Jupyter-book: Truncated notebooks

[sidneymbell]

Hi there! I've got jupyter-book mostly working for a course we're teaching next month (hooray!). Love the interface and super appreciate the project!

I'm experiencing an odd thing where most of my notebooks are being truncated. For example, this long notebook:
https://github.com/chanzuckerberg/scRNA-python-workshop/blob/master/content/preprocessing/01-basic-qc.ipynb

results in this short page:
https://chanzuckerberg.github.io/scRNA-python-workshop/preprocessing/01-basic-qc.html

even though the html file in _build/ contains the full notebook:
https://github.com/chanzuckerberg/scRNA-python-workshop/blob/master/_build/preprocessing/01-basic-qc.html

Could you point me in the right direction? (I assume there's just a setting I'm overlooking somewhere?). Thanks so much!

[emdupre]

Hi @sidneymbell --

It looks like your <details> tag is swallowing a lot of your text ! If I expand the arrow at the bottom of your linked book page (right above Solution) I'm able to recover the text (there's also one more <details> to expand in there to capture all of it). It seems we're not playing nicely with those tags when converting !

Could you try instead putting these items in their own cells ? You could then tag the cell content. In particular, you might want to tag these cells to hide their input !

[sidneymbell]

Hey @emdupre -- Thanks so much for your response!

The rest of the content is indeed getting collapsed in the dropdown somehow.

I did see the tag option; while it's a cool feature, I'd like to keep the dropdowns in these notebooks if possible. The notebooks will be run by students, and while the cell tag will hide the solution in the book rendering, it won't hide them in the notebooks themselves.

Interestingly, the individual HTML pages seem to render the dropdowns just fine; the odd collapsing behavior only occurs in the book context. Any idea why this occurs?

Thanks again for your help!

[choldgraf]

Ah - looking through your page's HTML:

view-source:https://chanzuckerberg.github.io/scRNA-python-workshop/preprocessing/01-basic-qc.html

Do a ctrl-f for the word "details". It seems like for some reason your first details tag is getting escaped into non-HTML characters (line ~797 I believe). I wonder if that's the problem. Figuring out why this is happening is another question :-)

I wonder if there's some wonkiness being introduced by mixing HTML + markdown in the same cell?

And another question: I believe that notebooks can have cell inputs or outputs marked as "collapsed" so that in a jupyter session they'll be closed when you first open the notebook. If that was the case, would that fit your usecase?

[sidneymbell]

Ahh, thanks for the catch. Ended up being a weird paragraph tag issue, but I've got it fixed now. Hooray!

And yes, being able to mark cells as "collapsed" in a jupyter session would also have met my use case.

Thanks again! :)

[choldgraf]

wohooo! that's great to hear :-)