Different type of errors

[P705]

Hi
I can't run your code and have error.
Most of these error comes from conehead and conehead.convolve_c.
How can i handle these errors ?

[ethanio12345]

Experienced the same issue.

[cwant]

Similar issues here (Ubuntu Linux, trying a few different Python versions and versions of supporting packages).

I'd love to see some guidance on how to get this software up and running well enough to run the tests.

[cwant]

I did get the code to compile and import correctly (and the test suite to pass), by replacing setup.py with the following:

from setuptools import setup, find_packages
from Cython.Build import cythonize
import numpy as np
import os

os.environ["CFLAGS"] = "-O0"

def find_pyx(path='.'):
    pyx_files = []
    for root, dirs, filenames in os.walk(path):
        for fname in filenames:
            if fname.endswith('.pyx'):
                pyx_files.append(os.path.join(root, fname))
    return pyx_files

setup(
    name="conehead",
    ext_modules=cythonize(find_pyx()),
    include_dirs=[np.get_include()]
)

[ethanio12345]

Hey @cwant! Thanks for your comment appreciate the solution; I only just got back to have a look here again and I couldn't seem to apply your fix. What steps did you take to get things working? Would appreciate your expertise, comments system params (i.e. if you have to adjust PYTHONPATH or anything else).

In both cases, with original setup and yours, if I build and install (which both successfully run), then try running any of the tests or example.py, it comes up with the ModuleNotFoundError as posted by P705 above. If I then open python and try the from conehead_convolve.c import convolve_c, it says

I haven't really come across these types of problems before, so would appreciate your help. I've had a read from some of the stackexchanges, but couldn't find a workable solution. Thanks again for your patience. :)

[ethanio12345]

Hi all,

Found a solution (potentially short-term) after mucking around for a while!

It required running the setup.py build_ext in place rather than the standard build process, which moved me forward from the original import error to a ImportError: dynamic module does not define module export function (PyInit_convolve_c). From here I recomplied the .pyx files through cython to generate the .c files, reran setup.p build_ext --inplace and I can now import the modules successfully.

[cwant]

Hi @ethanio12345, sorry but I don't use software myself but was helping out a researcher at my university (and haven't looked at it since).

Here are the notes that I shared with the researcher at the time, hope it helps:

Then build with:

python3 setup.py build_ext --inplace

I am then able to "import conehead" in a python interpreter, and I am also able to successfully run the test suite with:

python3 -m pytest --cov=conehead tests/

Give this a try and we'll see if this gets you further. My only other comment is that I originally had import problems with cython version 0.29 that went away when I used version 0.29.23.

P.S. The inspiration for this fix was provided by the demo cython project from the post on this page by "oz1":

https://stackoverflow.com/questions/44043620/how-to-prepare-cython-submodules

[ethanio12345]

Hi @cwant,

No worries at all mate, appreciate your input! Thanks for the help - it's at least importing things and running now. :)

[ethanio12345]

Sorry to keep bombing the thread, but to go along with the building in place, to make the code more extensible (and modules importable from any directory), the package works properly as most other packages when installed with pip install -e . and without any adaptations to the setup.py package. This creates a symlink in lib/site-packages to your current working directory (so if functionally equivalent to setup_py build_ext --inplace), but is handled by pip (and wheels things) and can be accessed from other folders.