#!/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()