VTK seems to break interactive window

This example requires pip install pymatgen vtk. VTK is the Visualization Toolkit which offers 1st party Python bindings.

# %%
from pymatgen.core import Structure
from pymatgen.vis.structure_vtk import StructureVis


# %%
struct = Structure(
    [[1, 0, 0], [0, 1, 0], [0, 0, 1]],
    ["O", "H", "H"],
    [[0, 0, 0], [0.5, 0.5, 0], [0.5, 0, 0.5]],
)

# %%
struct_vis = StructureVis()
struct_vis.set_structure(struct)
struct_vis.show()


# %%
print("hello")

Two odd things here:

1. The interactive crystal structure created by struct_vis.show() opens in a new Python window, i.e. is not captured by VS Code Jupyter and inlined into the notebook. Screenshot below.

2. When closing the Python window, I get a beach ball spinning endlessly until I force close Python.app and from then on, my interactive window is broken. Running any cell (e.g. print("hello")) now throws

   Error: Session cannot generate requests
   at S.executeCodeCell (/Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2021.10.1101450599/out/client/extension.js:66:301742)
   at runMicrotasks (<anonymous>)
   at processTicksAndRejections (internal/process/task_queues.js:93:5)
   at S.execute (/Users/janosh/.vscode/extensions/ms-toolsai.jupyter-2021.10.1101450599/out/client/extension.js:66:300721)
   

[DonJayamanne]

Same problem in Insiders. I still get a beach ball when trying to close the Python plot window.

PLease could you provide the logs from the Jupyter output panel. Looks like the kernel is dying. Also can you try this in Jupyter Notebook (outside vscode) and confirm the kernel doesn’t die there either.

Basically I don’t think this is a problem with VS Code, we don’t kill the kernel, here it looks like the kernel died for some external reason.

[janosh]

@DonJayamanne You’re right, same thing happening in Jupyter. Closing as unrelated to VS Code.