I have never done it myself, but I think there are ways to setup a debugger for mixed Python/Cython debugging for example see thisblog post.

TheCython documentation may have some useful info although part of it is out-of-date for example the part where it says Python 2 is needed, seecython/cython#4911.

There are also some reports of people managing to do it insideVSCode.

If you manage to do it, I think it would be great if you post how to do it because I am guessing this would be useful for others 🙏.

@lesteve thanks for your response. I will try out these. (On a high level it looks we need to run the py debugger and the gdg (or cygdb) independently). But since you have mentioned that you haven't tried or did this, I will keep this thread open.

I am in a similar boat debugging the K-D trees function calls from my user program. Unfortunately I did not get very far with PDB, all I saw was a step into a utility file and a function named checkarray. I also had no idea what was Cython and/or Python code