Add a max waiting time for computing meshes

[DrLeucine]

Hi Arian :)

Is your feature request related to a problem? Please describe.
Currently, we just wait until the object is created. At times these objects can take more than 5-10 minutes (!).

Describe the solution you'd like
A break clause that raises a TimeoutError if it has been longer than X amount of time.

Additional context
Something like this for example could work in meshes.py

    max_wait_seconds = 10  

    start_time = time.time()
    while not os.path.isfile(obj_file):
        if time.time() - start_time > max_wait_seconds:
            raise TimeoutError(f"{obj_file} not found after {max_wait_seconds} seconds")
        time.sleep(0.1)

The max_wait_seconds could be a parameter passed to create_mesh or to config.

Let me know what you think :)

[a-r-j]

Hi @DrLeucine thanks for the suggestion. I think this is a good idea in general although it'd be helpful if you could clarify why this needs to be in the library rather than users wrapping the function call in the while block (or a decorator to this effect).

[DrLeucine]

Hi @a-r-j ,

Yes, the main reason is that the while loop does not have a clear exit condition, so if PyMol crashes or some error prevents the mesh from being created, the user is left without any feedback or debug information. This is especially tricky to debug in a multiprocessing context.

I think adding a timeout makes the failure mode more explicit and easier to handle than wrapping the function externally.

What do you think? If you like the idea it'd be good to know what you think the default should be (eg. something like 10 minutes?)