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microsoft / vscode-jupyter

VS Code Jupyter extension
https://marketplace.visualstudio.com/items?itemName=ms-toolsai.jupyter
MIT License
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nglview not working with vscode-jupyter #15757

Open gcrth opened 4 months ago

gcrth commented 4 months ago

Related issue https://github.com/nglviewer/nglview/issues/1085.

pip install nglview==3.1.0
import nglview
view = nglview.show_pdbid("3pqr")  # load "3pqr" from RCSB PDB and display viewer widget
view

The example above works in jupyter notebook, but it does not work in vscode. Changing version of nglview and ipywidgets does not fix the problem.

The important part of the log is 

Failed to load model class 'ColormakerRegistryModel' from module 'nglview-js-widgets'
Error: No version of module nglview-js-widgets is registered

nglview-js-widgets is in the cdn https://cdn.jsdelivr.net/npm/nglview-js-widgets/. jupyter.widgetScriptSources has been configured per https://github.com/microsoft/vscode-jupyter/wiki/IPyWidget-Support-in-VS-Code-Python. It seems that something goes wrong when loading the module.

nightroxide commented 4 months ago

Same issue for me

DonJayamanne commented 4 months ago

There seems to be some change in nglview that seems to be causing this issue in VS code. Sorry for the trouble, will try to get to the bottom of this. Please can you try installing an older version of nglview and see if that makes a difference. You might need to re-load VS Code after doing that.

4doom4 commented 4 months ago

@DonJayamanne I tried it with 2.7.7 and get the same outcome. Maybe this trace helps (is from 3.1.2 nglview though)


Failed to load model class 'ColormakerRegistryModel' from module 'nglview-js-widgets'
Error: No version of module nglview-js-widgets is registered
    at ph.loadClass (https://file+.vscode-resource.vscode-cdn.net/Users/xxxxx/.vscode/extensions/ms-toolsai.jupyter-renderers-1.0.18/out/node_modules/%40vscode/jupyter-ipywidgets8/dist/ipywidgets.js:2:4099813)
    at ph.loadClass (https://file+.vscode-resource.vscode-cdn.net/Users/xxxxx/.vscode/extensions/ms-toolsai.jupyter-renderers-1.0.18/out/node_modules/%40vscode/jupyter-ipywidgets8/dist/ipywidgets.js:2:4403287)
    at ph.loadModelClass (https://file+.vscode-resource.vscode-cdn.net/Users/xxxxx/.vscode/extensions/ms-toolsai.jupyter-renderers-1.0.18/out/node_modules/%40vscode/jupyter-ipywidgets8/dist/ipywidgets.js:2:4097773)
    at ph._make_model (https://file+.vscode-resource.vscode-cdn.net/Users/xxxxx/.vscode/extensions/ms-toolsai.jupyter-renderers-1.0.18/out/node_modules/%40vscode/jupyter-ipywidgets8/dist/ipywidgets.js:2:4094616)
    at ph.new_model (https://file+.vscode-resource.vscode-cdn.net/Users/xxxxx/.vscode/extensions/ms-toolsai.jupyter-renderers-1.0.18/out/node_modules/%40vscode/jupyter-ipywidgets8/dist/ipywidgets.js:2:4092246)
    at ph.handle_comm_open (https://file+.vscode-resource.vscode-cdn.net/Users/xxxxx/.vscode/extensions/ms-toolsai.jupyter-renderers-1.0.18/out/node_modules/%40vscode/jupyter-ipywidgets8/dist/ipywidgets.js:2:4091039)
    at https://file+.vscode-resource.vscode-cdn.net/Users/xxxxx/.vscode/extensions/ms-toolsai.jupyter-renderers-1.0.18/out/node_modules/%40vscode/jupyter-ipywidgets8/dist/ipywidgets.js:2:4402511
    at n._handleCommOpen (https://file+.vscode-resource.vscode-cdn.net/Users/xxxxx/.vscode/extensions/ms-toolsai.jupyter-2024.5.0-darwin-arm64/dist/webviews/webview-side/ipywidgetsKernel/ipywidgetsKernel.js:3:80955)
    at async n._handleMessage (https://file+.vscode-resource.vscode-cdn.net/Users/xxxxx/.vscode/extensions/ms-toolsai.jupyter-2024.5.0-darwin-arm64/dist/webviews/webview-side/ipywidgetsKernel/ipywidgetsKernel.js:3:82830)
LuhuanWu commented 4 months ago

same issue here

laisFK commented 4 months ago

Helo, I have the same problem in VSC, please someone found a solution? Thanks

4doom4 commented 3 months ago

There seems to be some change in nglview that seems to be causing this issue in VS code. Sorry for the trouble, will try to get to the bottom of this. Please can you try installing an older version of nglview and see if that makes a difference. You might need to re-load VS Code after doing that.

@DonJayamanne I tried many different versions and got version 3.0.8 (installed via conda conda-forge::nglview=3.0.8) to work with VScode on linux version 1.91.1

Hope this helps

DonJayamanne commented 3 months ago

This seems to be caused by some upstream issue in nglview, I haven't had a chance to identify the root cause as of yet.

hainm commented 3 months ago

There is a change in NGL (which is being used by nglview) in the way it is packaged. The change happened after nglview 3.8. But nglview works fine with notebook (using lab) and lab.

DonJayamanne commented 3 months ago

@hainm its still failing at my end in Jupyter lab This is with the latest version of nglview

Image

hainm commented 3 months ago

Can you please try install nglview via conda/mamba from conda-forget channel?

I am surprised that it doesn't work for you since I tried myself before publishing the package. Cheers

hainm commented 3 months ago

@DonJayamanne I've tried again with my mac:

image

lab 4.2.4

Exact steps:

mamba create -n test python=3.11 -c conda-forge -y
source activate test
mamba install jupyterlab -c conda-forge -y
mamba install nglview=3.1.2 -c conda-forge -y
jupyter-lab
MarcSkovMadsen commented 2 months ago

There is the same problem for Bokeh/ Panel. See https://github.com/bokeh/jupyter_bokeh/issues/201

invemichele commented 1 month ago

@DonJayamanne With v2024.8.0 no matter the nglview version I try, I always get the error in the OP.

Reverting back to v2024.7.0 and nglview==3.0.8 works

DonJayamanne commented 1 month ago

@invemichele You are running into https://github.com/microsoft/vscode-jupyter/issues/16008