Support Bokeh Plots

[acocac]

I recently start experimenting JB2-alpha for upgrading the EDS book resource. Some published notebooks in EDS book use the Holoviz ecosystem which builds Bokeh/Matplotlib/Plotly plots.

It seems MyST has some issues to display bokeh-related plots. For instance the notebook, https://eds-book.github.io/b34facfa-cea8-48f5-89f6-f11ce00812a9/notebook#compute-ndvi-and-fdi-indices, using a bokeh backend, doesn't show up the plot in the output cell.

Neither importing output_notebook from bokeh.io import nor a print statement of the interactive plot works.

@stevejpurves mentioned a potential short term workaround similar to plotly which would be great to point/crossreference in this issue.

[acocac]

If it helps to test new fixes, I've created a new repository using simple examples from the hvplot library, see https://github.com/eds-book/test-hvplot. The published website confirms MyST can handle plotly but it fails when using the bokeh backend.

[acocac]

@stevejpurves - I wondered if there's any progress on supporting bokeh-related plots in MyST. I've tried in the test example some alternatives, preload jquery, export bokeh objects to html and embed them within the notebook, etc. When I explore/render the repo in nbviewer, it displays the bokeh plots.

[stevejpurves]

@acocac #544 should fix your immediate issues for porting a jupyter-book, with further work needed for all myst features in #545

[stevejpurves]

#544 was merged, awaiting release

[acocac]

@stevejpurves thanks for the update! I have some basic questions related how usually developers incorporate fixes from myst-theme.

• Will the fix be incorporated into a new release of JB2-beta?
• To experiment with the fix while the release, could I declare a particular commit from myst-theme within myst config/packages files? or shall I update myst-cli?

[agoose77]

@acocac Jupyter Book 2 for now uses the same themes that MyST-MD uses, which are pulled in by mystmd / jupyter-book in the _build/templates/site directory. You won't need to update JB explicitly to get the latest themes, but sometimes updates are required in the core MyST engine (e.g. for user-CSS and/or landing pages).

You can play around with a local theme by serving your content with MyST, and running the theme separately.
If you want to make a static build of your site, you need to actually package up the theme for deployment. Let me know if that's what you're aiming for, and I can walk you through it and update our contributing guide.

[acocac]

@acocac Jupyter Book 2 for now uses the same themes that MyST-MD uses, which are pulled in by mystmd / jupyter-book in the _build/templates/site directory. You won't need to update JB explicitly to get the latest themes, but sometimes updates are required in the core MyST engine (e.g. for user-CSS and/or landing pages).

Gotcha - thanks for the explanation on this!

You can play around with a local theme by serving your content with MyST, and running the theme separately.
If you want to make a static build of your site, you need to actually package up the theme for deployment. Let me know if that's what you're aiming for, and I can walk you through it and update our contributing guide.

By local theme, do you mean to customise a template as it's suggested in MyST doc? A walk through would be helpful with updates in the contribution guide of JB2.

[agoose77]

Could you clarify what you're trying to do?

• If you just want to see what the new theme looks like before it is released, you can run the theme application locally.
• If you want to build static HTML to publish, you can also do that, and I'd need to update our contributing guide for a walk through.

[stevejpurves]

@acocac once the theme is released then to test make sure that you run myst clean --templates to download latest theme when you next run myst start.

To jump ahead and test something before it is released:

1. clone/checkout jupyter-book/myst-theme (at the desired commit or just main to get the latest including merged pre-release changes)
2. cd myst-theme
3. npm install
4. npm run build
5. npm run theme:book
6. open a new terminal and cd into your content/book folder
7. run myst start --headless
8. visit http://localhost:3000 and you should see your book content rendered in the theme you have checked out

note you need a recent version of node installed e.g. >=20.

If you are looking to just test on a prerelease (1. from Angus) then this is fine, if you intended to statically publish I suggest you wait for an official release.

[acocac]

• run myst start --headless

I run jupyter book start --headless instead and it works! The fix exactly renders holoviews based plots 🚀

If you are looking to just test on a prerelease (1. from Angus) then this is fine, if you intended to statically publish I suggest you wait for an official release.

I'll wait until the official release then. In the meantime, I'll start checking the pre-release on the actual notebooks in EDS book. #545 looks also pertinent for future content by the EDS book community so I'll keep an eye out on this too!

Thanks @agoose77 and @stevejpurves!

[acocac]

Could you clarify what you're trying to do?

• If you just want to see what the new theme looks like before it is released, you can run the theme application locally.
• If you want to build static HTML to publish, you can also do that, and I'd need to update our contributing guide for a walk through.

I refer to 1, however it might be helpful some guidelines for "JB2 advanced users" on how to publish using pre-releases.

[stevejpurves]

in the meantime @acocac the (first round of) changes for holoviews/bokeh have been released - as this does not require a release of jupyter book but myst-theme instead. If you run jupyter book clean --templates you'll clear out old themes and the latest and greatest will be downloaded when you next run jupyter book start.