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setup.py
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from setuptools import find_packages
from setuptools import setup
import os
install_requires = [
"numpy>=1.21,<1.24",
"scikit-learn>=1.0,<1.2",
"anndata==0.8.*",
"scprep>=1.2.2",
"scipy>=1.7,<1.10",
"scanpy>=1.6",
"louvain==0.8.*",
"python-igraph==0.10.*",
"decorator<5.0", # pinned in #324
"memory-profiler==0.60",
"colorama==0.4.*",
"packaging==21.3",
"umap-learn==0.5.*",
"requests==2.28.*",
"pandas==1.3.5",
]
r_requires = [
"rpy2>=3.4,<3.4.3",
"anndata2ri==1.0.6",
]
evaluate_requires = ["snakemake>=7.8,<7.17", "tabulate<0.9"]
process_requires = ["numpyencoder==0.3.*"]
test_requires = [
"pytest==7.1.*",
"pytest-cov>=3.0,<4.1",
"pytest-timestamper==0.0.9",
"black==22.10.0",
"coverage>=6.4,<6.6",
"codecov==2.1.*",
"parameterized==0.8.*",
"requests==2.28.*",
"bibtexparser==1.4.*",
]
version_py = os.path.join(os.path.dirname(__file__), "openproblems", "version.py")
version = open(version_py).read().strip().split("=")[-1].replace('"', "").strip()
readme = open("README.md").read()
setup(
name="openproblems",
version=version,
packages=find_packages(),
license="MIT",
install_requires=install_requires,
python_requires=">=3.7",
extras_require={
"test": test_requires + r_requires,
"r": r_requires,
"evaluate": evaluate_requires,
"process": process_requires,
},
entry_points={
"console_scripts": ["openproblems-cli=openproblems.api.main:main"],
},
long_description=readme,
long_description_content_type="text/markdown",
include_package_data=True,
keywords=[
"computational-biology",
],
)