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setup.py
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setup.py
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import sys
import os
import io
from setuptools import setup
from distutils.core import Extension
from Cython.Build import cythonize
EXTRA_COMPILE_ARGS = ["-std=c++2a"]
EXTRA_LINK_ARGS = []
if sys.platform == "darwin":
EXTRA_COMPILE_ARGS += ["-stdlib=libc++", "-mmacosx-version-min=10.9"]
EXTRA_LINK_ARGS += ["-stdlib=libc++", "-mmacosx-version-min=10.9"]
weights = cythonize([
Extension("alphacluster.weights",
extra_compile_args=EXTRA_COMPILE_ARGS,
extra_link_args=EXTRA_LINK_ARGS,
sources=["alphacluster/weights.pyx",
"src/weighted_choice.cpp",
"src/simulate.cpp"],
include_dirs=["src/"],
language="c++"),
Extension("alphacluster.transcript",
extra_compile_args=EXTRA_COMPILE_ARGS,
extra_link_args=EXTRA_LINK_ARGS,
sources=[
"alphacluster/transcript.pyx",
"src/tx.cpp"],
include_dirs=["src/"],
language="c++"),
Extension("alphacluster.gencode",
extra_compile_args=EXTRA_COMPILE_ARGS,
extra_link_args=EXTRA_LINK_ARGS,
sources=[
"alphacluster/gencode.pyx",
"src/gencode.cpp",
"src/gtf.cpp",
"src/tx.cpp",
"src/gzstream/gzstream.C",
],
include_dirs=["src/", "src/gzstream"],
libraries=["z"],
language="c++"),
Extension("alphacluster.site_specific_rates",
extra_compile_args=EXTRA_COMPILE_ARGS,
extra_link_args=EXTRA_LINK_ARGS,
sources=[
"alphacluster/site_specific_rates.pyx",
"src/weighted_choice.cpp",
"src/tx.cpp",
"src/site_rates.cpp"],
include_dirs=["src/"],
language="c++"),
])
setup(name="alphacluster",
description='Package to examine de novo clustering',
long_description=io.open('README.md', encoding='utf-8').read(),
long_description_content_type='text/markdown',
version="1.0.0",
author="Joseph Obiajulu, Jeremy McRae",
author_email="joseph.obiajulu@gmail.com, jeremy.mcrae@gmail.com",
license="MIT",
url='https://github.com/ShenLab/MVP3D',
packages=["alphacluster"],
install_requires=[
'aiohttp >= 3.0',
'scipy >= 0.9.0',
'cython >= 0.19.0',
'pyfaidx >= 0.5.8',
],
package_data={"alphacluster": ['data/rates.txt', 'weights.pxd']},
entry_points={'console_scripts': ['alphacluster = alphacluster.__main__:main']},
classifiers=[
"Development Status :: 5 - Production/Stable",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"License :: OSI Approved :: MIT License",
],
python_requires='>=3.6',
ext_modules=weights,
test_suite="tests")