*path):
"""
Required for windows systems - functions defined in libutils.def.
"""
lines = open(os.path.join(*path), 'r').readlines()[2:]
return [s.strip() for s in lines if s.strip() != '']
def get_extensions(no_mkl=False):
from distutils.extension import Extension
if READ_THE_DOCS:
return []
# will use static linking if STATIC_FFTW_DIR defined
static_fftw_path = os.environ.get('STATIC_FFTW_DIR', None)
link_static_fftw = static_fftw_path is not None
common_extension_args = {
'include_dirs': get_include_dirs(),
'library_dirs': get_library_dirs()}
sources = [os.path.join('eqcorrscan', 'utils', 'src', 'multi_corr.c'),
os.path.join('eqcorrscan', 'utils', 'src', 'time_corr.c'),
os.path.join('eqcorrscan', 'utils', 'src', 'find_peaks.c'),
os.path.join('eqcorrscan', 'utils', 'src',
'distance_cluster.c')]
exp_symbols = export_symbols("eqcorrscan/utils/src/libutils.def")
if get_build_platform() not in ('win32', 'win-amd64'):
if get_build_platform().startswith('freebsd'):
# Clang uses libomp, not libgomp
extra_link_args = ['-lm', '-lomp']
else:
extra_link_args = ['-lm', '-lgomp']
extra_compile_args = ['-fopenmp']
if all(arch not in get_build_platform()
for arch in ['arm', 'aarch']):
extra_compile_args.extend(['-msse2', '-ftree-vectorize'])
else:
extra_link_args = []
extra_compile_args = ['/openmp', '/TP']
libraries = get_libraries()
if link_static_fftw:
if get_build_platform() in ('win32', 'win-amd64'):
lib_pre = ''
lib_ext = '.lib'
else:
lib_pre = 'lib'
lib_ext = '.a'
for lib in libraries:
extra_link_args.append(
os.path.join(static_fftw_path, lib_pre + lib + lib_ext))
common_extension_args['extra_link_args'] = extra_link_args
common_extension_args['libraries'] = []
common_extension_args['extra_compile_args'] = extra_compile_args
common_extension_args['export_symbols'] = exp_symbols
else:
# otherwise we use dynamic libraries
common_extension_args['extra_link_args'] = extra_link_args
common_extension_args['extra_compile_args'] = extra_compile_args
common_extension_args['export_symbols'] = exp_symbols
if no_mkl:
mkl = None
else:
mkl = get_mkl()
if mkl is not None:
# use MKL if we have it
common_extension_args['include_dirs'].extend(mkl[0])
common_extension_args['library_dirs'].extend(mkl[1])
common_extension_args['libraries'] = mkl[2]
else:
common_extension_args['libraries'] = libraries
ext_modules = [
Extension('eqcorrscan.utils.lib.libutils', sources=sources,
**common_extension_args)]
return ext_modules
class CustomBuildExt(build_ext):
def finalize_options(self):
build_ext.finalize_options(self)
if self.compiler is None:
compiler = get_default_compiler()
else:
compiler = self.compiler
cfg_vars = sysconfig.get_config_vars()
# Hack around OSX setting a -m flag
if "macosx" in get_build_platform() and "CFLAGS" in cfg_vars:
print("System C-flags:")
print(cfg_vars["CFLAGS"])
cflags = []
for flag in cfg_vars["CFLAGS"].split():
if flag in ["-m", "-isysroot"]:
continue
# Remove sdk links
if flag.endswith(".sdk"):
continue
cflags.append(flag)
cfg_vars["CFLAGS"] = " ".join(cflags)
print("Editted C-flags:")
print(cfg_vars["CFLAGS"])
# Remove unsupported C-flags
unsupported_flags = [
"-fuse-linker-plugin", "-ffat-lto-objects", "-flto-partition=none"]
for key in ["CFLAGS", "LDFLAGS", "LDSHARED"]:
if key in cfg_vars:
print("System {0}:".format(key))
print(cfg_vars[key])
flags = []
for flag in cfg_vars[key].split():
if flag in unsupported_flags:
continue
flags.append(flag)
cfg_vars[key] = " ".join(flags)
print("Editted {0}:".format(key))
print(cfg_vars[key])
if compiler == 'msvc':
# Add msvc specific hacks
# Sort linking issues with init exported symbols
def _get_export_symbols(self, ext):
return ext.export_symbols
build_ext.get_export_symbols = _get_export_symbols
if (sys.version_info.major, sys.version_info.minor) < (3, 3):
# The check above is a nasty hack. We're using the python
# version as a proxy for the MSVC version. 2008 doesn't
# have stdint.h, so is needed. 2010 does.
#
# We need to add the path to msvc includes
msvc_2008_path = (
os.path.join(os.getcwd(), 'include', 'msvc_2008'))
if self.include_dirs is not None:
self.include_dirs.append(msvc_2008_path)
else:
self.include_dirs = [msvc_2008_path]
elif (sys.version_info.major, sys.version_info.minor) < (3, 5):
# Actually, it seems that appveyor doesn't have a stdint that
# works, so even for 2010 we use our own (hacked) version
# of stdint.
# This should be pretty safe in whatever case.
msvc_2010_path = (
os.path.join(os.getcwd(), 'include', 'msvc_2010'))
if self.include_dirs is not None:
self.include_dirs.append(msvc_2010_path)
else:
self.include_dirs = [msvc_2010_path]
# We need to prepend lib to all the library names
_libraries = []
for each_lib in self.libraries:
_libraries.append('lib' + each_lib)
self.libraries = _libraries
def setup_package():
# Figure out whether to add ``*_requires = ['numpy']``.
build_requires = []
try:
import numpy
except ImportError:
build_requires = ['numpy>=1.6, <2.0']
if not READ_THE_DOCS:
install_requires = ['matplotlib>=1.3.0', 'scipy>=1.10',
'bottleneck', 'obspy>=1.0.3', 'numpy>=1.12',
'h5py']
else:
install_requires = ['matplotlib>=1.3.0', 'obspy>=1.0.3', 'mock']
install_requires.extend(build_requires)
setup_args = {
'name': 'EQcorrscan',
'version': VERSION,
'description':
'EQcorrscan - matched-filter earthquake detection and analysis',
'long_description': long_description,
'url': 'https://github.com/eqcorrscan/EQcorrscan',
'author': 'Calum Chamberlain',
'author_email': '[email protected]',
'license': 'LGPL',
'classifiers': [
'Development Status :: 4 - Beta',
'Intended Audience :: Science/Research',
'Topic :: Scientific/Engineering',
'License :: OSI Approved :: GNU Library or Lesser General Public '
'License (LGPL)',
'Programming Language :: Python :: 3.8',
'Programming Language :: Python :: 3.9',
'Programming Language :: Python :: 3.10',
],
'keywords': 'earthquake correlation detection match-filter',
'scripts': scriptfiles,
'install_requires': install_requires,
'setup_requires': ['pytest-runner'],
'tests_require': ['pytest>=2.0.0', 'pytest-cov', 'pytest-pep8',
'pytest-xdist', 'pytest-rerunfailures',
'obspy>=1.1.0'],
'cmdclass': {'build_ext': CustomBuildExt},
'packages': [
'eqcorrscan', 'eqcorrscan.utils', 'eqcorrscan.core',
'eqcorrscan.core.match_filter',
'eqcorrscan.core.match_filter.helpers', 'eqcorrscan.utils.lib',
'eqcorrscan.tutorials', 'eqcorrscan.helpers', 'eqcorrscan.tests'],
}
if using_setuptools:
setup_args['setup_requires'] = build_requires
setup_args['install_requires'] = install_requires
no_mkl = False
if "--no-mkl" in sys.argv:
no_mkl = True
sys.argv.remove("--no-mkl")
if len(sys.argv) >= 2 and (
'--help' in sys.argv[1:] or
sys.argv[1] in ('--help-commands', 'egg_info', '--version',
'clean')):
# For these actions, NumPy is not required.
pass
else:
setup_args['ext_modules'] = get_extensions(no_mkl=no_mkl)
setup_args['package_data'] = get_package_data()
setup_args['package_dir'] = get_package_dir()
if os.path.isdir("build"):
shutil.rmtree("build")
setup(**setup_args)
if __name__ == '__main__':
setup_package()