[MRG] add --distance-matrix option to sourmash compare

[ctb]

This PR addresses #2196 by adding a --distance-matrix flag to compare.

This flag simply subtracts every value in the matrix from 1, converting it from a similarity matrix to a distance matrix. Easy peasy!

Along the way, I decided to clean up the compare tests in tests/test_sourmash.py, which makes for a somewhat messier diff, sorry :(. Specifically, I

• renamed the compare tests to all have def test_compare at the beginning of the test fn;
• switched the tests from decorator c to test fixture runtmp;
• added comments;
• refactored some shared sig and matrix loading code out of a number of tests;

TODO:

• confirm that plot code needs no changes

Fixes #2196

[codecov]

Codecov Report

Merging #2225 (ef16462) into latest (718c9b5) will increase coverage by 7.37%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           latest    #2225      +/-   ##
==========================================
+ Coverage   84.66%   92.04%   +7.37%     
==========================================
  Files         131      100      -31     
  Lines       15512    11245    -4267     
  Branches     2210     2213       +3     
==========================================
- Hits        13134    10351    -2783     
+ Misses       2085      601    -1484     
  Partials      293      293              

Flag	Coverage Δ
python	92.04% <100.00%> (+<0.01%)	⬆️
rust	?

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

Impacted Files	Coverage Δ
src/sourmash/cli/compare.py	100.00% <100.00%> (ø)
src/sourmash/commands.py	90.72% <100.00%> (+0.07%)	⬆️
src/core/src/sketch/minhash.rs
src/core/src/from.rs
src/core/src/signature.rs
src/core/src/encodings.rs
src/core/src/index/search.rs
src/core/src/index/sbt/mhbt.rs
src/core/tests/test.rs
src/core/src/lib.rs
... and 23 more

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[ctb]

ready for review @sourmash-bio/devs !

[taylorreiter]

did you confirm that the plot code needs no changes as marked as a todo item?

[taylorreiter]

a couple of comments, otherwise LGTM.

[taylorreiter]

also why is the docs build failing? (sry if its a dumb question bc i haven't been keeping up with sourmash CI)

[ctb]

also why is the docs build failing? (sry if its a dumb question bc i haven't been keeping up with sourmash CI)

readthedocs is ALWAYS failing. Usually because I haven't pinned some version or something 😆

I'll take a look in a bit.

[ctb]

did you confirm that the plot code needs no changes as marked as a todo item?

unfortunately, it does indeed need changes. but I think I will do as a separate issue.

(oddly, I thought I'd made this comment ...somewhere, but apparently forgot it. yay.)

[ctb]

readthedocs builds failing issue: #2227

[ctb]

plot adjustment issue: #2228

[ctb]

thanks for the review @taylorreiter - I'm going to wait to merge until #2215 is in!