ipywidgets>=8.0 and pythreejs>=2.4 appear to error during analysis notebook interactive plot

[bpowell122]

Describe the bug
Running the cryodrgn_filtering_template.ipynb cell widget, fig, ind_table = analysis.ipy_plot_interactive(df); VBox((widget,fig,ind_table)) causes an error message and prevents rendering of the interactive plot. This appears to be due to specific ipywidgets (and potentially pythreejs) versions. It may be useful to temporarily add "ipywidgets<8.0" "pythreejs<2.4.0" constraints to the cryoDRGN installation instructions.

To Reproduce
My conda environment contains the following relevant versions:
ipywidgets 8.0.2 pyhd8ed1ab_1 conda-forge
pythreejs 2.4.1 pyhc268e32_0 conda-forge
Running the cryodrgn_filtering_template.ipynb notebook through the analysis.ipy_plot_interactive(df) cell causes (1) the x/y/color_by/colormap widget to load, (2) two identical error messages to appear, and (3) the figure and ind_table to not be rendered.

Expected behavior
Normally this command produces a plot to render and be interactively configurable for x axis / y axis / color_by column / colormap, and reports mouse-lasso-selected indices in a table below.

Additional context
Running the command conda install "pythreejs<2.4.0" "ipywidgets<8.0" -c conda-forge, re-launching the notebook, and re-running the cell in question causes the expected behavior to occur. The conda command caused the following environment changes:
ipywidgets conda-forge::ipywidgets-8.0.2-pyhd8ed~ --> pkgs/main::ipywidgets-7.6.5-pyhd3eb1b0_1
pythreejs conda-forge/noarch::pythreejs-2.4.1-p~ --> conda-forge/linux-64::pythreejs-2.1.0-py37_0
widgetsnbextension conda-forge/noarch::widgetsnbextensio~ --> pkgs/main/linux-64::widgetsnbextension-3.5.2-py37h06a4308_0
I've only tested this in jupyter notebook, not jupyter lab. This bug might be related to this one here. I'm attaching screenshots of the error message below rather than copying the error because the error message itself was rendered differently from typical python tracebacks in my experience and I'm not sure if others may find that useful.

[zhonge]

@vineetbansal can you take a look at this?

[vineetbansal]

Hello @bpowell122 - thanks for your investigations. Most helpful. I'm able to confirm that a new installation of cryoDRGN without being specific about ipywidgets version does cause issues with the interactive filtering cell (I see just the dropdown widgets but not the actual rendered interactive graph).

It seems to me that in the link that you have provided, the issues lies with ipywidgets 8 (and above). I tried specifying ipywidgets<8 in our setup.py and I see that things start working again, and I can filter the particles using the Lasso tool. So I'm inclined to pin ipywidgets as you suggest. I'm not seeing pythreejs installed in my environment at all. cryoDRGN certainly doesn't need that dependency directly, and it looks like nothing it depends on needs it either. I'm not sure how you ended up with it.

Let me know if the above fix would be acceptable, and I can incorporate it in today.

[bpowell122]

Thanks for checking and refining the bug+fix! Pinning ipywidgets<8 sounds like the appropriate solution here. pythreejs likely snuck in on my end as a dependency from ipyvolume for some other visualizations I'm trying out with cryodrgn, so not including that package sounds like the correct decision.

[zhonge]

Thanks for digging into this! Please re-open if there are any more issues.