run_custom_code is painfully slow

[christian-oreilly]

The following code

import ipyniivue
import time

nv = ipyniivue.Niivue()
t1 = time.time() 
is_pial = nv.run_custom_code('this.nv.isMeshExt("test.pial")')
print(time.time() - t1)

launched on Google Colab takes about 60s to run. My understanding is that this code just checks if "pial" is a mesh extension, which should be a very fast operation. All similar calls seem to be that slow. This can be tested using the example notebook on running custom code.

[christian-oreilly]

Let me wrap this also in this issue to avoid creating another issue just for that: The run_custom_code also seems to fail to return values. Printing is_pial in this example currently gives me None. With fixing this, we should add a test for pytest that avoids code regression on that. This is a fairly simple test to add.

[AnthonyAndroulakis]

Thank you for bringing this up. run_custom_code does not work online Jupyter environments, such as Google Colab, due to the way online Jupyter handles concurrent execution. See https://github.com/Kirill888/jupyter-ui-poll/issues/23#issuecomment-1321256681 for more info.

Concerning ipyniivue, we can either add note to the documentation specifying that run_custom_code (and therefore all getters that use run_custom_code) do not work in online Jupyter environments. Alternatively, we could explore implementing some solution that runs in online Jupyter environments. Currently, I don't know of any ways to do this.

[christian-oreilly]

What is the difference between local and "online" Jupyter environments exactly? The issue you referred to seems to make a difference between ipykernel (works) and jupyterlite (does not work). I may be mistaken but I did not see any clear restrictions (except in the version maybe) for ipykernel on the Colab...? Also, jupyter-ui-poll seems to work on Colab (https://github.com/Kirill888/jupyter-ui-poll/issues/18). It seems like there was some issues with ipykernel 4.x, which was the default for Colab at the time the ticket was created, but the current version is now 5.5.6.

[AnthonyAndroulakis]

I see, I think I was confused with JupyterLite and Google Colab, and just assumed they used the same kernel. I'll have to do more testing to see if I can get run_custom_code to work in Colab then. The reason it takes at most 60 seconds to run the run_custom_code function is because it times out at 60 seconds.

[christian-oreilly]

So, a deeper issue is the transparency of JS errors from Python side. This should cause a timeout exception on Python side so that the user knows what is happening.