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# My code has references to the following repositories:
# RefHiC: https://github.com/BlanchetteLab/RefHiC（Analysis code）
# Axial Attention: https://github.com/lucidrains/axial-attention (Model architecture)
# Peakachu: https://github.com/tariks/peakachu (Calculate intra reads)
# Thanks a lot for their implement.
"""
Setup script for Polaris.
A Versatile Framework for Chromatin Loop Annotation in Bulk and Single-cell Hi-C Data.
"""
from setuptools import setup
with open("README.md", "r") as readme:
long_des = readme.read()
setup(
name='polaris',
version='1.1.0',
author="Yusen HOU, Audrey Baguette, Mathieu Blanchette*, Yanlin Zhang*",
author_email="yhou925@connect.hkust-gz.edu.cn",
description="A Versatile Framework for Chromatin Loop Annotation in Bulk and Single-cell Hi-C Data",
long_description=long_des,
long_description_content_type="text/markdown",
url="https://github.com/ai4nucleome/Polaris",
packages=['polaris'],
include_package_data=True,
install_requires=[
'setuptools==75.1.0',
'appdirs==1.4.4',
'click==8.0.1',
'cooler==0.8.11',
'matplotlib==3.8.0',
'numpy==1.22.4',
'pandas==1.3.0',
'scikit-learn==1.4.2',
'scipy==1.7.3',
'torch==2.2.2',
'timm==0.6.12',
'tqdm==4.65.0',
],
entry_points={
'console_scripts': [
'polaris = polaris.polaris:cli',
],
},
classifiers=[
"Programming Language :: Python :: 3",
"License :: OSI Approved :: MIT License",
"Intended Audience :: Science/Research",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Operating System :: OS Independent",
],
python_requires='>=3.9',
)
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