Expand Reference table of contents one more level

[bdpedigo]

Is your feature request related to a problem? Please describe.

Currently in reference tab in docs, it looks like

Reference | |_____ Module 1 | |____ Topic 1 | |____ Topic 2 | |_____ Module 2 | |____ Topic 1 | |____ Topic 2 ...

So none of the actual classes/functions can be seen in the TOC.

I dislike this. I know many people miss certain functions because they don't scroll through everything in the actual page.

Describe the solution you'd like

I would like each function/class to show up in the TOC (basically just make it go one level further). I'd be okay with removing the intermediate categorizations that don't correspond to an actual module or anything like that.

Describe alternatives you've considered

Some libraries have something like this or this

Additional context

Seems related to #119 Is a solution to something I think @jovo was complaining about.

Would like to hear opinions on this.

[alyakin314]

Both seem options appropriate to me; removing the intermediate categorizations seem more user-friendly than nesting them, but both have pros and cons obviously.

[alyakin314]

i also wanted to add in that it might be time for us to re-arrange references in some sort of a logical order

[bdpedigo]

https://scanpy.readthedocs.io/en/stable/api/index.html#module-scanpy.tl curious what people think of this as a way of organizing the reference docs