Documentation

[mumichae]

Update docstrings and create sphinx docs for readthedocs.
Rendered documentation: https://scib--279.org.readthedocs.build/en/279/ (from in github checks at the bottom of this page)

[mumichae]

@LuckyMD

Can we add default values to the documentation? => mainly important for k0 in LISI scores

Afaik, default values are already included in the autodoc. Or do you want more specific explanations on which values to use?

[LuckyMD]

Afaik, default values are already included in the autodoc. Or do you want more specific explanations on which values to use?

I didn't see any in the readthedocs link...

[mumichae]

Afaik, default values are already included in the autodoc. Or do you want more specific explanations on which values to use?

I didn't see any in the readthedocs link...

Default values are shown in the function signature.

[LuckyMD]

Ah, I was looking at the parameter explanation. Okay,all good. Thanks!

[ivirshup]

Looks fantastic! A few minor points, but I think it would be good to merge.

---

A few general minor things which would be nice, but could/ should be separate PRs:

• Type information + autodoc-typehints would be nice
• It would be great if you can installation instructions for setting up an isolated environment (probably conda), especially due to the mixed language dependencies
  • Kinda related: wouldn't you need Seurat for read_seurat?
• I would strongly recommend turning on PR builds for docs: https://docs.readthedocs.io/en/stable/pull-requests.html