[MRG] Documentation updates for 4.0 release

[ctb]

URL for build: https://sourmash.readthedocs.io/en/docs_4.0/

Fixes #1168, sourmash sketch docs
Fixes #1142, docs for new top-level signature loading API
Fixes #919 - better docs for save/load signatures
Fixes #973 - better indexed database docs
Willfix #1069 once #1316 is merged into this PR.

TODO:

• integrate sourmash sketch docs
• change sourmash compute to sourmash sketch in the markdown docs
• search for --scaled and --track-abundance and change to -p format in the markdown docs
• change sourmash compute to sourmash sketch in tutorials and notebooks
• search for --scaled and --track-abundance and change to -p format in tutorials and notebooks
• do a once-over review of all the docs with singlehtml or latexpdf
• check internal references etc on docs build
• document new top-level API for loading signatures/databases, load_file_as_signatures and load_databases per make load_database and load_file_as_signatures the new top-level/public API for loading signatures. #1142
• resolve @ctb stuff
• add release notes Draft release notes for v4.0 #1309
• add migration doc, currently in hackmd at https://hackmd.io/KktN0rK0SHqbbZoKsRwBmw

Checklist

• Is it mergeable?
• make test Did it pass the tests?
• make coverage Is the new code covered?
• Did it change the command-line interface? Only additions are allowed
  without a major version increment. Changing file formats also requires a
  major version number increment.
• Was a spellchecker run on the source code and documentation after
  changes were made?

[codecov]

Codecov Report

Merging #1283 (71ef18d) into latest (6f2664e) will increase coverage by 5.32%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           latest    #1283      +/-   ##
==========================================
+ Coverage   88.74%   94.06%   +5.32%     
==========================================
  Files         123       96      -27     
  Lines       18124    14510    -3614     
  Branches     1399     1399              
==========================================
- Hits        16084    13649    -2435     
+ Misses       1801      622    -1179     
  Partials      239      239              

Flag	Coverage Δ
python	94.06% <ø> (ø)
rust	?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/core/src/sketch/minhash.rs
src/core/src/wasm.rs
src/core/src/sketch/nodegraph.rs
src/core/src/index/sbt/mod.rs
src/core/src/index/storage.rs
src/core/src/ffi/cmd/compute.rs
src/core/src/ffi/hyperloglog.rs
src/core/src/index/sbt/mhbt.rs
src/core/src/ffi/utils.rs
src/core/src/signature.rs
... and 17 more

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[ctb]

I think this is ready for review; the only remaining issues have to deal with tutorials, notebooks, and migration docs, and are pretty isolated (and can be reviewed piecemeal as PRs into this one).

@taylorreiter go for it!

[taylorreiter]

this is a wonderful docs update! some suggestions included.

[ctb]

OK, @luizirber, I think this is fully baked! ready for your review.

[luizirber]

Just a couple of comments, but LGTM!

[ctb]

🎉