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
  24 def main():
  25     if sys.version_info < (3, 9):
  26         sys.stderr.write("CRITICAL: Python version must >= 3.9!\n")
  27         sys.exit(1)
  28
  29     # NumPy include dir
  30     numpy_include_dir = [numpy.get_include()]
  31
  32     # CFLAG
  33     extra_c_args = ["-w", "-O3", "-g0"]
  34
  35     # CFLAG for fermi-lite related codes
  36     clang = False
  37     icc = False
  38     new_gcc = False
  39     try:
  40         if os.environ['CC'] == "clang":
  41             clang = True
  42     except KeyError:
  43         pass
  44
  45     if not clang:
  46         try:
  47             gcc_version_check = subprocess.check_output([os.environ.get('CC', 'gcc'), "--version"], universal_newlines=True)
  48             if gcc_version_check.find("clang") != -1:
  49                 clang = True
  50             else:
  51                 gcc_version_check = gcc_version_check.split('\n')[0]  # get the first line
  52                 m = re.search(r"\s+(\d+\.\d+)\.\d+", gcc_version_check)
  53                 if m:
  54                     gcc_version = float(m[1])
  55                     if gcc_version > 4.8:
  56                         new_gcc = True
  57         except subprocess.CalledProcessError:
  58             pass
  59
  60     try:
  61         if os.environ['CC'] == "icc":
  62             icc = True
  63     except KeyError:
  64         pass
  65
  66     extra_c_args_for_fermi = ["-std=gnu99", "-DUSE_SIMDE",
  67                               "-DSIMDE_ENABLE_NATIVE_ALIASES"]
  68
  69     if icc or sysconfig.get_config_vars()['CC'] == 'icc':
  70         extra_c_args_for_fermi.extend(['-qopenmp-simd',
  71                                        '-DSIMDE_ENABLE_OPENMP'])
  72     elif new_gcc or clang or sysconfig.get_config_vars()['CC'] == 'clang':
  73         extra_c_args_for_fermi.extend(['-fopenmp-simd',
  74                                        '-DSIMDE_ENABLE_OPENMP'])
  75
  76     # extensions, those have to be processed by Cython
  77     ext_modules = [Extension("MACS3.Signal.HMMR_EM",
  78                              ["MACS3/Signal/HMMR_EM.pyx"],
  79                              libraries=["m"],
  80                              include_dirs=numpy_include_dir,
  81                              extra_compile_args=extra_c_args),
  82                    Extension("MACS3.Signal.HMMR_Signal_Processing",
  83                              ["MACS3/Signal/HMMR_Signal_Processing.pyx"],
  84                              libraries=["m"],
  85                              include_dirs=numpy_include_dir,
  86                              extra_compile_args=extra_c_args),
  87                    Extension("MACS3.Signal.HMMR_HMM",
  88                              ["MACS3/Signal/HMMR_HMM.pyx"],
  89                              libraries=["m"],
  90                              include_dirs=numpy_include_dir,
  91                              extra_compile_args=extra_c_args),
  92                    Extension("MACS3.Signal.Prob",
  93                              ["MACS3/Signal/Prob.pyx"],
  94                              libraries=["m"],
  95                              include_dirs=numpy_include_dir,
  96                              extra_compile_args=extra_c_args),
  97                    Extension("MACS3.Signal.Region",
  98                              ["MACS3/Signal/Region.pyx"],
  99                              include_dirs=numpy_include_dir,
 100                              extra_compile_args=extra_c_args),
 101                    Extension("MACS3.Signal.Pileup",
 102                              ["MACS3/Signal/Pileup.pyx",
 103                               "MACS3/Signal/cPosValCalculation.c"],
 104                              include_dirs=numpy_include_dir,
 105                              extra_compile_args=extra_c_args),
 106                    Extension("MACS3.Signal.PileupV2",
 107                              ["MACS3/Signal/PileupV2.pyx"],
 108                              include_dirs=numpy_include_dir,
 109                              extra_compile_args=extra_c_args),
 110                    Extension("MACS3.Signal.PeakModel",
 111                              ["MACS3/Signal/PeakModel.pyx"],
 112                              include_dirs=numpy_include_dir,
 113                              extra_compile_args=extra_c_args),
 114                    Extension("MACS3.Signal.PeakDetect",
 115                              ["MACS3/Signal/PeakDetect.pyx"],
 116                              extra_compile_args=extra_c_args),
 117                    Extension("MACS3.Signal.SignalProcessing",
 118                              ["MACS3/Signal/SignalProcessing.pyx"],
 119                              include_dirs=numpy_include_dir,
 120                              extra_compile_args=extra_c_args),
 121                    Extension("MACS3.Signal.FixWidthTrack",
 122                              ["MACS3/Signal/FixWidthTrack.pyx"],
 123                              include_dirs=numpy_include_dir,
 124                              extra_compile_args=extra_c_args),
 125                    Extension("MACS3.Signal.PairedEndTrack",
 126                              ["MACS3/Signal/PairedEndTrack.pyx"],
 127                              include_dirs=numpy_include_dir,
 128                              extra_compile_args=extra_c_args),
 129                    Extension("MACS3.Signal.BedGraph",
 130                              ["MACS3/Signal/BedGraph.pyx"],
 131                              libraries=["m"],
 132                              include_dirs=numpy_include_dir,
 133                              extra_compile_args=extra_c_args),
 134                    Extension("MACS3.Signal.ScoreTrack",
 135                              ["MACS3/Signal/ScoreTrack.pyx"],
 136                              libraries=["m"],
 137                              include_dirs=numpy_include_dir,
 138                              extra_compile_args=extra_c_args),
 139                    Extension("MACS3.Signal.CallPeakUnit",
 140                              ["MACS3/Signal/CallPeakUnit.pyx"],
 141                              libraries=["m"],
 142                              include_dirs=numpy_include_dir,
 143                              extra_compile_args=extra_c_args),
 144                    Extension("MACS3.Signal.VariantStat",
 145                              ["MACS3/Signal/VariantStat.pyx"],
 146                              libraries=["m"],
 147                              include_dirs=numpy_include_dir,
 148                              extra_compile_args=extra_c_args),
 149                    Extension("MACS3.Signal.ReadAlignment",
 150                              ["MACS3/Signal/ReadAlignment.pyx"],
 151                              libraries=["m"],
 152                              include_dirs=numpy_include_dir,
 153                              extra_compile_args=extra_c_args),
 154                    Extension("MACS3.Signal.RACollection",
 155                              ["MACS3/Signal/RACollection.pyx",
 156                               "MACS3/fermi-lite/bfc.c",
 157                               "MACS3/fermi-lite/bseq.c",
 158                               "MACS3/fermi-lite/bubble.c",
 159                               "MACS3/fermi-lite/htab.c",
 160                               "MACS3/fermi-lite/ksw.c",
 161                               "MACS3/fermi-lite/kthread.c",
 162                               "MACS3/fermi-lite/mag.c",
 163                               "MACS3/fermi-lite/misc.c",
 164                               "MACS3/fermi-lite/mrope.c",
 165                               "MACS3/fermi-lite/rld0.c",
 166                               "MACS3/fermi-lite/rle.c",
 167                               "MACS3/fermi-lite/rope.c",
 168                               "MACS3/fermi-lite/unitig.c",
 169                               "MACS3/Signal/swalign.c"],
 170                              libraries=["m", "z"],
 171                              include_dirs=numpy_include_dir+["./",
 172                                                              "./MACS3/fermi-lite/",
 173                                                              "./MACS3/Signal/"],
 174                              extra_compile_args=extra_c_args+extra_c_args_for_fermi),
 175                    Extension("MACS3.Signal.UnitigRACollection",
 176                              ["MACS3/Signal/UnitigRACollection.pyx"],
 177                              libraries=["m"],
 178                              include_dirs=numpy_include_dir,
 179                              extra_compile_args=extra_c_args),
 180                    Extension("MACS3.Signal.PosReadsInfo",
 181                              ["MACS3/Signal/PosReadsInfo.pyx"],
 182                              libraries=["m"],
 183                              include_dirs=numpy_include_dir,
 184                              extra_compile_args=extra_c_args),
 185                    Extension("MACS3.Signal.PeakVariants",
 186                              ["MACS3/Signal/PeakVariants.pyx"],
 187                              libraries=["m"],
 188                              include_dirs=numpy_include_dir,
 189                              extra_compile_args=extra_c_args),
 190                    Extension("MACS3.IO.Parser",
 191                              ["MACS3/IO/Parser.pyx"],
 192                              include_dirs=numpy_include_dir,
 193                              extra_compile_args=extra_c_args),
 194                    Extension("MACS3.IO.PeakIO",
 195                              ["MACS3/IO/PeakIO.pyx"],
 196                              extra_compile_args=extra_c_args),
 197                    Extension("MACS3.IO.BedGraphIO",
 198                              ["MACS3/IO/BedGraphIO.pyx"],
 199                              extra_compile_args=extra_c_args),
 200                    Extension("MACS3.IO.BAM",
 201                              ["MACS3/IO/BAM.pyx",], libraries=["m"],
 202                              include_dirs=numpy_include_dir,
 203                              extra_compile_args=extra_c_args)]
 204
 205     setup(version=MACS_VERSION,
 206           package_dir={'MACS3': 'MACS3'},
 207           packages=['MACS3', 'MACS3.IO', 'MACS3.Signal', 'MACS3.Commands', 'MACS3.Utilities'],
 208           package_data={'MACS3': ['*.pxd']},
 209           scripts=['bin/macs3', ],
 210           ext_modules=cythonize(ext_modules))
 211
 212
 213 if __name__ == '__main__':
 214     main()