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setup.py
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setup.py
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import numpy as np
from setuptools import setup, find_namespace_packages
from Cython.Build import cythonize
with open("README.md", "r") as fh:
long_description = fh.read()
setup(
name="crispr-bean",
version="1.2.9",
python_requires=">=3.8.0",
author="Jayoung Ryu",
author_email="jayoung_ryu@g.harvard.edu",
description="Base Editor screen analysis with guide Activity Normalization",
long_description=long_description,
long_description_content_type="text/markdown",
url="https://github.com/pinellolab/crispr-bean",
packages=find_namespace_packages(),
ext_modules=cythonize(
["bean/mapping/CRISPResso2Align.pyx"], compiler_directives={"language_level": 2}
),
include_dirs=np.get_include(),
setup_requires=[
"setuptools>=18.0",
"Cython",
],
scripts=["bin/bean"],
install_requires=[
"numpy",
"pandas",
"scipy",
"perturb-tools>=0.3.5",
"matplotlib<3.9", # temporary error? https://github.com/DeepLabCut/DeepLabCut/issues/2581
"seaborn>=0.13.0",
"tqdm",
"bio",
"liftover",
"openpyxl>=3.0.10",
"papermill>=2.4.0",
"pyBigWig>=0.3.18",
"pyro-ppl>=1.8.5",
"scikit-learn",
"statsmodels>=0.12.1",
"ipykernel",
"pytest-order",
"nbconvert",
"logomaker",
"ipywidgets",
],
include_package_data=True,
package_data={
"bean.annotate": ["ldlr_exons.fa"],
"bean.notebooks": [
"sample_quality_report.ipynb",
"profile_editing_preference.ipynb",
],
},
classifiers=[
"Programming Language :: Python :: 3",
"Operating System :: OS Independent",
],
)