setup.py

   1 #!/usr/bin/env python3
   2 """Description:
   3
   4 Setup script for MACS -- Model Based Analysis for ChIP-Seq data
   5
   6 This code is free software; you can redistribute it and/or modify it
   7 under the terms of the BSD License (see the file LICENSE included with
   8 the distribution).
   9 """
  10
  11 import sys
  12 import os
  13 import re
  14 from setuptools import setup, Extension
  15 from Cython.Build import cythonize
  16 import subprocess
  17 import sysconfig
  18 import numpy
  19
  20 # get MACS version
  21 exec(open("MACS3/Utilities/Constants.py").read())
  22
  23 # classifiers
  24 classifiers =[\
  25               'Development Status :: 5 - Production/Stable',
  26               'Environment :: Console',
  27               'Intended Audience :: Developers',
  28               'Intended Audience :: Science/Research',
  29               'License :: OSI Approved :: BSD License',
  30               'Operating System :: MacOS :: MacOS X',
  31               'Operating System :: POSIX',
  32               'Operating System :: Unix',
  33               'Topic :: Scientific/Engineering :: Bio-Informatics',
  34               'Programming Language :: Python :: 3.9',
  35               'Programming Language :: Python :: 3.10',
  36               'Programming Language :: Python :: 3.11',
  37               'Programming Language :: Python :: 3.12',
  38               'Programming Language :: Cython', ]
  39
  40 install_requires = [ "numpy>=1.25",
  41                      "scipy>=1.12",
  42                      "hmmlearn>=0.3.2",
  43                      "scikit-learn>=1.3",
  44                      "cykhash>=2.0,<3.0"]
  45
  46
  47
  48 def main():
  49     if sys.version_info < (3,9):
  50         sys.stderr.write("CRITICAL: Python version must >= 3.9!\n")
  51         sys.exit(1)
  52
  53     # NumPy include dir
  54     numpy_include_dir = [ numpy.get_include() ]
  55
  56     # CFLAG
  57     # I intend to use -Ofast, however if gcc version < 4.6, this option is unavailable so...
  58     # should I care about old gcc compiler?...
  59     extra_c_args = ["-w","-Ofast", "-g0"] # for C, -Ofast implies -O3 and -ffast-math
  60
  61     # CFLAG for fermi-lite related codes
  62     clang = False
  63     icc = False
  64     new_gcc = False
  65     try:
  66         if os.environ['CC'] == "clang":
  67             clang = True
  68     except KeyError:
  69         pass
  70
  71     if not clang:
  72         try:
  73             gcc_version_check = subprocess.check_output( [os.environ.get('CC', 'gcc'), "--version"], universal_newlines=True)
  74             if gcc_version_check.find("clang") != -1:
  75                 clang = True
  76             else:
  77                 gcc_version_check = gcc_version_check.split('\n')[0] # get the first line
  78                 m = re.search(r"\s+(\d+\.\d+)\.\d+", gcc_version_check )
  79                 if m:
  80                     gcc_version = float( m[1] )
  81                     if gcc_version > 4.8:
  82                         new_gcc = True
  83         except subprocess.CalledProcessError:
  84             pass
  85
  86     try:
  87         if os.environ['CC'] == "icc":
  88             icc = True
  89     except KeyError:
  90         pass
  91
  92     extra_c_args_for_fermi = ["-std=gnu99","-DUSE_SIMDE", "-DSIMDE_ENABLE_NATIVE_ALIASES"]
  93     if icc or sysconfig.get_config_vars()['CC'] == 'icc':
  94         extra_c_args_for_fermi.extend(['-qopenmp-simd', '-DSIMDE_ENABLE_OPENMP'])
  95     elif new_gcc or clang or sysconfig.get_config_vars()['CC'] == 'clang':
  96         extra_c_args_for_fermi.extend(['-fopenmp-simd', '-DSIMDE_ENABLE_OPENMP'])
  97
  98     # extensions, those have to be processed by Cython
  99     ext_modules = [ \
 100                     Extension("MACS3.Signal.HMMR_EM", ["MACS3/Signal/HMMR_EM.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
 101                     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 ),
 102                     Extension("MACS3.Signal.HMMR_HMM", ["MACS3/Signal/HMMR_HMM.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
 103                     Extension("MACS3.Signal.Prob", ["MACS3/Signal/Prob.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
 104                     Extension("MACS3.Signal.Region", ["MACS3/Signal/Region.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
 105                     Extension("MACS3.Signal.Pileup", ["MACS3/Signal/Pileup.pyx","MACS3/Signal/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
 106                     Extension("MACS3.Signal.PileupV2", ["MACS3/Signal/PileupV2.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
 107                     Extension("MACS3.Signal.PeakModel", ["MACS3/Signal/PeakModel.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
 108                     Extension("MACS3.Signal.PeakDetect", ["MACS3/Signal/PeakDetect.pyx"], extra_compile_args=extra_c_args),
 109                     Extension("MACS3.Signal.SignalProcessing", ["MACS3/Signal/SignalProcessing.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
 110                     Extension("MACS3.Signal.FixWidthTrack", ["MACS3/Signal/FixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
 111                     Extension("MACS3.Signal.PairedEndTrack", ["MACS3/Signal/PairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
 112                     Extension("MACS3.Signal.BedGraph", ["MACS3/Signal/BedGraph.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
 113                     #Extension("MACS3.Signal.BedGraphV2", ["MACS3/Signal/BedGraphV2.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
 114                     Extension("MACS3.Signal.ScoreTrack", ["MACS3/Signal/ScoreTrack.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
 115                     Extension("MACS3.Signal.CallPeakUnit", ["MACS3/Signal/CallPeakUnit.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
 116                     Extension("MACS3.Signal.VariantStat",["MACS3/Signal/VariantStat.pyx",],libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
 117                     Extension("MACS3.Signal.ReadAlignment",["MACS3/Signal/ReadAlignment.pyx",],libraries=["m"],include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
 118                     Extension("MACS3.Signal.RACollection",["MACS3/Signal/RACollection.pyx","MACS3/fermi-lite/bfc.c","MACS3/fermi-lite/bseq.c",\
 119                                                            "MACS3/fermi-lite/bubble.c","MACS3/fermi-lite/htab.c","MACS3/fermi-lite/ksw.c","MACS3/fermi-lite/kthread.c",\
 120                                                            "MACS3/fermi-lite/mag.c","MACS3/fermi-lite/misc.c","MACS3/fermi-lite/mrope.c","MACS3/fermi-lite/rld0.c",\
 121                                                            "MACS3/fermi-lite/rle.c","MACS3/fermi-lite/rope.c","MACS3/fermi-lite/unitig.c", "MACS3/Signal/swalign.c" ], \
 122                               libraries=["m","z"], include_dirs=numpy_include_dir+["./","./MACS3/fermi-lite/","./MACS3/Signal/"], extra_compile_args=extra_c_args+extra_c_args_for_fermi),
 123                     Extension("MACS3.Signal.UnitigRACollection",["MACS3/Signal/UnitigRACollection.pyx"],libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
 124                     Extension("MACS3.Signal.PosReadsInfo",["MACS3/Signal/PosReadsInfo.pyx",],libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
 125                     Extension("MACS3.Signal.PeakVariants",["MACS3/Signal/PeakVariants.pyx",],libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
 126                     # IO
 127                     Extension("MACS3.IO.Parser",["MACS3/IO/Parser.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
 128                     Extension("MACS3.IO.PeakIO", ["MACS3/IO/PeakIO.pyx"], extra_compile_args=extra_c_args),
 129                     Extension("MACS3.IO.BedGraphIO", ["MACS3/IO/BedGraphIO.pyx"], extra_compile_args=extra_c_args),
 130                     Extension("MACS3.IO.BAM",["MACS3/IO/BAM.pyx",],libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args) ]
 131
 132
 133     with open("README.md", "r") as fh:
 134         long_description = fh.read()
 135
 136     setup( name = "MACS3",
 137            version = MACS_VERSION,
 138            description = "Model Based Analysis for ChIP-Seq data",
 139            long_description = long_description,
 140            long_description_content_type = "text/markdown",
 141            author = 'Tao Liu',
 142            author_email = 'vladimir.liu@gmail.com',
 143            url = 'http://github.com/macs3-project/MACS/',
 144            package_dir = {'MACS3' : 'MACS3'},
 145            packages = ['MACS3', 'MACS3.IO', 'MACS3.Signal', 'MACS3.Commands','MACS3.Utilities'],
 146            package_data = {'MACS3':['*.pxd']},
 147            scripts = ['bin/macs3', ],
 148            classifiers = classifiers,
 149            install_requires = install_requires,
 150            python_requires = '>=3.9',
 151            ext_modules=cythonize( ext_modules ) ),
 152 #                                  compiler_directives={'linetrace': True, 'binding': True}) )
 153
 154 if __name__ == '__main__':
 155     main()