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O3 -> Ofast
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@taoliu
taoliu committed Mar 12, 2015
1 parent f860986 commit ee79249
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32 changes: 16 additions & 16 deletions setup.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#!/usr/bin/env python
# Time-stamp: <2015-03-10 16:13:01 Tao Liu>
# Time-stamp: <2015-03-12 00:17:23 Tao Liu>

"""Description
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sys.stderr.write("CRITICAL: Python version must be 2.7!\n")
sys.exit(1)

ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"] ),
Extension("MACS2.IO.Parser",["MACS2/IO/Parser.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.Pileup", ["MACS2/Pileup.c","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"] ),
Extension("MACS2.PeakModel", ["MACS2/PeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.c"], extra_compile_args=["-w","-O3"]),
Extension("MACS2.Signal", ["MACS2/Signal.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.c"], extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.c"], extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.c"], libraries=["m"], extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"] ),
Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-O3"]),
Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-O3"]),
ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.Parser",["MACS2/IO/Parser.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.Pileup", ["MACS2/Pileup.c","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.PeakModel", ["MACS2/PeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.Signal", ["MACS2/Signal.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.c"], libraries=["m"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
]

setup(name="MACS2",
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62 changes: 31 additions & 31 deletions setup_w_cython.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
#!/usr/bin/env python
# Time-stamp: <2015-03-10 16:12:52 Tao Liu>
# Time-stamp: <2015-03-12 00:17:39 Tao Liu>

"""Description:
Expand Down Expand Up @@ -45,38 +45,38 @@ def main():
sys.exit(1)

if has_cython:
ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"] ),
Extension("MACS2.IO.Parser",["MACS2/IO/Parser.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.Pileup", ["MACS2/Pileup.pyx","MACS2/cPosValCalculation.pxd","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"] ),
Extension("MACS2.PeakModel", ["MACS2/PeakModel.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.pyx"], extra_compile_args=["-w","-O3"]),
Extension("MACS2.Signal", ["MACS2/Signal.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.pyx"], extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.pyx"], extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.pyx"], libraries=["m"], extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"] ),
Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.hashtable", ["MACS2/hashtable.pyx"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-O3"]),
Extension("MACS2.Statistics", ["MACS2/Statistics.pyx", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-O3"]),
ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.Parser",["MACS2/IO/Parser.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.Pileup", ["MACS2/Pileup.pyx","MACS2/cPosValCalculation.pxd","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.PeakModel", ["MACS2/PeakModel.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.pyx"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.Signal", ["MACS2/Signal.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.pyx"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.pyx"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.pyx"], libraries=["m"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.pyx"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.hashtable", ["MACS2/hashtable.pyx"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.Statistics", ["MACS2/Statistics.pyx", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
]
else:
ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"] ),
Extension("MACS2.IO.Parser",["MACS2/IO/Parser.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.Pileup", ["MACS2/Pileup.c","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"] ),
Extension("MACS2.PeakModel", ["MACS2/PeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.c"], extra_compile_args=["-w","-O3"]),
Extension("MACS2.Signal", ["MACS2/Signal.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.c"], extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.c"], extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.c"], libraries=["m"], extra_compile_args=["-w","-O3"]),
Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"] ),
Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-O3"]),
Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-O3"]),
Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-O3"]),
ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.Parser",["MACS2/IO/Parser.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.Pileup", ["MACS2/Pileup.c","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.PeakModel", ["MACS2/PeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.Signal", ["MACS2/Signal.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.c"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.c"], libraries=["m"], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"] ),
Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=["-w","-Ofast"]),
]

setup(name="MACS2",
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