Doc submodule

[ivirshup]

Overhaul of tutorials page

Tutorials can now be versioned with the docs by using a gitsubmodule of the tutorials repo (letting us avoid things like: scverse/scanpy-tutorials#85)

Possible additions, that can be left to later

• It's a lot more bare now, maybe we should use cards? I wasn't sure if there's a great way to do this while keeping overall organization.
• Some tutorials that have been removed may be worth keeping
  • 1.3 million mouse neurons
  • Cell cycle regression

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 75.49%. Comparing base (f5edd43) to head (b22084d).
Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #2901   +/-   ##
=======================================
  Coverage   75.49%   75.49%           
=======================================
  Files         116      116           
  Lines       12911    12911           
=======================================
  Hits         9747     9747           
  Misses       3164     3164           

Files	Coverage Δ
scanpy/datasets/_datasets.py	86.04% <ø> (ø)
scanpy/neighbors/__init__.py	80.75% <ø> (ø)
scanpy/plotting/_tools/scatterplots.py	86.48% <ø> (ø)
scanpy/tools/_ingest.py	77.23% <ø> (ø)

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[ivirshup]

@flying-sheep, docs are building now if you want to take a look

[flying-sheep]

The structure looks good, two main things:

1. The tutorial site looks a bit messy, with toc trees, paragraphs, and images interspersed. If you e.g. remove the sub-indices, put the text together and use a sphinx-design grid for the images, you’d get:

   

2. See Doc submodule #2901 (review)

   Bibtool should run either in CI or at least locally.

[ivirshup]

Seems like you accidentally force-pushed over my commits, please re-add:

This was intentional as those changes broke the doc build. sphinxcontrib-bibtex couldn't parse the reformatted bibtex file. Over here I requested that if you want to add bib tool working as a precommit, I would like you to do it in a separate branch.

[flying-sheep]

OK, now the only thing missing is to move the notebooks directory into docs and to make sure the bibtex isn’t a mess.

You said you don’t want to do that manually, so please add some way to do it automatically.

sphinxcontrib-bibtex couldn't parse the reformatted bibtex file.

hmm, so we can’t trust its parser to work properly, that’s a bit concerning. But we control what it sees so that isn’t too bad.

[ivirshup]

OK, now the only thing missing is to move the notebooks directory into docs

We have already discussed this, and it is staying as is for now. We can think about doing this in the future, but please make your case in an issue.

bibtex isn’t a mess.

I will be leaving the bibtex as is, I don't see an issue with the bibtex as it renders fine. As I requested last week, you can suggest a formatter for it in a separate PR. Notably this bibtex is copied directly from scverse-tutorials, which doesn't seem to have caused any issues.

FWIW there are some tools for working with bibtex recommended here:

• Extend Sect. Related Programs by 'betterbib', 'python-bibtexparser', 'BibDesk' and 'ebib' ge-ne/bibtool#58
  • bibtex-tidy has a pre-commit that doesn't do exactly what you're looking for
  • python-bibtexparser seems like it'd be able to do what you want, and is far more actively maintained than bibtool.