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#!/usr/bin/env python3
"""Description:
Setup script for MACS -- Model Based Analysis for ChIP-Seq data
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file LICENSE included with
the distribution).
"""
import sys
import os
import re
from setuptools import setup, Extension
from Cython.Build import cythonize
import subprocess
import sysconfig
import numpy
# get MACS version
exec(open("MACS3/Utilities/Constants.py").read())
# classifiers
classifiers =[\
'Development Status :: 5 - Production/Stable',
'Environment :: Console',
'Intended Audience :: Developers',
'Intended Audience :: Science/Research',
'License :: OSI Approved :: BSD License',
'Operating System :: MacOS :: MacOS X',
'Operating System :: POSIX',
'Operating System :: Unix',
'Topic :: Scientific/Engineering :: Bio-Informatics',
'Programming Language :: Python :: 3.9',
'Programming Language :: Python :: 3.10',
'Programming Language :: Python :: 3.11',
'Programming Language :: Python :: 3.12',
'Programming Language :: Cython', ]
install_requires = [ "numpy>=1.25,<2.0.0",
"scipy>=1.12",
"hmmlearn>=0.3.2",
"scikit-learn>=1.3",
"cykhash>=2.0,<3.0"]
def main():
if sys.version_info < (3,9):
sys.stderr.write("CRITICAL: Python version must >= 3.9!\n")
sys.exit(1)
# NumPy include dir
numpy_include_dir = [ numpy.get_include() ]
# CFLAG
extra_c_args = ["-w","-O3"]
# CFLAG for fermi-lite related codes
clang = False
icc = False
new_gcc = False
try:
if os.environ['CC'] == "clang":
clang = True
except KeyError:
pass
if not clang:
try:
gcc_version_check = subprocess.check_output( [os.environ.get('CC', 'gcc'), "--version"], universal_newlines=True)
if gcc_version_check.find("clang") != -1:
clang = True
else:
gcc_version_check = gcc_version_check.split('\n')[0] # get the first line
m = re.search(r"\s+(\d+\.\d+)\.\d+", gcc_version_check )
if m:
gcc_version = float( m[1] )
if gcc_version > 4.8:
new_gcc = True
except subprocess.CalledProcessError:
pass
try:
if os.environ['CC'] == "icc":
icc = True
except KeyError:
pass
extra_c_args_for_fermi = ["-std=gnu99","-DUSE_SIMDE", "-DSIMDE_ENABLE_NATIVE_ALIASES"]
if icc or sysconfig.get_config_vars()['CC'] == 'icc':
extra_c_args_for_fermi.extend(['-qopenmp-simd', '-DSIMDE_ENABLE_OPENMP'])
elif new_gcc or clang or sysconfig.get_config_vars()['CC'] == 'clang':
extra_c_args_for_fermi.extend(['-fopenmp-simd', '-DSIMDE_ENABLE_OPENMP'])
# extensions, those have to be processed by Cython
ext_modules = [ \
Extension("MACS3.Signal.HMMR_EM", ["MACS3/Signal/HMMR_EM.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
Extension("MACS3.Signal.HMMR_Signal_Processing", ["MACS3/Signal/HMMR_Signal_Processing.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
Extension("MACS3.Signal.HMMR_HMM", ["MACS3/Signal/HMMR_HMM.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
Extension("MACS3.Signal.Prob", ["MACS3/Signal/Prob.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
Extension("MACS3.Signal.Region", ["MACS3/Signal/Region.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
Extension("MACS3.Signal.Pileup", ["MACS3/Signal/Pileup.pyx","MACS3/Signal/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
Extension("MACS3.Signal.PileupV2", ["MACS3/Signal/PileupV2.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
Extension("MACS3.Signal.PeakModel", ["MACS3/Signal/PeakModel.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS3.Signal.PeakDetect", ["MACS3/Signal/PeakDetect.pyx"], extra_compile_args=extra_c_args),
Extension("MACS3.Signal.SignalProcessing", ["MACS3/Signal/SignalProcessing.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS3.Signal.FixWidthTrack", ["MACS3/Signal/FixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS3.Signal.PairedEndTrack", ["MACS3/Signal/PairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS3.Signal.BedGraph", ["MACS3/Signal/BedGraph.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
#Extension("MACS3.Signal.BedGraphV2", ["MACS3/Signal/BedGraphV2.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS3.Signal.ScoreTrack", ["MACS3/Signal/ScoreTrack.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
Extension("MACS3.Signal.CallPeakUnit", ["MACS3/Signal/CallPeakUnit.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS3.Signal.VariantStat",["MACS3/Signal/VariantStat.pyx",],libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS3.Signal.ReadAlignment",["MACS3/Signal/ReadAlignment.pyx",],libraries=["m"],include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS3.Signal.RACollection",["MACS3/Signal/RACollection.pyx","MACS3/fermi-lite/bfc.c","MACS3/fermi-lite/bseq.c",\
"MACS3/fermi-lite/bubble.c","MACS3/fermi-lite/htab.c","MACS3/fermi-lite/ksw.c","MACS3/fermi-lite/kthread.c",\
"MACS3/fermi-lite/mag.c","MACS3/fermi-lite/misc.c","MACS3/fermi-lite/mrope.c","MACS3/fermi-lite/rld0.c",\
"MACS3/fermi-lite/rle.c","MACS3/fermi-lite/rope.c","MACS3/fermi-lite/unitig.c", "MACS3/Signal/swalign.c" ], \
libraries=["m","z"], include_dirs=numpy_include_dir+["./","./MACS3/fermi-lite/","./MACS3/Signal/"], extra_compile_args=extra_c_args+extra_c_args_for_fermi),
Extension("MACS3.Signal.UnitigRACollection",["MACS3/Signal/UnitigRACollection.pyx"],libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS3.Signal.PosReadsInfo",["MACS3/Signal/PosReadsInfo.pyx",],libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS3.Signal.PeakVariants",["MACS3/Signal/PeakVariants.pyx",],libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
# IO
Extension("MACS3.IO.Parser",["MACS3/IO/Parser.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
Extension("MACS3.IO.PeakIO", ["MACS3/IO/PeakIO.pyx"], extra_compile_args=extra_c_args),
Extension("MACS3.IO.BedGraphIO", ["MACS3/IO/BedGraphIO.pyx"], extra_compile_args=extra_c_args),
Extension("MACS3.IO.BAM",["MACS3/IO/BAM.pyx",],libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args) ]
with open("README.md", "r") as fh:
long_description = fh.read()
setup( name = "MACS3",
version = MACS_VERSION,
description = "Model Based Analysis for ChIP-Seq data",
long_description = long_description,
long_description_content_type = "text/markdown",
author = 'Tao Liu',
author_email = 'vladimir.liu@gmail.com',
url = 'http://github.com/macs3-project/MACS/',
package_dir = {'MACS3' : 'MACS3'},
packages = ['MACS3', 'MACS3.IO', 'MACS3.Signal', 'MACS3.Commands','MACS3.Utilities'],
package_data = {'MACS3':['*.pxd']},
scripts = ['bin/macs3', ],
classifiers = classifiers,
install_requires = install_requires,
python_requires = '>=3.9',
ext_modules=cythonize( ext_modules ) ),
# compiler_directives={'linetrace': True, 'binding': True}) )
if __name__ == '__main__':
main()
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