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