Doc overhaul

[adamgayoso]

This is a version of Sphix-book-based scanpy docs.

What's lost?

• Docsearch
• Edit on github button (was weird anyway as no other package does that)

What's gained?

• Aesthetics, easier to read
• Git submodule for tutorials
• sphinx.ext.viewcode so each function has a source button (effectively replaces edit on github button)

What else changed?

• I removed the release latest stuff, not sure what value it was adding
• API docs are split logically

View the rendered docs here:

https://icb-scanpy--2220.com.readthedocs.build/en/2220/index.html

What's left to do:

• Update tutorials index page to use nbgallery feature of nbsphinx
• Make home index page use a grid of cards, two columns
• Add to contributing guide how to manage the git submodule (really just occasionally do git submodule update --remote)
• Annotate CSS overrides
• Exchange sphinx ext viewcode for linkcode (probably in scanpydoc)

[codecov]

Codecov Report

Merging #2220 (524df7f) into master (1313f7b) will decrease coverage by 0.01%.
The diff coverage is n/a.

Additional details and impacted files

@@            Coverage Diff            @@
##           master   #2220      +/-   ##
=========================================
- Coverage    0.31%   0.31%   -0.01%     
=========================================
  Files          97      97              
  Lines       11485   11486       +1     
=========================================
  Hits           36      36              
- Misses      11449   11450       +1     

Impacted Files	Coverage Δ
scanpy/readwrite.py	0.00% <0.00%> (ø)

[adamgayoso]

Ok @Zethson it's ready to merge

[Zethson]

Thank you @adamgayoso !
We should consider removing the ecosystem page in favor our scverse ecosystem page in the future to not have to maintain both.

[flying-sheep]

Wait a second, how could I miss this.

This is an absolute no-go. This makes it very hard to go back to functional docs where nothing is broken, since broken stuff can accumulate after this.

Someone needs to spend far too much time to fix this, and I fear it’s going to be me. Can we please never do this again?