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setup.py
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setup.py
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from setuptools import setup, find_packages
from Cython.Build import cythonize
from distutils.extension import Extension
from setuptools.command.build_ext import build_ext as _build_ext
import os
USE_CYTHON = os.environ.get("USE_CYTHON", False)
ext = ".pyx" if USE_CYTHON else ".c"
cython_root = "pmaf/internal/_extensions/_cython/"
cpython_root = "pmaf/internal/_extensions/_cpython/"
class build_ext(_build_ext):
def finalize_options(self):
super().finalize_options()
self.inplace = True
ext_modules = [
Extension(
"pmaf.internal._extensions.PMAFCEXT",
sources=[
cpython_root + "_pmafc_extension/_source/c_parser.c",
cpython_root + "_pmafc_extension/_source/c_hmerizer.c",
],
include_dirs=[cpython_root + "_pmafc_extension/_source"],
),
Extension(
"pmaf.internal._extensions.cython_functions",
[cython_root + "_source/cython_functions" + ext],
),
]
# ext_modules = [
# Extension(
# "pmaf.internal._extensions.PMAFCEXT",
# sources=[
# cpython_root + "_pmafc_extension/_source/c_parser.c",
# cpython_root + "_pmafc_extension/_source/c_hmerizer.c",
# ],
# include_dirs=[cpython_root + "_pmafc_extension/_source"],
# ),
# ] + cythonize(
# Extension(
# "pmaf.internal._extensions.cython_functions",
# [cython_root + "_source/cython_functions" + ext],
# ),
# compiler_directives={"language_level": "3"},
# )
setup(
name="PhyloMAF",
version="1.0",
packages=find_packages(),
url="https://github.com/mmtechslv/PhyloMAF",
license="BSD-3-Clause",
author="Farid Musa",
author_email="farid.musa.h@gmail.com",
install_requires=[
"execnet",
"biom-format",
"Cython",
"fuzzywuzzy",
"pandas",
"dateparser",
"numpy",
#"pytest",
"urllib3",
"ete3",
"tables",
"biopython",
"scikit-bio",
],
ext_modules=cythonize(ext_modules),
tests_require=['pytest', 'coverage'],
compiler_directives={"language_level": "3"},
cmdclass={"build_ext": build_ext},
description="Phylogenetic Microbiome Analysis Framework",
)