forked from hyperspy/hyperspy
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathsetup.py
413 lines (372 loc) · 15.6 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
# -*- coding: utf-8 -*-
# Copyright 2007-2020 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# HyperSpy is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with HyperSpy. If not, see <http://www.gnu.org/licenses/>.
from __future__ import print_function
import hyperspy.Release as Release
from distutils.errors import CompileError, DistutilsPlatformError
import distutils.ccompiler
import distutils.sysconfig
import itertools
import subprocess
import os
import warnings
from tempfile import TemporaryDirectory
from setuptools import setup, Extension, Command
import sys
v = sys.version_info
if v[0] != 3:
error = "ERROR: From version 0.8.4 HyperSpy requires Python 3. " \
"For Python 2.7 install Hyperspy 0.8.3 e.g. " \
"$ pip install --upgrade hyperspy==0.8.3"
print(error, file=sys.stderr)
sys.exit(1)
# stuff to check presence of compiler:
setup_path = os.path.dirname(__file__)
install_req = ['scipy>=1.1',
'matplotlib>=3.1.3,<3.5',
'numpy>=1.17.1',
'traits>=4.5.0',
'natsort',
'requests',
'tqdm>=4.9.0',
'sympy',
'dill',
'h5py>=2.3',
'jinja2',
'packaging',
'python-dateutil>=2.5.0',
'ipyparallel',
# https://github.com/ipython/ipython/pull/13466
'ipython!=8.0.*',
'dask[array]>=2.11.0',
# fsspec is missing from dask dependencies for dask < 2021.3.1
'fsspec',
'scikit-image>=0.15',
'pint>=0.10',
'numexpr',
'sparse',
'imageio',
'pyyaml',
# prettytable and ptable are API compatible
# prettytable is maintained and ptable is an unmaintained fork
'prettytable',
'tifffile>=2020.2.16',
# non-uniform axis requirement
'numba>=0.52',
# included in stdlib since v3.8, but this required version requires Python 3.10
# We can remove this requirement when the minimum supported version becomes Python 3.10
'importlib_metadata>=3.6',
# numcodecs currently only supported on x86_64/AMD64 machines
'zarr;platform_machine=="x86_64" or platform_machine=="AMD64"',
]
extras_require = {
# exclude scikit-learn==1.0 on macOS (wheels issue)
# See https://github.com/scikit-learn/scikit-learn/pull/21227
"learning": ['scikit-learn!=1.0;sys_platform=="darwin"'],
"gui-jupyter": ["hyperspy_gui_ipywidgets>=1.1.0"],
"gui-traitsui": ["hyperspy_gui_traitsui>=1.1.0"],
"mrcz": ["blosc>=1.5", 'mrcz>=0.3.6'],
"speed": ["cython", "imagecodecs>=2020.1.31"],
"usid": ["pyUSID>=0.0.7", "sidpy"],
"scalebar": ["matplotlib-scalebar"],
# bug in pip: matplotib is ignored here because it is already present in
# install_requires.
"tests": ["pytest>=3.6", "pytest-mpl", "pytest-xdist", "pytest-rerunfailures", "pytest-instafail", "matplotlib>=3.1"],
"coverage":["pytest-cov", "codecov"],
# required to build the docs
"build-doc": ["sphinx>=1.7", "sphinx_rtd_theme", "sphinx-toggleprompt", "sphinxcontrib-mermaid", "sphinxcontrib-towncrier"],
}
# Don't include "tests" and "docs" requirements since "all" is designed to be
# used for user installation.
runtime_extras_require = {x: extras_require[x] for x in extras_require.keys()
if x not in ["tests", "coverage", "build-doc"]}
extras_require["all"] = list(itertools.chain(*list(
runtime_extras_require.values())))
extras_require["dev"] = list(itertools.chain(*list(extras_require.values())))
def update_version(version):
release_path = "hyperspy/Release.py"
lines = []
with open(release_path, "r") as f:
for line in f:
if line.startswith("version = "):
line = "version = \"%s\"\n" % version
lines.append(line)
with open(release_path, "w") as f:
f.writelines(lines)
# Extensions. Add your extension here:
raw_extensions = [Extension("hyperspy.io_plugins.unbcf_fast",
[os.path.join('hyperspy', 'io_plugins', 'unbcf_fast.pyx')]),
]
cleanup_list = []
for leftover in raw_extensions:
path, ext = os.path.splitext(leftover.sources[0])
if ext in ('.pyx', '.py'):
cleanup_list.append(''.join([os.path.join(setup_path, path), '.c*']))
if os.name == 'nt':
bin_ext = '.cpython-*.pyd'
else:
bin_ext = '.cpython-*.so'
cleanup_list.append(''.join([os.path.join(setup_path, path), bin_ext]))
def count_c_extensions(extensions):
c_num = 0
for extension in extensions:
# if first source file with extension *.c or *.cpp exists
# it is cythonised or pure c/c++ extension:
sfile = extension.sources[0]
path, ext = os.path.splitext(sfile)
if os.path.exists(path + '.c') or os.path.exists(path + '.cpp'):
c_num += 1
return c_num
def cythonize_extensions(extensions):
try:
from Cython.Build import cythonize
return cythonize(extensions, compiler_directives={'language_level' : "3"})
except ImportError:
warnings.warn("""WARNING: cython required to generate fast c code is not found on this system.
Only slow pure python alternative functions will be available.
To use fast implementation of some functions writen in cython either:
a) install cython and re-run the installation,
b) try alternative source distribution containing cythonized C versions of fast code,
c) use binary distribution (i.e. wheels, egg).""")
return []
def no_cythonize(extensions):
for extension in extensions:
sources = []
for sfile in extension.sources:
path, ext = os.path.splitext(sfile)
if ext in ('.pyx', '.py'):
if extension.language == 'c++':
ext = '.cpp'
else:
ext = '.c'
sfile = path + ext
sources.append(sfile)
extension.sources[:] = sources
return extensions
# to cythonize, or not to cythonize... :
if len(raw_extensions) > count_c_extensions(raw_extensions):
extensions = cythonize_extensions(raw_extensions)
else:
extensions = no_cythonize(raw_extensions)
# to compile or not to compile... depends if compiler is present:
compiler = distutils.ccompiler.new_compiler()
assert isinstance(compiler, distutils.ccompiler.CCompiler)
distutils.sysconfig.customize_compiler(compiler)
try:
with TemporaryDirectory() as tmpdir:
compiler.compile([os.path.join(setup_path, 'hyperspy', 'misc', 'etc',
'test_compilers.c')], output_dir=tmpdir)
except (CompileError, DistutilsPlatformError):
warnings.warn("""WARNING: C compiler can't be found.
Only slow pure python alternative functions will be available.
To use fast implementation of some functions writen in cython/c either:
a) check that you have compiler (EXACTLY SAME as your python
distribution was compiled with) installed,
b) use binary distribution of hyperspy (i.e. wheels, egg, (only osx and win)).
Installation will continue in 5 sec...""")
extensions = []
from time import sleep
sleep(5) # wait 5 secs for user to notice the message
class Recythonize(Command):
"""cythonize all extensions"""
description = "(re-)cythonize all changed cython extensions"
user_options = []
def initialize_options(self):
"""init options"""
pass
def finalize_options(self):
"""finalize options"""
pass
def run(self):
# if there is no cython it is supposed to fail:
from Cython.Build import cythonize
global raw_extensions
global extensions
cythonize(extensions)
class update_version_when_dev:
def __enter__(self):
self.release_version = Release.version
# Get the hash from the git repository if available
self.restore_version = False
if self.release_version.endswith(".dev"):
p = subprocess.Popen(["git", "describe",
"--tags", "--dirty", "--always"],
stdout=subprocess.PIPE,
shell=True)
stdout = p.communicate()[0]
if p.returncode != 0:
# Git is not available, we keep the version as is
self.restore_version = False
self.version = self.release_version
else:
gd = stdout[1:].strip().decode()
# Remove the tag
gd = gd[gd.index("-") + 1:]
self.version = self.release_version + "+git."
self.version += gd.replace("-", ".")
update_version(self.version)
self.restore_version = True
else:
self.version = self.release_version
return self.version
def __exit__(self, type, value, traceback):
if self.restore_version is True:
update_version(self.release_version)
with update_version_when_dev() as version:
setup(
name="hyperspy",
package_dir={'hyperspy': 'hyperspy'},
version=version,
ext_modules=extensions,
packages=['hyperspy',
'hyperspy.datasets',
'hyperspy._components',
'hyperspy.datasets',
'hyperspy.io_plugins',
'hyperspy.docstrings',
'hyperspy.drawing',
'hyperspy.drawing._markers',
'hyperspy.drawing._widgets',
'hyperspy.learn',
'hyperspy._signals',
'hyperspy.utils',
'hyperspy.tests',
'hyperspy.tests.axes',
'hyperspy.tests.component',
'hyperspy.tests.datasets',
'hyperspy.tests.drawing',
'hyperspy.tests.io',
'hyperspy.tests.learn',
'hyperspy.tests.model',
'hyperspy.tests.samfire',
'hyperspy.tests.signals',
'hyperspy.tests.utils',
'hyperspy.tests.misc',
'hyperspy.models',
'hyperspy.misc',
'hyperspy.misc.eels',
'hyperspy.misc.eds',
'hyperspy.misc.io',
'hyperspy.misc.holography',
'hyperspy.misc.machine_learning',
'hyperspy.external',
'hyperspy.external.mpfit',
'hyperspy.external.astropy',
'hyperspy.samfire_utils',
'hyperspy.samfire_utils.segmenters',
'hyperspy.samfire_utils.weights',
'hyperspy.samfire_utils.goodness_of_fit_tests',
],
python_requires='~=3.6',
install_requires=install_req,
tests_require=["pytest>=3.0.2"],
extras_require=extras_require,
package_data={
'hyperspy':
[
'tests/drawing/*.png',
'tests/drawing/data/*.hspy',
'tests/drawing/plot_signal/*.png',
'tests/drawing/plot_signal1d/*.png',
'tests/drawing/plot_signal2d/*.png',
'tests/drawing/plot_markers/*.png',
'tests/drawing/plot_model1d/*.png',
'tests/drawing/plot_model/*.png',
'tests/drawing/plot_roi/*.png',
'misc/dask_widgets/*.html.j2',
'misc/eds/example_signals/*.hspy',
'misc/holography/example_signals/*.hdf5',
'tests/drawing/plot_mva/*.png',
'tests/drawing/plot_widgets/*.png',
'tests/drawing/plot_signal_tools/*.png',
'tests/io/blockfile_data/*.blo',
'tests/io/dens_data/*.dens',
'tests/io/dm_stackbuilder_plugin/test_stackbuilder_imagestack.dm3',
'tests/io/dm3_1D_data/*.dm3',
'tests/io/dm3_2D_data/*.dm3',
'tests/io/dm3_3D_data/*.dm3',
'tests/io/dm4_1D_data/*.dm4',
'tests/io/dm4_2D_data/*.dm4',
'tests/io/dm4_3D_data/*.dm4',
'tests/io/dm3_locale/*.dm3',
'tests/io/FEI_new/*.emi',
'tests/io/FEI_new/*.ser',
'tests/io/FEI_old/*.emi',
'tests/io/FEI_old/*.ser',
'tests/io/FEI_old/*.npy',
'tests/io/FEI_old/*.tar.gz',
'tests/io/impulse_data/*.csv',
'tests/io/impulse_data/*.log',
'tests/io/impulse_data/*.npy',
'tests/io/msa_files/*.msa',
'tests/io/hdf5_files/*.hdf5',
'tests/io/hdf5_files/*.hspy',
'tests/io/JEOL_files/*',
'tests/io/JEOL_files/Sample/00_View000/*',
'tests/io/JEOL_files/InvalidFrame/*',
'tests/io/JEOL_files/InvalidFrame/Sample/00_Dummy-Data/*',
'tests/io/tiff_files/*.tif',
'tests/io/tiff_files/*.tif.gz',
'tests/io/tiff_files/*.dm3',
'tests/io/npy_files/*.npy',
'tests/io/unf_files/*.unf',
'tests/io/bruker_data/*.bcf',
'tests/io/bruker_data/*.json',
'tests/io/bruker_data/*.npy',
'tests/io/bruker_data/*.spx',
'tests/io/ripple_files/*.rpl',
'tests/io/ripple_files/*.raw',
'tests/io/emd_files/*.emd',
'tests/io/emd_files/fei_emd_files.zip',
'tests/io/protochips_data/*.npy',
'tests/io/protochips_data/*.csv',
'tests/io/nexus_files/*.nxs',
'tests/io/empad_data/*.xml',
'tests/io/phenom_data/*.elid',
'tests/io/sur_data/*.pro',
'tests/io/sur_data/*.sur',
'tests/signals/data/test_find_peaks1D_ohaver.hdf5',
'tests/signals/data/*.hspy',
'hyperspy_extension.yaml',
],
},
author=Release.authors['all'][0],
description=Release.description,
long_description=open('README.rst').read(),
license=Release.license,
platforms=Release.platforms,
url=Release.url,
project_urls=Release.PROJECT_URLS,
keywords=Release.keywords,
cmdclass={
'recythonize': Recythonize,
},
classifiers=[
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: 3.8",
"Programming Language :: Python :: 3.9",
"Development Status :: 4 - Beta",
"Environment :: Console",
"Intended Audience :: Science/Research",
"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
"Natural Language :: English",
"Operating System :: OS Independent",
"Topic :: Scientific/Engineering",
"Topic :: Scientific/Engineering :: Physics",
],
)