Cython fails to run for a python3.6 installed in custom location.

[gwk]

I have built/installed python from source on OSX to a custom framework location. The exact configure command is:

CC=clang CXX=clang++ CFLAGS='-flto=thin -Wno-deprecated-declarations' MACOSX_DEPLOYMENT_TARGET=10.9 ../configure --cache-file=config.cache --prefix=/usr/local/py --enable-framework=/usr/local/py/Library/Frameworks --quiet --with-lto 

I then install cython using the corresponding pip:

/usr/local/py/Library/Frameworks/Python.framework/Versions/3.6/bin/pip3 install cython

The cython install succeeds, but the installation is broken:

 $ cython
Traceback (most recent call last):
  File "/usr/local/py/Library/Frameworks/Python.framework/Versions/3.6/bin/cython", line 7, in <module>
    from Cython.Compiler.Main import setuptools_main
  File     "/usr/local/py/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/Cython/Compiler/Main.py",     line 30, in <module>
    from .Symtab import ModuleScope
  File     "/usr/local/py/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/Cython/Compiler/Symtab.py",     line 18, in <module>
    from . import PyrexTypes
  File     "/usr/local/py/Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/Cython/Compiler/PyrexTypes.    py", line 17, in <module>
    from .Code import UtilityCode, LazyUtilityCode, TempitaUtilityCode
  File "Cython/Compiler/Code.py", line 39, in init Cython.Compiler.Code     (/private/var/folders/vy/rcv48w3j4w79llzf_x6qnvw40000gn/T/pip-uioc89se-build/Cython/Compiler/Code.c:80038)
    def runsource(self, source, filename="<input>", symbol="single"):
ModuleNotFoundError: No module named '__builtin__'

I believe this is a Cython bug, as I can successfully install many other packages using pip for custom python locations. If anyone has an idea of how to debug this issue please let me know; I realize that these setups can be time consuming to reproduce. Thanks!

[gwk]

I am able to work around this bug by installing cython in developer mode: pip3 install -e . from the cython project root, master branch.

From there I was able to build pyzmq using pip3 install --no-binary=pyzmq pyzmq (it fails without the --no-binary option).

[scoder]

The name "__builtin__" suggests that there is something going wrong at a Py2/Py3 compatibility level. It's supposed to use the name "builtins" in Py3 instead. Difficult to say how this could happen, but could you check in your install/build output if there is any hint of interference of a Python 2.x version? And could you make sure that the shebang lines in you Python installation all use the correct Python 3.6 runtime?