#setup.py from distutils.core import setup, Extension from sysconfig import get_python_version import sys import os @USING_PGI_COMPILER_TRUE@using_pgi=True @USING_PGI_COMPILER_FALSE@using_pgi=False @BUILD_MINGW_TRUE@mingw = 1 @BUILD_MINGW_FALSE@mingw = 0 # TODO temporary workaround for mingw + cmake # When running with mingw-cmake, the path of the form C:/msys64/xyz # needs to be transformed to C:\msys64/xyz. def get_escaped_path(path): if mingw: return path.replace(":/", ":\\") else: return path # NRNPYTHON_DEFINES which were enabled at configure time extern_defines = "@NRNPYTHON_DEFINES@" nrnpython_exec = get_escaped_path("@NRNPYTHON_EXEC@") nrnpython_pyver = "@NRNPYTHON_PYVER@" nrnpython_pyver10 = "nrnpython" use_libnrnpython_majorminor = @USE_LIBNRNPYTHON_MAJORMINOR@ nrn_srcdir = get_escaped_path(os.path.relpath("@NRN_SRCDIR@")) build_rx3d = @BUILD_RX3D@ ivlibdir = get_escaped_path("@IV_LIBDIR@") if ivlibdir == "" : ivlibdir = '.' destdir = os.getenv("DESTDIR") if not destdir: destdir = "" # install into build directory and then copy to install prefix instdir = destdir + get_escaped_path(os.path.relpath("@CMAKE_BINARY_DIR@")) if nrn_srcdir[0] != '/' : if mingw: nrn_srcdir = nrn_srcdir if "@BUILD_NRNPYTHON_DYNAMIC_TRUE@" == "": # can do all the setup.py without re-configure. nrnpython_pyver = get_python_version() nrnpython_exec = sys.executable nrnpython_pyver10 = "nrnpython" + str(sys.version_info[0]) if use_libnrnpython_majorminor == 1: nrnpython_pyver10 = "nrnpython" + str(sys.version_info[0]) + str(sys.version_info[1]) else: if nrnpython_pyver!=get_python_version(): print ("Error:") print ("NEURON configure time python: "+nrnpython_exec+" "+ nrnpython_pyver) print ("Python presently executing setup.py: "+sys.executable+" "+ get_python_version()) print ("These do not match, and they should!") sys.exit(1) ldefs = extern_defines.split('-D') # if using MPI then at least for linking need special paths and libraries import os c_compiler_path = get_escaped_path("@CC@") cxx_compiler_path = get_escaped_path("@CXX@") # setup.py tries to compile C++ code with the C compiler. This works with # gcc and intel but fails with at least PGI compiler. Hence, use C++ compiler # if PGI compiler is used. os.environ['CC'] = cxx_compiler_path if using_pgi else c_compiler_path os.environ["CXX"] = cxx_compiler_path if using_pgi: # Spack installed Python includes patches that require setting LDSHARED # and LDCXXSHARED environmental variables to ensure the PGI/NVIDIA linker # is used as well as the compiler. Otherwise GCC is used and it chokes on # PGI/NVIDIA-specific compiler flags. os.environ["LDSHARED"] = os.environ['CC'] + " -shared" os.environ["LDCXXSHARED"] = os.environ["CXX"] + " -shared" # apparently we do not need the following ################################# ## following http://code.google.com/p/maroonmpi/wiki/Installation ## hack into distutils to replace the compiler in "linker_so" with mpicxx_bin # #import distutils #import distutils.unixccompiler # #class MPI_UnixCCompiler(distutils.unixccompiler.UnixCCompiler): # __set_executable = distutils.unixccompiler.UnixCCompiler.set_executable # # def set_executable(self,key,value): # print "MPI_UnixCCompiler ", key, " | ", value # if key == 'linker_so' and type(value) == str: # value = mpicxx_bin + ' ' + ' '.join(value.split()[1:]) # # return self.__set_executable(key,value) # #distutils.unixccompiler.UnixCCompiler = MPI_UnixCCompiler ################################# #include_dirs for hoc module include_dirs = [nrn_srcdir+'/src/nrnpython', nrn_srcdir+'/src/oc', '../oc', nrn_srcdir+'/src/nrnmpi'] #include dirs for all modules include_dirs_common = [] #not needed with clang,clang++ and on my beta catalina does not #work anyway with /Library/Developer/CommandLineTools/usr/bin/cc #for the ctng module #@MAC_DARWIN_TRUE@include_dirs_common.append("@CMAKE_OSX_SYSROOT@/usr/include") defines = [] libdirs = [destdir + get_escaped_path("@NRN_LIBDIR@"), ivlibdir ] # prepare rpath flags for neuron and iv libs directories rpath_prefix_flag='-Wl,-R' extra_link_args = [@NRN_LINK_FLAGS_COMMA_SEPARATED_STRINGS@] @MAC_DARWIN_FALSE@extra_link_args += [rpath_prefix_flag+lib_path for lib_path in libdirs] @MAC_DARWIN_TRUE@extra_link_args.append("-Wl,-rpath,@loader_path/../../") @MAC_DARWIN_TRUE@extra_link_args.append("-Wl,-rpath,%s" % ivlibdir) # as neuron module will be built during make, add build/lib # directory for linking. Note that build/lib shouldn't be # added to rpath to avoid issues with dlopen. libdirs.append(destdir + get_escaped_path(os.path.relpath("@CMAKE_BINARY_DIR@/lib"))) @MAC_DARWIN_FALSE@readline="readline@READLINE_SOSUFFIX@" @MAC_DARWIN_TRUE@readline="readline@READLINE_SOSUFFIX@" pgi_compiler_flags = "-noswitcherror" libs = [@BUILD_NRNPYTHON_DYNAMIC_TRUE@nrnpython_pyver10, "nrniv" ] if "@IVHINES@" != "": libs.append("@IVHINES@") extra_compile_args = [@NRN_COMPILE_FLAGS_COMMA_SEPARATED_STRINGS@] if using_pgi: extra_link_args.append(pgi_compiler_flags) extra_compile_args.append(pgi_compiler_flags) hoc_module = Extension( "neuron.hoc", ["inithoc.cpp"], library_dirs=libdirs, extra_link_args=extra_link_args, #extra_objects = [], extra_compile_args = extra_compile_args, libraries = libs , include_dirs = include_dirs+include_dirs_common, define_macros=defines ) # specify that the data_files paths are relative to same place as python files # from http://stackoverflow.com/questions/1612733/including-non-python-files-with-setup-py from distutils.command.install import INSTALL_SCHEMES for scheme in list(INSTALL_SCHEMES.values()): scheme['data'] = scheme['purelib'] ext_modules = [hoc_module] # The rx3d extensions are built using the setup.py.in in # nrn/share/lib/python/neuron/rxd/geometry3d which contains Cython pyx files # These files on Windows have to be compiled with the msvc compiler to avoid # issues with hypot, a #define, and some DL_IMPORT statements. At least for # Python3.5, the module must be built with the msvc toolchain to prevent a # crash, possibly due to incompatible c runtime libraries. The following # section is left here with the idea that someday the entire build on windows # may be done with the msvc toolchain. Note, although the extensions are not # built here, the python files are copied because of the call to setup here. if build_rx3d: try: import numpy # TODO: do we need to use os.path.join? src_path = nrn_srcdir + '/share/lib/python/neuron/rxd/geometry3d/' build_path = '../../share/lib/python/neuron/rxd/geometry3d/' include_dirs = [nrn_srcdir + '/share/lib/python/neuron/rxd/geometry3d', '.', numpy.get_include()] include_dirs += include_dirs_common extra_compile_args=["-O@NRN_RX3D_OPT_LEVEL@"] + extra_compile_args define_macros = [] if mingw: #Avoid undefined __imp_Py_InitModule4 and hypot problem define_macros.append(("MS_WIN64", None)) ext_modules=[hoc_module, Extension("neuron.rxd.geometry3d.graphicsPrimitives", sources=[build_path + "graphicsPrimitives.cpp"], extra_compile_args = extra_compile_args, extra_link_args=extra_link_args, define_macros = define_macros, include_dirs=include_dirs), Extension("neuron.rxd.geometry3d.ctng", sources=[build_path + "ctng.cpp"], extra_compile_args = extra_compile_args, extra_link_args=extra_link_args, define_macros = define_macros, include_dirs=include_dirs), Extension("neuron.rxd.geometry3d.surfaces", sources=[build_path + "surfaces.cpp", nrn_srcdir + "/src/nrnpython/rxd_marching_cubes.cpp", nrn_srcdir + "/src/nrnpython/rxd_llgramarea.cpp"], define_macros = define_macros, extra_compile_args = extra_compile_args, extra_link_args=extra_link_args, include_dirs=include_dirs)] except: pass packages=['neuron','neuron.neuroml','neuron.tests', 'neuron.rxd', 'neuron.crxd', 'neuron.gui2'] if build_rx3d: packages +=['neuron.rxd.geometry3d'] pkg_dir = os.path.relpath("@CMAKE_BINARY_DIR@") + '/share/nrn/lib/python' setup(name="NEURON", version="@PACKAGE_VERSION@", description = "NEURON bindings for python", package_dir = {'': pkg_dir}, packages=packages, data_files = [('neuron', [nrn_srcdir + '/share/lib/python/neuron/help_data.dat'])], ext_modules=ext_modules )