Equations not rendering properly

[rsbyrne]

Me yet again - this time about equations.

My equations are rendering just fine in the usual Jupyter notebook markdown cell context:

(screengrab of https://github.com/rsbyrne/thesis/blob/main/book/content/chapter_02_methods/section1.ipynb)

But are all borked on the actual Github pages upload:

(screengrab of https://rsbyrne.github.io/thesis/content/chapter_02_methods/section1.html)

Presumably the LaTeX engine that Jupyter Book is using has lesser or different syntax support for equations. Some of them render okay, but many don't. I'm sure there's a way to configure this, but I don't know how.

My versions:

Thanks for all the help - y'all are really saving my bacon.

-Rohan

[choldgraf]

If you use dollar signs does it render? It looks like you don't have the [ ] set to render as math in jupyter book. You may need to manually set this in sphinx. See here for how this is done in myst: https://myst-parser.readthedocs.io/en/latest/using/syntax.html#mathjax-and-math-parsing

[rsbyrne]

Hmm, that can't be it because whereas this renders fine:
\\[ Pr \equiv \frac{\nu_r}{\kappa_r} = \frac{\frac{\mu_r}{\rho_r}}{\frac{k_r}{\rho_r c_{p_r}}} \\]

This does not:
\\[ Nu = 1 + \left| \frac{\partial \theta^*}{\partial y^*} \right| _S \\]

Scroll down the page and you'll find heaps of examples: some work, some don't, and I can't figure out what the pattern is:
https://rsbyrne.github.io/thesis/content/chapter_02_methods/section1.html

My config file is here FYI:
https://github.com/rsbyrne/thesis/blob/main/book/_config.yml

I'll keep poking around.

[rsbyrne]

Okay, so it turns out that actually none of the equations are rendering anymore: the seemingly ad hoc quality of the problem was just due to caching of notebook cells.

So I must have some general Sphinx problem on my hands.

On a related note, is there a Docker container or anything like that that would demonstrate a properly configured environment for a Jupyter Book? Presumably the official Jupyter Book documentation is built by some VM somewhere - if I knew how that machine is configured, I could compare it to my own build and figure out what I'm missing.

[rsbyrne]

Alright, so I seem to have them working now. The key was forcing an upgrade to myst-parser. It raised a bunch of scary error messages saying that Jupyter Book would prefer the older version, but the newer version caused everything to render properly immediately.

My myst-parser version is now:

Is it possible that Jupyter Book's requirements are out of date?

[choldgraf]

@rsbyrne definitely possible, we are about to release a new version of Jupyter Book and I think some other versions will upgrade soon that will result in more alignment

[rsbyrne]

Pumped for the next release. Thanks so much to you and the other maintainers for driving forward this transformative project.

[rsbyrne]

TL;DR, the key was forcing an upgrade to myst-parser:
pip3 install -U myst-parser

In general, while doing so seems kind of slapdash, I'm having a lot of success with just forcing upgrades to everything as soon as I run into a problem!