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# ----------------------------------------------------------------------------
# Copyright (c) 2013--, BP development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ----------------------------------------------------------------------------
import os
from setuptools import setup
from setuptools.extension import Extension
from setuptools.command.build_py import build_py
from setuptools.command.install import install
from setuptools.command.develop import develop
from setuptools.command.egg_info import egg_info
import versioneer
import subprocess
import numpy as np
classes = """
Development Status :: 4 - Beta
License :: OSI Approved :: BSD License
Topic :: Scientific/Engineering
Programming Language :: Python
Programming Language :: Python :: 3.7
Programming Language :: Python :: 3.8
Programming Language :: Python :: 3.9
Operating System :: Unix
Operating System :: POSIX
Operating System :: MacOS :: MacOS X
Operating System :: Linux
"""
classifiers = [s.strip() for s in classes.split('\n') if s]
with open('README.md') as f:
long_description = f.read()
curdir = os.path.abspath(__file__).rsplit('/', 1)[0]
bitarr = os.path.join(curdir, 'bp/BitArray')
class common:
def build_bitarray(self):
subprocess.run(['make', '-C', bitarr, 'libbitarr.a'])
class BitArrayBuild(build_py, common):
def run(self):
self.build_bitarray()
build_py.run(self)
class BitArrayInstall(install, common):
def run(self):
self.build_bitarray()
install.run(self)
class BitArrayDevelop(develop, common):
def run(self):
self.build_bitarray()
develop.run(self)
class BitArrayEggInfo(egg_info, common):
def run(self):
self.build_bitarray()
egg_info.run(self)
USE_CYTHON = os.environ.get('USE_CYTHON', True)
ext = '.pyx' if USE_CYTHON else '.c'
extensions = [Extension("bp._bp",
["bp/_bp" + ext],
include_dirs=[bitarr],
library_dirs=[bitarr],
libraries=['bitarr']),
Extension("bp._io",
["bp/_io" + ext], ),
Extension("bp._conv",
["bp/_conv" + ext], ),
Extension("bp._binary_tree",
["bp/_binary_tree" + ext], ),
Extension("bp._insert",
["bp/_insert" + ext], ),
Extension("bp.tests.test_bp_cy",
["bp/tests/test_bp_cy" + ext],
include_dirs=['bp/BitArray/'],
library_dirs=['bp/BitArray/'],
libraries=['bitarr']),
]
extensions.extend([Extension("bp._ba",
["bp/_ba" + ext],
include_dirs=['bp/BitArray/'],
library_dirs=['bp/BitArray/'],
libraries=['bitarr'])])
if USE_CYTHON:
from Cython.Build import cythonize
extensions = cythonize(extensions,
language_level=3)
setup(name='iow',
version=versioneer.get_version(),
description='Balanced parentheses',
author='Daniel McDonald',
author_email='damcdonald@ucsd.edu',
maintainer='Daniel McDonald',
maintainer_email='damcdonald@ucsd.edu',
url='https://github.com/biocore/improved-octo-waddle',
packages=['bp'],
ext_modules=extensions,
include_dirs=[np.get_include(), bitarr],
setup_requires=['numpy >= 1.9.2'],
package_data={'bp': ['BitArray/*', ]},
install_requires=[
'numpy >= 1.9.2',
'pandas',
'click',
'scikit-bio >= 0.5.0'],
long_description=long_description,
long_description_content_type='text/markdown',
cmdclass=versioneer.get_cmdclass({'build_py': BitArrayBuild,
'install': BitArrayInstall,
'develop': BitArrayDevelop,
'egg_info': BitArrayEggInfo}),
entry_points='''
[console_scripts]
bp=bp._cli:cli
''')
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