[WIP] Store and retrieve hash abundances in LCA DBs.

[ctb]

NOTE: this is a PR into #1013.

Currently, the LCA/revindex databases cannot store or retrieve hashval abundances, which means that signatures with track_abundances are not represented faithfully. As suggested in #581 (comment), this PR enables abundance storage in LCA_Database objects by storing them in hashval_to_idx values as tuples (idx, abund).

After #1013, I think this is the last change to LCA_Database to bring it into full compliance as a signature storage database, i.e. all inserted signatures can be full reconstructed from the database. w00t!

Also see #634 and #1013 for motivation.

TODO:

• start filling in abundances
• test reconstruction of input sequences
• add ignore abundance parameters and flags
• test command line build

PR 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 #1015 into protein_lca_db will decrease coverage by 0.29%.
The diff coverage is 100.00%.

@@                Coverage Diff                 @@
##           protein_lca_db    #1015      +/-   ##
==================================================
- Coverage           92.33%   92.03%   -0.30%     
==================================================
  Files                  72       72              
  Lines                5413     5439      +26     
==================================================
+ Hits                 4998     5006       +8     
- Misses                415      433      +18     

Impacted Files	Coverage Δ
sourmash/lca/command_gather.py	84.47% <100.00%> (+0.60%)	⬆️
sourmash/lca/command_rankinfo.py	89.13% <100.00%> (ø)
sourmash/lca/lca_db.py	94.94% <100.00%> (+0.32%)	⬆️
sourmash/nodegraph.py	77.67% <0.00%> (-16.08%)	⬇️

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[ctb]

I'm going to close this for now, as I don't think we actually need it for anything useful :)