无法将cpplist导入Cython？

Question

I'm trying to figure out how to work lists/arrays in Cython, which seems impossibly complex, so I would prefer to just use C++ lists as I saw some people use on SO. However when I've ran their code, I'm getting a gcc+ compile error in ipynb. Cython data structures are infuriating.

When ran alone in a cell I get this error, I've tried importing with and without the %%cython magic call and both error...

'''

%%cython

from libcpp.list cimport list as cpplist 

'''
def main(int t):

cdef cpplist[int] temp

for x in range(t):
    if x> 0:
        temp.push_back(x)

cdef int N = temp.size()
cdef list OutputList = N*[0]

for i in range(N):
    OutputList[i] = temp.front()
    temp.pop_front()

return OutputList
'''

'''

 ---------------------------------------------------------------------------
DistutilsExecError                        Traceback (most recent call last)
/anaconda3/lib/python3.6/distutils/unixccompiler.py in _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts)
    117             self.spawn(compiler_so + cc_args + [src, '-o', obj] +
--> 118                        extra_postargs)
    119         except DistutilsExecError as msg:

/anaconda3/lib/python3.6/distutils/ccompiler.py in spawn(self, cmd)
    908     def spawn(self, cmd):
--> 909         spawn(cmd, dry_run=self.dry_run)
    910 

/anaconda3/lib/python3.6/distutils/spawn.py in spawn(cmd, search_path, verbose, dry_run)
     35     if os.name == 'posix':
---> 36         _spawn_posix(cmd, search_path, dry_run=dry_run)
     37     elif os.name == 'nt':

/anaconda3/lib/python3.6/distutils/spawn.py in _spawn_posix(cmd, search_path, verbose, dry_run)
    158                           "command %r failed with exit status %d"
--> 159                           % (cmd, exit_status))
    160             elif os.WIFSTOPPED(status):

DistutilsExecError: command 'gcc' failed with exit status 1

During handling of the above exception, another exception occurred:

CompileError                              Traceback (most recent call last)
<ipython-input-6-70891eecfa66> in <module>()
----> 1 get_ipython().run_cell_magic('cython', '--cplus', '\n# distutils: language = c++\nfor i in range(10):\n    print(i)\n    \n\n\n#from libc.math cimport log\nfrom libcpp.list cimport list as cpplist')

/anaconda3/lib/python3.6/site-packages/IPython/core/interactiveshell.py in run_cell_magic(self, magic_name, line, cell)
   2165             magic_arg_s = self.var_expand(line, stack_depth)
   2166             with self.builtin_trap:
-> 2167                 result = fn(magic_arg_s, cell)
   2168             return result
   2169 

<decorator-gen-127> in cython(self, line, cell)

/anaconda3/lib/python3.6/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
    185     # but it's overkill for just that one bit of state.
    186     def magic_deco(arg):
--> 187         call = lambda f, *a, **k: f(*a, **k)
    188 
    189         if callable(arg):

/anaconda3/lib/python3.6/site-packages/Cython/Build/IpythonMagic.py in cython(self, line, cell)
    327 
    328         self._build_extension(extension, lib_dir, pgo_step_name='use' if args.pgo else None,
--> 329                               quiet=args.quiet)
    330 
    331         module = imp.load_dynamic(module_name, module_path)

/anaconda3/lib/python3.6/site-packages/Cython/Build/IpythonMagic.py in _build_extension(self, extension, lib_dir, temp_dir, pgo_step_name, quiet)
    437             if not quiet:
    438                 old_threshold = distutils.log.set_threshold(distutils.log.DEBUG)
--> 439             build_extension.run()
    440         finally:
    441             if not quiet and old_threshold is not None:

/anaconda3/lib/python3.6/distutils/command/build_ext.py in run(self)
    337 
    338         # Now actually compile and link everything.
--> 339         self.build_extensions()
    340 
    341     def check_extensions_list(self, extensions):

/anaconda3/lib/python3.6/distutils/command/build_ext.py in build_extensions(self)
    446             self._build_extensions_parallel()
    447         else:
--> 448             self._build_extensions_serial()
    449 
    450     def _build_extensions_parallel(self):

/anaconda3/lib/python3.6/distutils/command/build_ext.py in _build_extensions_serial(self)
    471         for ext in self.extensions:
    472             with self._filter_build_errors(ext):
--> 473                 self.build_extension(ext)
    474 
    475     @contextlib.contextmanager

/anaconda3/lib/python3.6/distutils/command/build_ext.py in build_extension(self, ext)
    531                                          debug=self.debug,
    532                                          extra_postargs=extra_args,
--> 533                                          depends=ext.depends)
    534 
    535         # XXX outdated variable, kept here in case third-part code

/anaconda3/lib/python3.6/distutils/ccompiler.py in compile(self, sources, output_dir, macros, include_dirs, debug, extra_preargs, extra_postargs, depends)
    572             except KeyError:
    573                 continue
--> 574             self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
    575 
    576         # Return *all* object filenames, not just the ones we just built.

/anaconda3/lib/python3.6/distutils/unixccompiler.py in _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts)
    118                        extra_postargs)
    119         except DistutilsExecError as msg:
--> 120             raise CompileError(msg)
    121 
    122     def create_static_lib(self, objects, output_libname,

CompileError: command 'gcc' failed with exit status 1

---

When ran alone in a cell I get this error, I've tried importing with and without the %%cython magic call and both error...

in Cython, I get the object of type 'None' has no length (the ONLY error message in Cython language)

or

invalid syntax

Please advise, Cython has me ready to rip my hair out 2 days in.

EDITS: I've tried using:

%%cython --cplus
#distutils: language = c++

same error message. Also, JUST RUNNING '%%cython --cplus' GIVES ME AN ERROR MESSAGE, SAME ONE? With anything in the cell, a simple print or anything. Something is wrong with my cpp extension I think... how do I resolve?

In terminal (using runipy -- don't know how else to run ipynb in terminal aside from compiling via a setup.py and distutils Build)

zacharys-mbp:Cython zoakes$ runipy CSTL.ipynb
08/08/2019 08:47:47 PM INFO: Reading notebook CSTL.ipynb
08/08/2019 08:47:49 PM INFO: Running cell:
%load_ext cython 


08/08/2019 08:47:49 PM INFO: Cell returned
08/08/2019 08:47:49 PM INFO: Running cell:
%%cython 

#distutils: language = c++
from libcpp.list cimport list as cpplist

    warning: include path for stdlibc++ headers not found; pass '-    stdlib=libc++' on
      the command line to use the libc++ standard library instead
      [-Wstdlibcxx-not-found]
/Users/zoakes/.ipython/cython/_cython_magic_5a0764b273da2aafc5775e4dd20b1249.cpp:592:10: fatal error: 
      'ios' file not found
#include "ios"
         ^~~~~
1 warning and 1 error generated.
08/08/2019 08:47:50 PM INFO: Cell raised uncaught exception: 
---------------------------------------------------------------------------
DistutilsExecError                        Traceback (most recent call last)
/anaconda3/lib/python3.6/distutils/unixccompiler.py in _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts)
    117             self.spawn(compiler_so + cc_args + [src, '-o', obj] +
--> 118                        extra_postargs)
    119         except DistutilsExecError as msg:

/anaconda3/lib/python3.6/distutils/ccompiler.py in spawn(self, cmd)
    908     def spawn(self, cmd):
--> 909         spawn(cmd, dry_run=self.dry_run)
    910 

/anaconda3/lib/python3.6/distutils/spawn.py in spawn(cmd, search_path, verbose, dry_run)
     35     if os.name == 'posix':
---> 36         _spawn_posix(cmd, search_path, dry_run=dry_run)
     37     elif os.name == 'nt':

/anaconda3/lib/python3.6/distutils/spawn.py in _spawn_posix(cmd, search_path, verbose, dry_run)
    158                           "command %r failed with exit status %d"
--> 159                           % (cmd, exit_status))
    160             elif os.WIFSTOPPED(status):

DistutilsExecError: command 'gcc' failed with exit status 1

During handling of the above exception, another exception occurred:

CompileError                              Traceback (most recent call last)
<ipython-input-2-e4f283bb7389> in <module>()
----> 1 get_ipython().run_cell_magic('cython', '', '\n#distutils: language = c++\nfrom libcpp.list cimport list as cpplist')

/anaconda3/lib/python3.6/site-packages/IPython/core/interactiveshell.py in run_cell_magic(self, magic_name, line, cell)
   2165             magic_arg_s = self.var_expand(line, stack_depth)
   2166             with self.builtin_trap:
-> 2167                 result = fn(magic_arg_s, cell)
   2168             return result
   2169 

<decorator-gen-127> in cython(self, line, cell)

/anaconda3/lib/python3.6/site-packages/IPython/core/magic.py in <lambda>(f, *a, **k)
    185     # but it's overkill for just that one bit of state.
    186     def magic_deco(arg):
--> 187         call = lambda f, *a, **k: f(*a, **k)
    188 
    189         if callable(arg):

/anaconda3/lib/python3.6/site-packages/Cython/Build/IpythonMagic.py in cython(self, line, cell)
    327 
    328         self._build_extension(extension, lib_dir, pgo_step_name='use' if args.pgo else None,
--> 329                               quiet=args.quiet)
    330 
    331         module = imp.load_dynamic(module_name, module_path)

/anaconda3/lib/python3.6/site-packages/Cython/Build/IpythonMagic.py in _build_extension(self, extension, lib_dir, temp_dir, pgo_step_name, quiet)
    437             if not quiet:
    438                 old_threshold = distutils.log.set_threshold(distutils.log.DEBUG)
--> 439             build_extension.run()
    440         finally:
    441             if not quiet and old_threshold is not None:

/anaconda3/lib/python3.6/distutils/command/build_ext.py in run(self)
    337 
    338         # Now actually compile and link everything.
--> 339         self.build_extensions()
    340 
    341     def check_extensions_list(self, extensions):

/anaconda3/lib/python3.6/distutils/command/build_ext.py in build_extensions(self)
    446             self._build_extensions_parallel()
    447         else:
--> 448             self._build_extensions_serial()
    449 
    450     def _build_extensions_parallel(self):

/anaconda3/lib/python3.6/distutils/command/build_ext.py in _build_extensions_serial(self)
    471         for ext in self.extensions:
    472             with self._filter_build_errors(ext):
--> 473                 self.build_extension(ext)
    474 
    475     @contextlib.contextmanager

/anaconda3/lib/python3.6/distutils/command/build_ext.py in build_extension(self, ext)
    531                                          debug=self.debug,
    532                                          extra_postargs=extra_args,
--> 533                                          depends=ext.depends)
    534 
    535         # XXX outdated variable, kept here in case third-part code

/anaconda3/lib/python3.6/distutils/ccompiler.py in compile(self, sources, output_dir, macros, include_dirs, debug, extra_preargs, extra_postargs, depends)
    572             except KeyError:
    573                 continue
--> 574             self._compile(obj, src, ext, cc_args, extra_postargs, pp_opts)
    575 
    576         # Return *all* object filenames, not just the ones we just built.

/anaconda3/lib/python3.6/distutils/unixccompiler.py in _compile(self, obj, src, ext, cc_args, extra_postargs, pp_opts)
    118                        extra_postargs)
    119         except DistutilsExecError as msg:
--> 120             raise CompileError(msg)
    121 
    122     def create_static_lib(self, objects, output_libname,

CompileError: command 'gcc' failed with exit status 1
08/08/2019 08:47:50 PM INFO: Shutdown kernel
08/08/2019 08:47:50 PM WARNING: Exiting with nonzero exit status

Answer 1

I think this is a Mac issue, which limits my ability to help. However, the key error message seems to be:

warning: include path for stdlibc++ headers not found; pass '-stdlib=libc++' on
      the command line to use the libc++ standard library instead
      [-Wstdlibcxx-not-found]

If you search for (part of) this message it looks like it's related to XCode. At some point Apple switched the compiler from GCC to Clang, and this changed which implementation of the C++ standard library it uses.

I think the best solution is to install "stdlibc++" on XCode. Unfortunately I have no idea how you'd practically do this.

The second best solution involves adding the suggested command line argument for Cython - I think this is second-best because it's using a slightly mismatched implementation of the C++ standard library.

%%cython --compile-args=-stdlib=libc++ --link-args=-stdlib=libc++

I'm not sure if it needs to be in both compile and link args or just compile args.