[WIP] Use a Nodegraph for searching in internal nodes

[luizirber]

Direct similarity calculation of Nodegraphs avoid calling get_mins and copying then from C++ to Python all the time...

Depends on dib-lab/khmer#1842 (and updating our dependency on khmer to 3.0+)

• 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 #395 into master will decrease coverage by 0.08%.
The diff coverage is 83.33%.

@@            Coverage Diff             @@
##           master     #395      +/-   ##
==========================================
- Coverage   89.47%   89.39%   -0.09%     
==========================================
  Files          27       27              
  Lines        4238     4242       +4     
  Branches       39       39              
==========================================
  Hits         3792     3792              
- Misses        446      450       +4

Impacted Files	Coverage Δ
sourmash/sbtmh.py	85.51% <83.33%> (+0.51%)	⬆️
sourmash/signature_json.py	95.62% <0%> (-1.25%)	⬇️
sourmash/lca/lca_utils.py	95.23% <0%> (-0.8%)	⬇️
sourmash/lca/command_index.py	90.3% <0%> (-0.45%)	⬇️
sourmash/sbt.py	85.71% <0%> (ø)	⬆️
sourmash/sbt_storage.py	96.59% <0%> (+1.08%)	⬆️

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[luizirber]

Turns out that this... works. Tests are failing because this depends on an unreleased branch of khmer, which dropped Python 2.7.

Still need to run some benchmarks with real SBT indexes, only tried with a small subset of genbank (it's 30% faster, I suspect it will even better with large indexes)

[luizirber]

There are better ways of doing this once #424 is merged (including not depending on khmer releases).