Not able to compile the cython library.

[Schiboni]

Hi, hope you can help me, I am really desperate. I need to make some modification to the forward algorithm and compile my custom version of pomegranate. When i run setup.py with the command "python3 setup.py build_ext --inplace". I receive the following error:

/usr/bin/clang -bundle -undefined dynamic_lookup -arch i386 -arch x86_64 -g build/temp.macosx-10.6-intel-3.5/pomegranateplus/utils.o -o build/lib.macosx-10.6-intel-3.5/POWERSPOTTING/codes/pomegranateplus/utils.cpython-35m-darwin.so
copying build/lib.macosx-10.6-intel-3.5/POWERSPOTTING/codes/pomegranateplus/BayesClassifier.cpython-35m-darwin.so -> POWERSPOTTING/codes/pomegranateplus
error: could not create 'POWERSPOTTING/codes/pomegranateplus/BayesClassifier.cpython-35m-darwin.so': No such file or directory

Do you have any suggestions what to do? My machine is a Mac with Sierra 10.12.6 and python 3.

Thanks in advance

[jmschrei]

Can you try removing all of the files that are not .py, .pyx, or .pxd from the library and recompile? Also, potentially try running python3 setup.py install instead.

[jmschrei]

Did this work out?

[vpicouet]

It seems that deleting init.py works!

[enjoysmath]

Well, how do you build a cython package that requires an init.py if you have to delete it!!! This is driving me nuts.

[timonviola]

it also doesn't compile if __init__.py is present

[zwei-beiner]

@enjoysmath @timonviola
A fix that worked for me is described here:
https://stackoverflow.com/questions/71983019/why-does-adding-an-init-py-change-cython-build-ext-inplace-behavior

Essentially, you can keep the __init__.py file and the setup file has to be

from setuptools import Extension, setup
from Cython.Build import cythonize

extensions = [Extension("hello", ["hello.pyx"])]

setup(
    ext_modules=cythonize(extensions),
)

instead of

# WRONG!!
from setuptools import setup
from Cython.Build import cythonize

setup(
    ext_modules=cythonize("hello.pyx"),
)

[jmschrei]

Thanks for the comments. I'm currently in the process of rewriting pomegranate using a PyTorch backend so hopefully that will resolve all these issues.