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setup.py
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from setuptools import find_packages, Extension, setup
from Cython.Build import cythonize
def read(path):
with open(path, 'r') as f:
return f.read()
long_description = read('README.md')
include_dirs = ['pyseq_align/seq-align/src', 'pyseq_align/seq-align/libs']
extra_compile_args = [
'-Wno-strict-prototypes', '-Wno-unused-variable', '-Wno-unused-function'
]
to_cythonize = [
Extension(
'pyseq_align.needleman_wunsch',
[
'pyseq_align/needleman_wunsch.pyx',
'pyseq_align/seq-align/src/alignment.c',
'pyseq_align/seq-align/src/alignment_scoring.c',
'pyseq_align/seq-align/src/needleman_wunsch.c',
],
include_dirs=include_dirs,
extra_compile_args=extra_compile_args,
),
Extension(
'pyseq_align.smith_waterman',
[
'pyseq_align/smith_waterman.pyx',
'pyseq_align/seq-align/src/alignment.c',
'pyseq_align/seq-align/src/alignment_scoring.c',
'pyseq_align/seq-align/src/smith_waterman.c',
],
include_dirs=include_dirs,
extra_compile_args=extra_compile_args,
),
Extension(
'pyseq_align.alignment',
[
'pyseq_align/alignment.pyx',
'pyseq_align/seq-align/src/alignment.c',
'pyseq_align/seq-align/src/alignment_scoring.c',
],
include_dirs=include_dirs,
extra_compile_args=extra_compile_args,
),
Extension(
'pyseq_align.scoring',
[
'pyseq_align/scoring.pyx',
'pyseq_align/seq-align/src/alignment_scoring.c',
],
include_dirs=include_dirs,
extra_compile_args=extra_compile_args,
),
]
setup(
name='pyseq-align',
version='1.0.2',
url='https://github.com/Lioscro/pyseq-align',
author='Kyung Hoi (Joseph) Min',
author_email='[email protected]',
description='', # noqa
long_description=long_description,
long_description_content_type='text/markdown',
keywords='',
python_requires='>=3.6',
license='MIT',
packages=find_packages(exclude=('tests', 'docs')),
zip_safe=False,
include_package_data=True,
setup_requires=['cython'],
install_requires=read('requirements.txt').strip().split('\n'),
ext_modules=cythonize(to_cythonize, language_level='3'),
classifiers=[
'Intended Audience :: Science/Research',
'License :: OSI Approved :: MIT License',
'Operating System :: OS Independent',
'Programming Language :: Python :: 3.7',
'Programming Language :: Python :: 3.8',
'Programming Language :: Python :: 3.9',
'Programming Language :: Cython',
'Topic :: Scientific/Engineering :: Bio-Informatics',
],
)