Optionally weight lca summarize output by hashval abundance.

[ctb]

Adds --with-abundance to sourmash lca summarize, to weight output by hashval abundance in query signatures, per #1011 #634

This flag is off by default in 3.x but will be on by default in 4.0.

Also adds many unit tests for relevant functions in lca_utils.

Fixes #1011
Fixes #634

Still TODO:

• add new tests with hmp-sigs
• do deprecation tagging etc for 4.0
• build some simulated data and make sure it works end-to-end
• document

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• 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?

[ctb]

This is exposing some "interesting" design considerations in the unweighted code... Looks like lca_utils.gather_assignments and count_lca_for_assignments may flatten abundances in unintended ways.

[codecov]

Codecov Report

Merging #1022 into master will increase coverage by 0.02%.
The diff coverage is 95.65%.

@@            Coverage Diff             @@
##           master    #1022      +/-   ##
==========================================
+ Coverage   92.34%   92.37%   +0.02%     
==========================================
  Files          72       72              
  Lines        5421     5454      +33     
==========================================
+ Hits         5006     5038      +32     
- Misses        415      416       +1     

Impacted Files	Coverage Δ
sourmash/lca/lca_utils.py	95.83% <90.90%> (-0.72%)	⬇️
sourmash/lca/command_summarize.py	89.10% <97.05%> (+1.88%)	⬆️
sourmash/cli/lca/summarize.py	100.00% <100.00%> (ø)

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[ctb]

ready for review @bluegenes @taylorreiter

[ctb]

If we follow pandas deprecation policy per #655, I think what we want to do is --

• for next release (3.4?), make sure we've put deprecation warnings around "default" lca summarize, warning that default behavior will change to --with-abundance in 4.0;
• for 4.0, switch that warning so that we tell people, hey, default behavior is now --with-abundance
• for 5.0, remove that warning.

yes?

[bluegenes]

lgtm!

[ctb]

🥳 🎉