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
|
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# ----------------------------------------------------------------------------
# Copyright (c) 2011-2017, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
import os
import sys
from setuptools import setup, find_packages
from setuptools.extension import Extension
from setuptools.command.test import test as TestCommand
try:
import numpy as np
except ImportError:
raise ImportError("numpy must be installed prior to installing biom")
# Hack to prevent stupid "TypeError: 'NoneType' object is not callable" error
# in multiprocessing/util.py _exit_function when running `python
# setup.py test` (see
# http://www.eby-sarna.com/pipermail/peak/2010-May/003357.html),
# borrowed from https://github.com/getsentry/sentry/blob/master/setup.py
for m in ('multiprocessing', 'logging'):
try:
__import__(m)
except ImportError:
pass
__author__ = "Daniel McDonald"
__copyright__ = "Copyright 2011-2017, The BIOM Format Development Team"
__credits__ = ["Greg Caporaso", "Daniel McDonald", "Jose Clemente",
"Jai Ram Rideout", "Jorge Cañardo Alastuey", "Michael Hall"]
__license__ = "BSD"
__version__ = "2.1.7"
__maintainer__ = "Daniel McDonald"
__email__ = "mcdonadt@colorado.edu"
# derived from https://docs.pytest.org/en/3.8.0/goodpractices.html
class PyTest(TestCommand):
user_options = [("pytest-args=", "a", "Arguments to pass to pytest")]
def initialize_options(self):
TestCommand.initialize_options(self)
self.pytest_args = ""
def run_tests(self):
try:
import numpy
try:
# NumPy 1.14 changed repr output breaking our doctests,
# request the legacy 1.13 style
numpy.set_printoptions(legacy="1.13")
except TypeError:
# Old Numpy, output should be fine as it is :)
# TypeError: set_printoptions() got an unexpected
# keyword argument 'legacy'
pass
except ImportError:
numpy = None
import shlex
# import here, cause outside the eggs aren't loaded
import pytest
errno = pytest.main(shlex.split(self.pytest_args))
sys.exit(errno)
long_description = """BIOM: Biological Observation Matrix
http://www.biom-format.org
The Biological Observation Matrix (BIOM) format or: how I learned to stop
worrying and love the ome-ome
Daniel McDonald, Jose C Clemente, Justin Kuczynski, Jai Ram Rideout,
Jesse Stombaugh, Doug Wendel, Andreas Wilke, Susan Huse, John Hufnagle,
Folker Meyer, Rob Knight, J Gregory Caporaso
GigaScience 2012, 1:7.
"""
classes = """
Development Status :: 4 - Beta
License :: OSI Approved :: BSD License
Topic :: Scientific/Engineering :: Bio-Informatics
Topic :: Software Development :: Libraries :: Application Frameworks
Topic :: Software Development :: Libraries :: Python Modules
Programming Language :: Python
Programming Language :: Python :: 2.7
Programming Language :: Python :: 3.4
Programming Language :: Python :: 3.5
Programming Language :: Python :: 3.6
Programming Language :: Python :: Implementation :: CPython
Operating System :: OS Independent
Operating System :: POSIX :: Linux
Operating System :: MacOS :: MacOS X
"""
classifiers = [s.strip() for s in classes.split('\n') if s]
# Dealing with Cython
USE_CYTHON = os.environ.get('USE_CYTHON', False)
ext = '.pyx' if USE_CYTHON else '.c'
extensions = [Extension("biom._filter",
["biom/_filter" + ext],
include_dirs=[np.get_include()]),
Extension("biom._transform",
["biom/_transform" + ext],
include_dirs=[np.get_include()]),
Extension("biom._subsample",
["biom/_subsample" + ext],
include_dirs=[np.get_include()])]
if USE_CYTHON:
from Cython.Build import cythonize
extensions = cythonize(extensions)
install_requires = ["click", "numpy >= 1.9.2", "future >= 0.16.0",
"scipy >= 0.13.0", 'pandas >= 0.20.0',
"six >= 1.10.0"]
# HACK: for backward-compatibility with QIIME 1.9.x, pyqi must be installed.
# pyqi is not used anymore in this project.
if sys.version_info[0] < 3:
install_requires.append("pyqi")
import warnings
warnings.warn("Python 2.7 support will be removed on the next release",
DeprecationWarning)
setup(name='biom-format',
version=__version__,
description='Biological Observation Matrix (BIOM) format',
long_description=long_description,
license=__license__,
author=__maintainer__,
author_email=__email__,
maintainer=__maintainer__,
maintainer_email=__email__,
url='http://www.biom-format.org',
packages=find_packages(),
tests_require=['pytest',
'pytest-cov',
'flake8',
'nose'],
include_package_data=True,
ext_modules=extensions,
include_dirs=[np.get_include()],
install_requires=install_requires,
extras_require={'hdf5': ["h5py >= 2.2.0"]
},
classifiers=classifiers,
cmdclass={"pytest": PyTest},
entry_points='''
[console_scripts]
biom=biom.cli:cli
''')
|
