setup.py

   1 #!/usr/bin/env python3
   2 # Time-stamp: <2019-12-12 13:04:02 taoliu>
   3
   4 """Description:
   5
   6 Setup script for MACS -- Model Based Analysis for ChIP-Seq data
   7
   8 This code is free software; you can redistribute it and/or modify it
   9 under the terms of the BSD License (see the file LICENSE included with
  10 the distribution).
  11 """
  12
  13 import sys
  14 from setuptools import setup, Extension
  15
  16 from numpy import get_include as numpy_get_include
  17 numpy_include_dir = [numpy_get_include()]
  18
  19 def main():
  20     if float(sys.version[:3])<3.6:
  21         sys.stderr.write("CRITICAL: Python version must >= 3.6!\n")
  22         sys.exit(1)
  23
  24     # I intend to use -Ofast, however if gcc version < 4.6, this option is unavailable so...
  25     extra_c_args = ["-w","-O3","-ffast-math","-g0"] # for C, -Ofast implies -O3 and -ffast-math
  26
  27     ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
  28                    Extension("MACS2.IO.Parser",["MACS2/IO/Parser.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
  29                    Extension("MACS2.Pileup", ["MACS2/Pileup.pyx","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
  30                    Extension("MACS2.PeakModel", ["MACS2/PeakModel.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
  31                    Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.pyx"], extra_compile_args=extra_c_args),
  32                    Extension("MACS2.Signal", ["MACS2/Signal.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
  33                    Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.pyx"], extra_compile_args=extra_c_args),
  34                    Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.pyx"], extra_compile_args=extra_c_args),
  35                    Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
  36                    Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
  37                    Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.pyx"], libraries=["m"], extra_compile_args=extra_c_args),
  38                    Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ),
  39                    Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args),
  40                    Extension("MACS2.Statistics", ["MACS2/Statistics.pyx"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args),
  41     ]
  42
  43     with open("README.md", "r") as fh:
  44         long_description = fh.read()
  45
  46     setup(name="MACS2",
  47           version="2.2.6",
  48           description="Model Based Analysis for ChIP-Seq data",
  49           long_description = long_description,
  50           long_description_content_type="text/markdown",
  51           author='Tao Liu',
  52           author_email='vladimir.liu@gmail.com',
  53           url='http://github.com/taoliu/MACS/',
  54           package_dir={'MACS2' : 'MACS2'},
  55           packages=['MACS2', 'MACS2.IO'],
  56           package_data={'MACS2':['*.pxd']},
  57           scripts=['bin/macs2', ],
  58           classifiers=[
  59               'Development Status :: 5 - Production/Stable',
  60               'Environment :: Console',
  61               'Intended Audience :: Developers',
  62               'Intended Audience :: Science/Research',
  63               'License :: OSI Approved :: BSD License',
  64               'Operating System :: MacOS :: MacOS X',
  65               'Operating System :: POSIX',
  66               'Topic :: Scientific/Engineering :: Bio-Informatics',
  67               'Programming Language :: Python :: 3.6',
  68               'Programming Language :: Python :: 3.7',
  69               'Programming Language :: Python :: 3.8',
  70               'Programming Language :: Cython',
  71               ],
  72           install_requires=['numpy>=1.17'],
  73           ext_modules = ext_modules
  74           )
  75
  76 if __name__ == '__main__':
  77     main()