def main(): if float(sys.version[:3]) < 2.7 or float(sys.version[:3]) >= 2.8: sys.stderr.write("CRITICAL: Python version must be 2.7!\n") sys.exit(1) ext_modules = [ Extension("MACS2.cProb", ["MACS2/cProb.c"], libraries=["m"], include_dirs=numpy_include_dir), Extension("MACS2.IO.cParser", ["MACS2/IO/cParser.c"], include_dirs=numpy_include_dir), Extension("MACS2.cPileup", ["MACS2/cPileup.c"], include_dirs=numpy_include_dir), Extension("MACS2.cArray", ["MACS2/cArray.c"]), Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.c"], include_dirs=numpy_include_dir), Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.c"]), Extension("MACS2.cSignal", ["MACS2/cSignal.c"], include_dirs=numpy_include_dir), Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.c"]), Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.c"]), Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.c"], include_dirs=numpy_include_dir), Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.c"], include_dirs=numpy_include_dir), Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.c"], libraries=["m"]), Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.c"], include_dirs=numpy_include_dir), # Extension("MACS2.IO.cDiffScore", ["MACS2/IO/cDiffScore.c"], include_dirs=numpy_include_dir ), Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.c"], include_dirs=numpy_include_dir), Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/", numpy_get_include()]), Extension( "MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/", numpy_get_include()], ), ] setup( name="MACS2", version="2.1.0.20140616", description="Model Based Analysis for ChIP-Seq data", author="Tao Liu", author_email="*****@*****.**", url="http://github.com/taoliu/MACS/", package_dir={"MACS2": "MACS2"}, packages=["MACS2", "MACS2.IO"], # , 'MACS2.data'], # package_data={'MACS2': ['data/*.dat']}, scripts=["bin/macs2"], classifiers=[ "Development Status :: 4 - Beta", "Environment :: Console", "Intended Audience :: Developers", "Intended Audience :: Science/Research", "License :: OSI Approved :: BSD License", "Operating System :: MacOS :: MacOS X", "Operating System :: POSIX", "Topic :: Scientific/Engineering :: Bio-Informatics", "Programming Language :: Python", ], install_requires=[ "numpy>=1.6", #'scipy', ], cmdclass=command_classes, ext_modules=ext_modules, )
def doall(): setup(name='HRTime', version='1.0', description = 'a package providing access to the high resolution timer', ext_modules = [Extension('HRTime', sources=['HRTime.c'], )]) setup(name='rtsched', version='1.0', description = 'a package providing (limited) real-time processing/priority functionality', ext_modules = [Extension('rtsched', sources=['rtsched/rtsched.c'], )]) # these come from the SciPy cookbook: setup(name='rebin', version='1.0', description = 'a package providing the rebin "resampling function', py_modules=['rebin'], cmdclass={'build_py':build_py}, ) setup(name='DataFrame', version='1.0', description = 'a package providing R-like data.frame functionality', py_modules=['DataFrame'], cmdclass={'build_py':build_py} ) # these depend on numpy: if has_numpy: setup(name='sincos', version='1.0', description = 'a package providing a sincos function', ext_modules = [Extension('sincos', sources=['sincos.c','mips_sincos.c','cephes_sincos.c'], depends=['sse_mathfun/sse_mathfun.h'], include_dirs = [numpy_get_include()], extra_compile_args =['-g','-msse2','-faltivec','-DHAVE_VECLIB','-framework','Accelerate'], extra_link_args =['-g','-msse2','-faltivec','-framework','Accelerate'] )]) setup(name='rjvbFilt', version='1.0', description = 'a package providing some filtring functions', ext_modules = [Extension('rjvbFilt', sources=['rjvbFilters.cpp','rjvbFilt.c'], depends=['ParsedSequence.h','rjvbFilters.c','rjvbFilters.h'], include_dirs = [numpy_get_include()], extra_compile_args =['-g','-msse2','-faltivec','-framework','macstl','-UNDEBUG'], extra_link_args =['-g','-msse2','-faltivec'] )]) setup(name='fmadd', version='1.0', description = 'a package providing an fmadd function', ext_modules = [Extension('fmadd', sources=['fmadd.cpp'], depends=['fmadd.c'], extra_compile_args =['-g','-msse2','-faltivec','-UNDEBUG'], include_dirs = [numpy_get_include()] )])
def __init__(self): compile_args = "@CYTHON_BINDINGS_COMPILE_DEFINITIONS@" self.compile_args = [ "-D" + x for x in compile_args.split(';') if len(x) ] self.compile_args = list(set(self.compile_args)) include_dirs = "@CYTHON_BINDINGS_INCLUDE_DIRECTORIES@" include_dirs += ';{}'.format(numpy_get_include()) self.include_dirs = [x for x in include_dirs.split(';') if len(x)] self.include_dirs.append('@CMAKE_CURRENT_SOURCE_DIR@/include') self.include_dirs = list(set(self.include_dirs)) library_dirs = "@CYTHON_BINDINGS_LINK_FLAGS@" self.library_dirs = [x for x in library_dirs.split(';') if len(x)] self.libraries = [ re.sub("^lib", "", get_lib_name(l)) for l in "@CYTHON_BINDINGS_LIBRARIES@".split(";") if len(l) ] self.libraries = list(set(self.libraries)) self.library_dirs += [ os.path.dirname(l) for l in "@CYTHON_BINDINGS_TARGET_FILES@".split(';') if len(l) ] self.library_dirs = list(set(self.library_dirs)) self.link_args = [] if linux_build: for l in self.libraries: self.link_args += ['-Wl,--no-as-needed', '-l{}'.format(l)] self.libraries = [] if not win32_build: self.extra_objects = [ l for l in '@CYTHON_BINDINGS_STATIC_LIBRARIES@'.split(';') if len(l) ] else: self.extra_objects = []
def __init__(self): compile_args = "@CYTHON_BINDINGS_COMPILE_DEFINITIONS@" self.compile_args = [ "-D" + x for x in compile_args.split(';') if len(x) ] self.compile_args = list(set(self.compile_args)) include_dirs = "@CYTHON_BINDINGS_INCLUDE_DIRECTORIES@" include_dirs += ';{}'.format(numpy_get_include()) self.include_dirs = [x for x in include_dirs.split(';') if len(x)] self.include_dirs.append('@CMAKE_CURRENT_SOURCE_DIR@/include') self.include_dirs = list(set(self.include_dirs)) library_dirs = "@CYTHON_BINDINGS_LINK_FLAGS@" self.library_dirs = [x for x in library_dirs.split(';') if len(x)] self.libraries = [ re.sub("^lib", "", os.path.splitext(os.path.basename(l))[0]) for l in "@CYTHON_BINDINGS_LIBRARIES@".split(";") if len(l) ] self.libraries = list(set(self.libraries)) self.library_dirs += [ os.path.dirname(l) for l in "@CYTHON_BINDINGS_TARGET_FILES@".split(';') if len(l) ] self.library_dirs = list(set(self.library_dirs)) self.link_args = []
def def_ext_modules(self): # Overloading compilers. os.environ["CXX"] = "c++" os.environ["CC"] = "gcc" BITPIT_ENABLE_MPI = 0 include_libs = "-I" + self.PABLO_include_path include_libs = include_libs + " -I" + self.IO_include_path if ((not (not self.mpi_include_path)) and (ENABLE_MPI4PY)): BITPIT_ENABLE_MPI = 1 include_libs = include_libs + " -I" + self.mpi_include_path os.environ["CXX"] = "mpic++" os.environ["CC"] = "mpicc" _extra_compile_args = [ "-std=c++11", "-O3", "-fPIC", include_libs, "-DBITPIT_ENABLE_MPI=" + str(BITPIT_ENABLE_MPI) ] _extra_link_args = ["-fPIC" ] # Needed? We have already the same flag for # the compiler args above. _cython_directives = { "boundscheck": False, "wraparound": False, # http://stackoverflow.com/questions/23351813/how-to-declare-an-ndarray-in-cython-with-a-general-floating-point-type "nonecheck": False } _language = "c++" _extra_objects = ["libbitpit_MPI.a" if (BITPIT_ENABLE_MPI) \ else "libbitpit.a"] src_dir = os.path.dirname(self.IO_include_path.rstrip("/")) common_dir = src_dir + "/common/" operators_dir = src_dir + "/operators/" containers_dir = src_dir + "/containers/" _include_dirs = [ ".", self.PABLO_include_path, self.IO_include_path, common_dir, operators_dir, containers_dir, numpy_get_include() ] # Cython compile time environment. _cc_time_env = {"BITPIT_ENABLE_MPI": BITPIT_ENABLE_MPI} ext_modules = [ Extension( os.path.splitext(self.extensions_source)[0], [self.extensions_source], extra_compile_args=_extra_compile_args, extra_link_args=_extra_link_args, cython_directives=_cython_directives, language=_language, extra_objects=_extra_objects, include_dirs=_include_dirs, cython_compile_time_env=_cc_time_env, ) ] #return cythonize(ext_modules) return ext_modules
def _extension_named(name): return Extension( f"cnn.{name}", [f"src/cnn/{name}.pyx"], define_macros=[("NPY_NO_DEPRECATED_API", None)], include_dirs=[numpy_get_include(),], #language='c++', )
def doall(): setup(name='HRTime', version='1.0', description = 'a package providing access to the high resolution timer', ext_modules = [Extension('HRTime', sources=['HRTime.c'], libraries=['rt'], )]) setup(name='rtsched', version='1.0', description = 'a package providing (limited) real-time processing/priority functionality', ext_modules = [Extension('rtsched', sources=['rtsched/rtsched.c'], )]) # these come from the SciPy cookbook: setup(name='rebin', version='1.0', description = 'a package providing the rebin "resampling function', py_modules=['rebin'], cmdclass={'build_py':build_py}, ) setup(name='DataFrame', version='1.0', description = 'a package providing R-like data.frame functionality', py_modules=['DataFrame'], cmdclass={'build_py':build_py} ) # these depend on numpy: setup(name='rjvbFilt', version='1.0', description = 'a package providing some filtring functions', ext_modules = [Extension('rjvbFilt', sources=['rjvbFilt.c','rjvbFilters.c'], depends=['ParsedSequence.h'], include_dirs = [numpy_get_include()], extra_compile_args =['-mfpmath=sse','-msse','-msse2','-msse3','-msse4','-ftree-vectorize'] )]) setup(name='sincos', version='1.0', description = 'a package providing a sincos function', ext_modules = [Extension('sincos', sources=['sincos.c','mips_sincos.c','cephes_sincos.c'], include_dirs = [numpy_get_include()], extra_compile_args =['-mfpmath=sse','-msse','-msse2','-msse3','-msse4','-ftree-vectorize'] )]) setup(name='fmadd', version='1.0', description = 'a package providing an fmadd function', ext_modules = [Extension('fmadd', sources=['fmadd.c'], include_dirs = [numpy_get_include()] )])
def main(): if float(sys.version[:3])<2.7 or float(sys.version[:3])>=2.8: sys.stderr.write("CRITICAL: Python version must be 2.7!\n") sys.exit(1) ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.c"], libraries=["m"], include_dirs=numpy_include_dir ), Extension("MACS2.IO.cParser",["MACS2/IO/cParser.c"], include_dirs=numpy_include_dir), Extension("MACS2.cPileup", ["MACS2/cPileup.c"], include_dirs=numpy_include_dir ), Extension("MACS2.cArray", ["MACS2/cArray.c"]), Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.c"], include_dirs=numpy_include_dir), Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.c"]), Extension("MACS2.cSignal", ["MACS2/cSignal.c"], include_dirs=numpy_include_dir), Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.c"],), Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.c"],), Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.c"], include_dirs=numpy_include_dir), Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.c"], include_dirs=numpy_include_dir), Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.c"], libraries=["m"]), Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.c"], include_dirs=numpy_include_dir ), Extension("MACS2.IO.cCompositeScoreTrack", ["MACS2/IO/cCompositeScoreTrack.c"],), Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()]), ] setup(name="MACS2", version="2.0.10.09132012", description="Model Based Analysis for ChIP-Seq data", author='Tao Liu', author_email='*****@*****.**', url='http://github.com/taoliu/MACS/', package_dir={'MACS2' : 'MACS2'}, packages=['MACS2', 'MACS2.IO'],#, 'MACS2.data'], #package_data={'MACS2': ['data/*.dat']}, scripts=['bin/macs2', ], classifiers=[ 'Development Status :: 4 - Beta', 'Environment :: Console', 'Intended Audience :: Developers', 'Intended Audience :: Science/Research', 'License :: OSI Approved :: Artistic License', 'Operating System :: MacOS :: MacOS X', 'Operating System :: POSIX', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Programming Language :: Python', ], install_requires=[ 'numpy>=1.6', ], cmdclass = command_classes, ext_modules = ext_modules )
def GenExtension( name, pkg, ): pyx_src = name.replace('.', '/') pyx_src = pyx_src + '.pyx' ext_src = pyx_src if pkg.found: return Extension(name, [ext_src], extra_compile_args=pkg.compile_args, include_dirs=pkg.include_dirs + [numpy_get_include()], library_dirs=pkg.library_dirs, libraries=pkg.libraries) else: print("Failed to find {}".format(pkg.name)) return None
# # This script can be run using the following command: # # python setup_cython.py build_ext --inplace # from distutils.core import setup from distutils.extension import Extension from Cython.Distutils import build_ext from numpy import get_include as numpy_get_include numpy_includes = numpy_get_include() ext_modules = [ Extension("nuc_dynamics.dyn_util", ["nuc_dynamics/dyn_util.pyx"], libraries=["m"], include_dirs=[numpy_includes]) ] setup(name='NucDynamics Cython utilities', cmdclass={'build_ext': build_ext}, ext_modules=ext_modules)
def GenExtension(name, pkg, ): pyx_src = name.replace('.', '/') pyx_src = pyx_src + '.pyx' ext_src = pyx_src if pkg.found: return Extension(name, [ext_src], extra_compile_args = pkg.compile_args, include_dirs = pkg.include_dirs + [numpy_get_include()], library_dirs = pkg.library_dirs, libraries = pkg.libraries) else: print("Failed to find {}".format(pkg.name)) return None
## Copyright (C) 2012 Max-Planck-Society ## Author: Marco Selig from distutils.core import setup from distutils.extension import Extension as extension from Cython.Distutils import build_ext from numpy import get_include as numpy_get_include srcs = ["wrapper.pyx", "interfacer.cpp"] libs = ["sharp", "fftpack", 'c_utils'] idirs = [numpy_get_include(), "../libsharp-code/c_utils", "../libsharp-code/libfftpack", "../libsharp-code/libsharp"] ldirs = ["../libsharp-code/auto/lib"] exmod = [extension("libsharp_wrapper_gl", srcs, language="c++", include_dirs=idirs, library_dirs=ldirs, libraries=libs)] setup(name="libsharp_wrapper_gl", version="0.1",
def def_ext_modules(self): # Define \"Extension\" being cythonized. # Overloading compilers. os.environ["CXX"] = "c++" os.environ["CC"] = "gcc" BITPIT_ENABLE_MPI = 0 include_paths = [ self.bitpit_path + "/include/bitpit/", self.madeleine_path + "../../src/" ] mpi_lib = "" if ((not (not self.mpi_include_path)) and (ENABLE_MPI4PY)): BITPIT_ENABLE_MPI = 1 include_paths.append(self.mpi_include_path) os.environ["CXX"] = "mpic++" os.environ["CC"] = "mpicc" mpi_lib = "/usr/local/openmpi-1.10.5_intel/lib/libmpi.so" mpi_lib = "/usr/lib64/openmpi-1.10/lib/libmpi.so" _extra_compile_args = [ "-std=c++11", "-g", "-O0", "-fPIC", #include_paths, "-DBITPIT_ENABLE_MPI=" + str(BITPIT_ENABLE_MPI) ] _extra_link_args = ["-fPIC" ] # Needed? We have already the same flag for # the compiler args above. _cython_directives = { "boundscheck": False, "wraparound": False, # http://stackoverflow.com/questions/23351813/how-to-declare-an-ndarray-in-cython-with-a-general-floating-point-type "nonecheck": False } _language = "c++" bitpit_lib = self.bitpit_path + "/lib/" if (BITPIT_ENABLE_MPI): bitpit_lib = bitpit_lib + "libbitpit_MPI_D.so" else: bitpit_lib = bitpit_lib + "libbitpit_D.so" madeleine_lib = self.madeleine_path + "libmadeleine.so" _extra_objects = [mpi_lib, bitpit_lib, madeleine_lib, "-lxml2"] ##FINO QUI! #print(os.path.dirname(self.bitpit_include_path)) #piercedVector_subdir = os.path.dirname(self.bitpit_include_path) + "/containers/" _include_dirs = [".", numpy_get_include()] _include_dirs.extend(include_paths) # Cython compile time environment. _cc_time_env = {"BITPIT_ENABLE_MPI": BITPIT_ENABLE_MPI} ext_modules = [ Extension( os.path.splitext(self.extensions_source)[0], [self.extensions_source], extra_compile_args=_extra_compile_args, extra_link_args=_extra_link_args, cython_directives=_cython_directives, language=_language, extra_objects=_extra_objects, include_dirs=_include_dirs, cython_compile_time_env=_cc_time_env, ) ] return cythonize(ext_modules, gdb_debug=True)
def main(): if float(sys.version[:3])<2.7 or float(sys.version[:3])>=2.8: sys.stderr.write("CRITICAL: Python version must be 2.7!\n") sys.exit(1) # I intend to use -Ofast, however if gcc version < 4.6, this option is unavailable so... extra_c_args = ["-w","-O3","-ffast-math"] # for C, -Ofast implies -O3 and -ffast-math ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ), Extension("MACS2.IO.Parser",["MACS2/IO/Parser.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.Pileup", ["MACS2/Pileup.c","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ), Extension("MACS2.PeakModel", ["MACS2/PeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.c"], extra_compile_args=extra_c_args), Extension("MACS2.Signal", ["MACS2/Signal.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.c"], extra_compile_args=extra_c_args), Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.c"], extra_compile_args=extra_c_args), Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.c"], libraries=["m"], extra_compile_args=extra_c_args), Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ), Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args), Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args), ] setup(name="MACS2", version="2.1.1.20160226", description="Model Based Analysis for ChIP-Seq data", author='Tao Liu', author_email='*****@*****.**', url='http://github.com/taoliu/MACS/', package_dir={'MACS2' : 'MACS2'}, packages=['MACS2', 'MACS2.IO'],#, 'MACS2.data'], #package_data={'MACS2': ['data/*.dat']}, scripts=['bin/macs2', ], classifiers=[ 'Development Status :: 4 - Beta', 'Environment :: Console', 'Intended Audience :: Developers', 'Intended Audience :: Science/Research', 'License :: OSI Approved :: BSD License', 'Operating System :: MacOS :: MacOS X', 'Operating System :: POSIX', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Programming Language :: Python', ], install_requires=[ 'numpy>=1.6', #'scipy', ], cmdclass = command_classes, ext_modules = ext_modules )
extra_compile_args.append('-Wno-shift-negative-value') extra_compile_args.append('-Wno-parentheses-equality') extra_compile_args.append('-Wno-deprecated-declarations') else: # Remove the "-Wstrict-prototypes" compiler option that swig adds, which isn't valid for C++. cfg_vars = sysconfig.get_config_vars() for key, value in cfg_vars.items(): if type(value) == str: cfg_vars[key] = value.replace("-Wstrict-prototypes", "") extra_compile_args.append('-Wno-maybe-uninitialized') # the libgip.so module containing all the C++ code gip_module = Extension( name=os.path.join("gippy", "libgip"), sources=glob.glob('GIP/*.cpp'), include_dirs=['GIP', numpy_get_include()] + gdal_config.include, library_dirs=lib_dirs, libraries=[ 'pthread' ] + gdal_config.libs, extra_compile_args=extra_compile_args, extra_link_args=extra_link_args ) # the swig .so modules containing the C++ code that wraps libgip.so swig_modules = [] for n in ['gippy', 'algorithms']: src = os.path.join('gippy', n + '.i') cppsrc = os.path.join('gippy', n + '_wrap.cpp') src = cppsrc if os.path.exists(cppsrc) else src swig_modules.append(
from distutils.core import setup from distutils.extension import Extension from distutils.sysconfig import get_python_inc from Cython.Distutils import build_ext from numpy import get_include as numpy_get_include ext_modules = [Extension("_regions", ["src/_regions.pyx"], include_dirs = [numpy_get_include()])] setup( name = '_regions', cmdclass = {'build_ext': build_ext}, ext_modules = ext_modules )
from distutils.core import setup, Extension try: from numpy import get_include as numpy_get_include numpy_includes=numpy_get_include() del numpy_get_include except: print("falling back to hardcoded numpy header directory") numpy_includes='/usr/lib/python3.2/site-packages/numpy/core/include' try: from distutils.command.build_py import build_py_2to3 as build_py except ImportError: from distutils.command.build_py import build_py def doall(): setup(name='HRTime', version='1.0', description = 'a package providing access to the high resolution timer', ext_modules = [Extension('HRTime', sources=['HRTime.c'], )]) setup(name='rtsched', version='1.0', description = 'a package providing (limited) real-time processing/priority functionality', ext_modules = [Extension('rtsched', sources=['rtsched/rtsched.c'], )]) # these come from the SciPy cookbook: # setup(name='rebin', version='1.0', # description = 'a package providing the rebin "resampling function', # py_modules=['rebin'], cmdclass={'build_py':build_py}, )
@status: beta @version: $Revision$ @author: Tao Liu @contact: [email protected] """ import os import sys from setuptools import setup, Extension # Use build_ext from Cython if found command_classes = {} try: from numpy import get_include as numpy_get_include numpy_include_dir = [numpy_get_include()] except: numpy_include_dir = [] sys.stderr.write("CRITICAL:Numpy must be installed!\n") sys.exit(1) def main(): if float(sys.version[:3]) < 2.7 or float(sys.version[:3]) >= 2.8: sys.stderr.write("CRITICAL: Python version must be 2.7!\n") sys.exit(1) ext_modules = [ Extension("MACS2.cProb", ["MACS2/cProb.c"], libraries=["m"], include_dirs=numpy_include_dir,
def main(): if float(sys.version[:3])<2.7 or float(sys.version[:3])>=2.8: sys.stderr.write("CRITICAL: Python version must be 2.7!\n") sys.exit(1) if has_cython: ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.pyx"], libraries=["m"]), Extension("MACS2.IO.cParser",["MACS2/IO/cParser.pyx"]), Extension("MACS2.cPileup", ["MACS2/cPileup.pyx"], include_dirs=numpy_include_dir ), Extension("MACS2.cArray", ["MACS2/cArray.pyx"]), Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.pyx"], include_dirs=numpy_include_dir), Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.pyx"]), Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.pyx"],), Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.pyx"],), Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.pyx"], include_dirs=numpy_include_dir), Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.pyx"], libraries=["m"]), Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.pyx"], include_dirs=numpy_include_dir ), Extension("MACS2.IO.cCompositeScoreTrack", ["MACS2/IO/cCompositeScoreTrack.pyx"],), Extension("MACS2.hashtable", ["MACS2/hashtable.pyx"],include_dirs=["MACS2/",numpy_get_include()]), ] else: ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.c"], libraries=["m"]), Extension("MACS2.IO.cParser",["MACS2/IO/cParser.c"]), Extension("MACS2.cPileup", ["MACS2/cPileup.c"], include_dirs=numpy_include_dir), Extension("MACS2.cArray", ["MACS2/cArray.c"]), Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.c"], include_dirs=numpy_include_dir), Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.c"]), Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.c"],), Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.c"],), Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.c"], include_dirs=numpy_include_dir), Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.c"], libraries=["m"]), Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.c"], include_dirs=numpy_include_dir), Extension("MACS2.IO.cCompositeScoreTrack", ["MACS2/IO/cCompositeScoreTrack.c"],), Extension("MACS2.hashtable", ["MACS2/hashtable.c"],include_dirs=["MACS2/",numpy_get_include()]), ] setup(name="MACS", version="2.0.10", description="Model Based Analysis for ChIP-Seq data", author='Tao Liu', author_email='*****@*****.**', url='http://github.com/taoliu/MACS/', package_dir={'MACS2' : 'MACS2'}, packages=['MACS2', 'MACS2.IO', 'MACS2.data'], package_data={'MACS2': ['data/*.dat']}, scripts=['bin/macs2', 'bin/MLEPostPoisRatios', 'bin/MCMCPostPoisRatios', ], classifiers=[ 'Development Status :: 4 - experimental', 'Environment :: Console', 'Intended Audience :: Developers', 'License :: OSI Approved :: Artistic License', 'Operating System :: MacOS :: MacOS X', 'Operating System :: Microsoft :: Windows', 'Operating System :: POSIX', 'Programming Language :: Python', ], cmdclass = command_classes, ext_modules = ext_modules )
extra_compile_args.append('-Wno-absolute-value') extra_compile_args.append('-Wno-shift-negative-value') extra_compile_args.append('-Wno-parentheses-equality') extra_compile_args.append('-Wno-deprecated-declarations') else: # Remove the "-Wstrict-prototypes" compiler option that swig adds, which isn't valid for C++. cfg_vars = sysconfig.get_config_vars() for key, value in cfg_vars.items(): if type(value) == str: cfg_vars[key] = value.replace("-Wstrict-prototypes", "") extra_compile_args.append('-Wno-maybe-uninitialized') # the libgip.so module containing all the C++ code gip_module = Extension(name=os.path.join("gippy", "libgip"), sources=glob.glob('GIP/*.cpp'), include_dirs=['GIP', numpy_get_include()] + gdal_config.include, library_dirs=lib_dirs, libraries=['pthread'] + gdal_config.libs, extra_compile_args=extra_compile_args, extra_link_args=extra_link_args) # the swig .so modules containing the C++ code that wraps libgip.so swig_modules = [] for n in ['gippy', 'algorithms']: src = os.path.join('gippy', n + '.i') cppsrc = os.path.join('gippy', n + '_wrap.cpp') src = cppsrc if os.path.exists(cppsrc) else src swig_modules.append( Extension(name=os.path.join('gippy', '_' + n), sources=[src],
def GenExtension(name): pyx_src = name.replace('.', '/') pyx_src = pyx_src + '.pyx' ext_src = pyx_src return Extension(name, [ext_src], extra_compile_args = config.compile_args, include_dirs = config.include_dirs + [numpy_get_include()], library_dirs = config.library_dirs, libraries = config.libraries, extra_link_args = config.link_args)
def main(): if float(sys.version[:3])<3.6: sys.stderr.write("CRITICAL: Python version must >= 3.6!\n") sys.exit(1) cwd = os.path.abspath(os.path.dirname(__file__)) # install required numpy p = subprocess.call([sys.executable, "-m", 'pip', 'install', f'numpy{numpy_requires}'],cwd=cwd) if p != 0: # Could be due to a too old pip version and build isolation, check that try: # Note, pip may not be installed or not have been used import pip if LooseVersion(pip.__version__) < LooseVersion('18.0.0'): raise RuntimeError("Installing requirements failed. Possibly due " "to `pip` being too old, found version {}, " "needed is >= 18.0.0.".format(pip.__version__)) else: raise RuntimeError("Installing requirements failed!") except ImportError: raise RuntimeError("Installing requirement failed! `pip` has to be installed!") from numpy import get_include as numpy_get_include numpy_include_dir = [numpy_get_include()] # I intend to use -Ofast, however if gcc version < 4.6, this option is unavailable so... extra_c_args = ["-w","-O3","-ffast-math","-g0"] # for C, -Ofast implies -O3 and -ffast-math ext_modules = [Extension("MACS2.Prob", ["MACS2/Prob.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ), Extension("MACS2.IO.Parser",["MACS2/IO/Parser.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.Pileup", ["MACS2/Pileup.pyx","MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ), Extension("MACS2.PeakModel", ["MACS2/PeakModel.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.pyx"], extra_compile_args=extra_c_args), Extension("MACS2.Signal", ["MACS2/Signal.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.pyx"], extra_compile_args=extra_c_args), Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.pyx"], extra_compile_args=extra_c_args), Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.pyx"], libraries=["m"], extra_compile_args=extra_c_args), Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args ), Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), #Extension("MACS2.Statistics", ["MACS2/Statistics.pyx"], libraries=["m"], include_dirs=["MACS2/",numpy_get_include()], extra_compile_args=extra_c_args), ] with open("README.md", "r") as fh: long_description = fh.read() setup(name="MACS2", version="2.2.7.1", description="Model Based Analysis for ChIP-Seq data", long_description = long_description, long_description_content_type="text/markdown", author='Tao Liu', author_email='*****@*****.**', url='http://github.com/taoliu/MACS/', package_dir={'MACS2' : 'MACS2'}, packages=['MACS2', 'MACS2.IO'], package_data={'MACS2':['*.pxd']}, scripts=['bin/macs2', ], classifiers=[ 'Development Status :: 5 - Production/Stable', 'Environment :: Console', 'Intended Audience :: Developers', 'Intended Audience :: Science/Research', 'License :: OSI Approved :: BSD License', 'Operating System :: MacOS :: MacOS X', 'Operating System :: POSIX', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Programming Language :: Python :: 3.6', 'Programming Language :: Python :: 3.7', 'Programming Language :: Python :: 3.8', 'Programming Language :: Cython', ], install_requires=install_requires, setup_requires=install_requires, python_requires='>=3.6', ext_modules = ext_modules )
@status: beta @version: $Revision$ @author: Tao Liu @contact: [email protected] """ import os import sys from distutils.core import setup, Extension # Use build_ext from Cython if found command_classes = {} try: from numpy import get_include as numpy_get_include numpy_include_dir = [numpy_get_include()] except: numpy_include_dir = [] sys.stderr.write("CRITICAL:Numpy must be installed!\n") sys.exit(1) def main(): if float(sys.version[:3])<2.7 or float(sys.version[:3])>=2.8: sys.stderr.write("CRITICAL: Python version must be 2.7!\n") sys.exit(1) ext_modules = [Extension("MACS2.cProb", ["MACS2/cProb.c"], libraries=["m"], include_dirs=numpy_include_dir ), Extension("MACS2.IO.cParser",["MACS2/IO/cParser.c"], include_dirs=numpy_include_dir), Extension("MACS2.cPileup", ["MACS2/cPileup.c"], include_dirs=numpy_include_dir ), Extension("MACS2.cArray", ["MACS2/cArray.c"]), Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.c"], include_dirs=numpy_include_dir),
def main(): if float(sys.version[:3]) < 2.7 or float(sys.version[:3]) >= 2.8: sys.stderr.write("CRITICAL: Python version must be 2.7!\n") sys.exit(1) # I intend to use -Ofast, however if gcc version < 4.6, this option is unavailable so... extra_c_args = ["-w", "-O3", "-ffast-math"] # for C, -Ofast implies -O3 and -ffast-math if has_cython: ext_modules = [ Extension("MACS2.Prob", ["MACS2/Prob.pyx"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.Parser", ["MACS2/IO/Parser.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.Pileup", [ "MACS2/Pileup.pyx", "MACS2/cPosValCalculation.pxd", "MACS2/cPosValCalculation.c" ], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.PeakModel", ["MACS2/PeakModel.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.pyx"], extra_compile_args=extra_c_args), Extension("MACS2.Signal", ["MACS2/Signal.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.pyx"], extra_compile_args=extra_c_args), Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.pyx"], extra_compile_args=extra_c_args), Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.pyx"], libraries=["m"], extra_compile_args=extra_c_args), Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.pyx"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.hashtable", ["MACS2/hashtable.pyx"], include_dirs=["MACS2/", numpy_get_include()], extra_compile_args=extra_c_args), Extension("MACS2.Statistics", ["MACS2/Statistics.pyx"], libraries=["m"], include_dirs=["MACS2/", numpy_get_include()], extra_compile_args=extra_c_args), ] else: ext_modules = [ Extension("MACS2.Prob", ["MACS2/Prob.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.Parser", ["MACS2/IO/Parser.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.Pileup", ["MACS2/Pileup.c", "MACS2/cPosValCalculation.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.PeakModel", ["MACS2/PeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.PeakDetect", ["MACS2/PeakDetect.c"], extra_compile_args=extra_c_args), Extension("MACS2.Signal", ["MACS2/Signal.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.PeakIO", ["MACS2/IO/PeakIO.c"], extra_compile_args=extra_c_args), Extension("MACS2.IO.BedGraphIO", ["MACS2/IO/BedGraphIO.c"], extra_compile_args=extra_c_args), Extension("MACS2.IO.FixWidthTrack", ["MACS2/IO/FixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.PairedEndTrack", ["MACS2/IO/PairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.BedGraph", ["MACS2/IO/BedGraph.c"], libraries=["m"], extra_compile_args=extra_c_args), Extension("MACS2.IO.ScoreTrack", ["MACS2/IO/ScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.IO.CallPeakUnit", ["MACS2/IO/CallPeakUnit.c"], include_dirs=numpy_include_dir, extra_compile_args=extra_c_args), Extension("MACS2.hashtable", ["MACS2/hashtable.c"], include_dirs=["MACS2/", numpy_get_include()], extra_compile_args=extra_c_args), Extension("MACS2.Statistics", ["MACS2/Statistics.c", "MACS2/cStatistics.c"], libraries=["m"], include_dirs=["MACS2/", numpy_get_include()], extra_compile_args=extra_c_args), ] with open("README.md", "r") as fh: long_description = fh.read() setup( name="MACS2", version="2.1.3", description="Model Based Analysis for ChIP-Seq data", long_description=long_description, long_description_content_type="text/markdown", author='Tao Liu', author_email='*****@*****.**', url='http://github.com/taoliu/MACS/', package_dir={'MACS2': 'MACS2'}, packages=['MACS2', 'MACS2.IO', 'MACS2.data'], #package_data={'MACS2': ['data/*.dat']}, scripts=[ 'bin/macs2', ], classifiers=[ 'Development Status :: 5 - Production/Stable', 'Environment :: Console', 'Intended Audience :: Developers', 'Intended Audience :: Science/Research', 'License :: OSI Approved :: BSD License', 'Operating System :: MacOS :: MacOS X', 'Operating System :: POSIX', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Programming Language :: Python :: 2 :: Only', 'Programming Language :: Cython', ], install_requires=[ 'numpy>=1.15', 'cython>=0.25', #'scipy', ], cmdclass=command_classes, ext_modules=cythonize(ext_modules, language_level="2"))
def main(): if float(sys.version[:3]) < 2.7 or float(sys.version[:3]) >= 2.8: sys.stderr.write("CRITICAL: Python version must be 2.7!\n") sys.exit(1) ext_modules = [ Extension("MACS2.cProb", ["MACS2/cProb.c"], libraries=["m"], include_dirs=numpy_include_dir, extra_compile_args=["-w", "-Ofast"]), Extension("MACS2.IO.cParser", ["MACS2/IO/cParser.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w", "-Ofast"]), Extension("MACS2.cPileup", ["MACS2/cPileup.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w", "-Ofast"]), Extension("MACS2.cArray", ["MACS2/cArray.c"], extra_compile_args=["-w", "-Ofast"]), Extension("MACS2.cPeakModel", ["MACS2/cPeakModel.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w", "-Ofast"]), Extension("MACS2.cPeakDetect", ["MACS2/cPeakDetect.c"], extra_compile_args=["-w", "-Ofast"]), Extension("MACS2.cSignal", ["MACS2/cSignal.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w", "-Ofast"]), Extension("MACS2.IO.cPeakIO", ["MACS2/IO/cPeakIO.c"], extra_compile_args=["-w", "-Ofast"]), Extension("MACS2.IO.cBedGraphIO", ["MACS2/IO/cBedGraphIO.c"], extra_compile_args=["-w", "-Ofast"]), Extension("MACS2.IO.cFixWidthTrack", ["MACS2/IO/cFixWidthTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w", "-Ofast"]), Extension("MACS2.IO.cPairedEndTrack", ["MACS2/IO/cPairedEndTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w", "-Ofast"]), Extension("MACS2.IO.cBedGraph", ["MACS2/IO/cBedGraph.c"], libraries=["m"], extra_compile_args=["-w", "-Ofast"]), Extension("MACS2.IO.cScoreTrack", ["MACS2/IO/cScoreTrack.c"], include_dirs=numpy_include_dir, extra_compile_args=["-w", "-Ofast"]), Extension("MACS2.IO.cCallPeakUnit", ["MACS2/IO/cCallPeakUnit.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", version="2.1.0.20141030", description="Model Based Analysis for ChIP-Seq data", author='Tao Liu', author_email='*****@*****.**', url='http://github.com/taoliu/MACS/', package_dir={'MACS2': 'MACS2'}, packages=['MACS2', 'MACS2.IO'], #, 'MACS2.data'], #package_data={'MACS2': ['data/*.dat']}, scripts=[ 'bin/macs2', ], classifiers=[ 'Development Status :: 4 - Beta', 'Environment :: Console', 'Intended Audience :: Developers', 'Intended Audience :: Science/Research', 'License :: OSI Approved :: BSD License', 'Operating System :: MacOS :: MacOS X', 'Operating System :: POSIX', 'Topic :: Scientific/Engineering :: Bio-Informatics', 'Programming Language :: Python', ], install_requires=[ 'numpy>=1.6', #'scipy', ], cmdclass=command_classes, ext_modules=ext_modules)
## Max-Planck-Institute for Astrophysics. ## ## Copyright (C) 2012 Max-Planck-Society ## Author: Marco Selig from distutils.core import setup from distutils.extension import Extension as extension from Cython.Distutils import build_ext from numpy import get_include as numpy_get_include srcs = ["wrapper.pyx", "interfacer.cpp"] libs = ["sharp", "fftpack", 'c_utils'] idirs = [ numpy_get_include(), "../libsharp-code/c_utils", "../libsharp-code/libfftpack", "../libsharp-code/libsharp" ] ldirs = ["../libsharp-code/auto/lib"] exmod = [ extension("libsharp_wrapper_gl", srcs, language="c++", include_dirs=idirs, library_dirs=ldirs, libraries=libs) ] setup(name="libsharp_wrapper_gl",