[MRG] subtantial refactoring of CounterGather and related Index code.

[ctb]

Note: PR into #2111

This PR does a bunch of cleanup and refactoring of gather related things:

• renames search.make_gather_query to search.make_containment_query
• adds support for best_only in Index.prefetch
• renames Index.gather to Index.best_containment, and changes method to return None or an IndexSearchResult, rather than a list => much confusion reduction.
• consolidates threshold calculation code in search.py into a single function 🎉
• adds flatten_and_* utility functions in sourmash.minhash.
• adjusts CounterGather classes to take SourmashSignature instead of MinHash object, in line with Better conceptual definition on minhash/signature/query #616
• changes CounterGather.siglist and locations to use dictionaries instead of lists
• adds CounterGather.signatures()
• adds a CounterGather_LCA() test implementation

The net result is a lot of code reduction in the Python codebase plus (IMO) more readable code.

A note to CounterGather aficionados

The change to using dictionaries instead of lists to store signatures and locations in CounterGather means that only one signature per md5sum will be stored. For the default CounterGather test, this will be the last one added.

See test test_index.py:test_counter_gather_identical_md5sum for the specific implementation test for CounterGather, and test_index_protocol.py::test_counter_gather_multiple_identical_matches for the general protocol test.

TODO

• make a CounterGather technique to provide list of locations, list of signatures??
• should CounterGather classes take a list of index databases to prefetch on, instead of current creation API?
• remove/rename Index.gather?

[codecov]

Codecov Report

Merging #2116 (61624fc) into latest (0bc9dbd) will increase coverage by 7.38%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           latest    #2116      +/-   ##
==========================================
+ Coverage   84.30%   91.69%   +7.38%     
==========================================
  Files         130       99      -31     
  Lines       15278    11002    -4276     
  Branches     2171     2166       -5     
==========================================
- Hits        12880    10088    -2792     
+ Misses       2095      611    -1484     
  Partials      303      303              

Flag	Coverage Δ
python	91.69% <100.00%> (ø)
rust	?

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

Impacted Files	Coverage Δ
src/sourmash/commands.py	88.88% <100.00%> (ø)
src/sourmash/index/__init__.py	96.66% <100.00%> (-0.12%)	⬇️
src/sourmash/minhash.py	94.02% <100.00%> (+0.22%)	⬆️
src/sourmash/search.py	97.92% <100.00%> (-0.02%)	⬇️
src/core/tests/storage.rs
src/core/src/sketch/nodegraph.rs
src/core/src/cmd.rs
src/core/src/sketch/minhash.rs
src/core/tests/test.rs
src/core/src/ffi/hyperloglog.rs
... and 25 more

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[ctb]

@mr-eyes ready for review!

[bluegenes]

a few comments/questions -- otherwise I think this looks good to me. cleaner and better descriptions, for sure