[WIP] Use a Nodegraph for searching in internal nodes

[luizirber]

Updated version of #395, fixes #203

This builds up on #1137 and uses a Nodegraph for querying internal nodes. It actually passes the test currently failing in #1137, so I'm starting to think there is something fishy going on with node.data.matches(mh)...

TODO:

• It is slower than the previous way, which is annoying. Might need to change how containment and similarity are calculated in Rust (can do popcnt over the bitsets, instead of building intersection and union)

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?

[ctb]

I'm starting to think there is something fishy going on with node.data.matches(mh)...
oh no!

[codecov]

Codecov Report

Merging #1138 (4ab065d) into remove_min_n_below (fc2ee33) will decrease coverage by 0.13%.
The diff coverage is 37.03%.

@@                  Coverage Diff                   @@
##           remove_min_n_below    #1138      +/-   ##
======================================================
- Coverage               89.39%   89.26%   -0.14%     
======================================================
  Files                     122      122              
  Lines                   19001    19044      +43     
  Branches                 1448     1451       +3     
======================================================
+ Hits                    16986    16999      +13     
- Misses                   1796     1827      +31     
+ Partials                  219      218       -1     

Flag	Coverage Δ
python	94.64% <68.96%> (-0.05%)	⬇️
rust	66.60% <0.00%> (-0.41%)	⬇️

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

Impacted Files	Coverage Δ
src/core/src/ffi/nodegraph.rs	0.00% <0.00%> (ø)
src/core/src/sketch/nodegraph.rs	78.07% <0.00%> (-1.44%)	⬇️
src/sourmash/nodegraph.py	65.87% <25.00%> (-5.18%)	⬇️
src/sourmash/sbtmh.py	95.83% <100.00%> (+2.13%)	⬆️

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[ctb]

curious if the changes in #1392 help or hurt this effort.

(I don't like all of the function/class names in that PR, but it does some nice code cleanup and consolidation so I plan to propose it for merge in a few weeks.)

[luizirber]

I'm starting to think there is something fishy going on with node.data.matches(mh)...
oh no!

turns out I was doing ng.containment(ng2) wrong, oops!
(I was using sum(len(hash_tables)) as denominator, which underestimated containment; the fix was to use sum(set_bits), only considering the bits that are set in the nodegraph)

[luizirber]

Not focusing on SBTs anymore