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setup.py
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setup.py
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import platform
import os
import shutil
from setuptools import setup
import numpy
# Work around https://github.com/pypa/pip/issues/7953
import site
import sys
site.ENABLE_USER_SITE = "--user" in sys.argv[1:]
# Version number
version = "0.6.11"
def readme():
with open("README.md") as f:
return f.read()
# python setup.py sdist bdist_wininst upload
setup(
name="fastlmm",
version=version,
description="Fast GWAS",
long_description=readme(),
long_description_content_type="text/markdown",
keywords="gwas bioinformatics LMMs MLMs linear mixed models genomics genetics python",
url="https://fastlmm.github.io/",
author="FaST-LMM Team",
author_email="fastlmm-dev@python.org",
project_urls={
"Bug Tracker": "https://github.com/fastlmm/FaST-LMM/issues",
"Documentation": "http://fastlmm.github.io/FaST-LMM",
"Source Code": "https://github.com/fastlmm/FaST-LMM",
},
license="Apache 2.0",
classifiers=[
"Programming Language :: Python :: 3.9",
"Programming Language :: Python :: 3.10",
"Programming Language :: Python :: 3.11",
"Programming Language :: Python :: 3.12",
"Programming Language :: Python :: 3",
"Programming Language :: Python",
],
packages=[ # basically, everything with a __init__.py
"fastlmm",
"fastlmm/association",
"fastlmm/association/altset_list",
"fastlmm/association/tests",
"fastlmm/external",
"fastlmm/external/util",
"fastlmm/feature_selection",
"fastlmm/inference",
"fastlmm/inference/tests",
"fastlmm/pyplink", # old snpreader
"fastlmm/pyplink/altset_list", # old snpreader
"fastlmm/pyplink/snpreader", # old snpreader
"fastlmm/pyplink/snpset", # old snpreader
"fastlmm/util",
"fastlmm/util/matrix",
"fastlmm/util/standardizer",
"fastlmm/util/stats",
],
package_data={
"fastlmm/association": [
"Fastlmm_autoselect/FastLmmC.exe",
"Fastlmm_autoselect/libiomp5md.dll",
"Fastlmm_autoselect/fastlmmc",
"Fastlmm_autoselect/FastLmmC.Manual.pdf",
],
"fastlmm/feature_selection": [
"examples/bronze.txt",
"examples/ScanISP.Toydata.config.py",
"examples/ScanLMM.Toydata.config.py",
"examples/ScanOSP.Toydata.config.py",
"examples/toydata.5chrom.bed",
"examples/toydata.5chrom.bim",
"examples/toydata.5chrom.fam",
"examples/toydata.cov",
"examples/toydata.map",
"examples/toydata.phe",
"examples/toydata.shufflePlus.phe",
"examples/toydata.sim",
"examples/toydataTest.phe",
"examples/toydataTrain.phe",
],
"fastlmm": ["util/fastlmm.hashdown.json"],
},
install_requires=[
"pandas>=1.1.1",
"matplotlib>=1.5.1",
"scikit-learn>=0.19.1",
"bed-reader>=1.0.5",
"pysnptools>=0.5.13",
"cloudpickle>=2.2.0",
"statsmodels>=0.14.2",
"psutil>=5.6.7",
"fastlmmclib>=0.0.6",
],
extras_require={"bgen": ["pysnptools[bgen]>=0.5.13"]},
)