Link to cellrank.org

[Marius1311]

Once that's done, we can use a fix by @VolkerBergen to make sure that even when the user clicks on a tutorial, the visible url remains cellrank.readthedocs/xxx. @VolkerBergen , can you point me to the part of the code where you do this?

[michalk8]

@Marius1311 I think you need to set this up, since you're the owner, see here: https://docs.readthedocs.io/en/stable/custom_domains.html#custom-domain-support

[VolkerBergen]

You can retrieve the notebooks from the notebook-repo (see here), which downloads the notebooks behind the scenes and converts them to html via nbsphinx. This way, you would have your tutorials-docs also being hosted directly at cellrank.readthedocs.org.

[Marius1311]

Linking to cellrank.org is done. @michalk8, we can set up the notebook download in our call on Wednesday together.

[michalk8]

Thanks @VolkerBergen for the suggestion, it's done. @Marius1311 the figures look a bit off, do you know how to fix it? Afterwards, we can close this.

[michalk8]

Also @VolkerBergen , upgrading to sphinx-3.1.1 leads to the following problem (no links are present for some functions, such as tl.partition):

I think this is because of all the warnings we're getting (not included in toc tree) when building the docs (I'd like to fix them, but have no idea how + I want to be a bit stricter and have warnings as error). Do you know what might be the cause?
`

[VolkerBergen]

@michalk8 I get the following error when trying to generate the html

Extension error:
Handler <function process_docstring at 0x12b6bbc20> for event 'autodoc-process-docstring' threw an exception
make: *** [html] Error 2

Maybe related?

[michalk8]

Yes and no, but it has led me to this (didn't see this because of all the other warnings...).
Furthermore, I don't get that error, but digging deeper, this is the warning which causes the issue:

WARNING: don't know which module to import for autodocumenting 'pl.cluster_fates' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)

Here's the related issue for sphinx version 3.1.1: sphinx-doc/sphinx#7844

[matthewfeickert]

👋 @michalk8, I was checking on the Sphinx Issue that I opened today and noticed that you had linked to it here. Could you please mention on the Issue that you're also running into this? The more people that are reporting the sooner it will probably get attention from the Sphinx devs.

FWIW, pyhf is considering temporarily pinning to have Sphinx be sphinx<3.1.0, so might be worth looking into for cellrank as well(?).

[Marius1311]

@michalk8, we had that figure issue before, you remember? Last time you fixed it somehow, I can't remember how you did it though. This was a couple of months ago.

@VolkerBergen , do you know how to fix this? We run into trouble when we have several figures in one row in the tutorials.

[Marius1311]

By the way, @michalk8, very nice clean up of the notebooks repo! I love it!

[michalk8]

This has been done, closing this. I will create a separate issue for removal of the warnings.

[VolkerBergen]

Sorry, forgot to reply. I know the issue and can help you with getting the right fig sizes in the converted tutorials. It's a little longer explanation. Let's disc next week.