[WIP] Save unique kmers count in Nodegraph

[luizirber]

Both khmer and sourmash Nodegraph keep track of unique kmers during insertion, but this info is lost when serializing to disk. This PR updated the binary format, adding an extra field to keep this info. This makes sourmash Nodegraphs incompatible with khmer, but they sort of are incompatible already because khmer doesn't support compressed Nodegraphs.

(both changes can be ported back to khmer, but not today =] )

I copied over the version 4 binary format documentation from khmer and added the new changes for version 5 of the Nodegraph.

cc @olgabot

TODO

• need to expose a save_v4 method to Python, to keep compatibility with khmer (the save method defaults to v5)
• Fix the rust tests, they still assume everything is v4-only

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 #1009 into master will increase coverage by 8.79%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #1009      +/-   ##
==========================================
+ Coverage   83.30%   92.09%   +8.79%     
==========================================
  Files          97       72      -25     
  Lines        8749     5454    -3295     
==========================================
- Hits         7288     5023    -2265     
+ Misses       1461      431    -1030     

Flag	Coverage Δ
#rusttests	?

Impacted Files	Coverage Δ
sourmash/nodegraph.py	77.67% <0.00%> (-16.08%)	⬇️
src/core/tests/test.rs
src/core/src/ffi/utils.rs
src/core/src/ffi/mod.rs
src/core/src/ffi/signature.rs
src/core/src/sketch/ukhs.rs
src/core/src/ffi/nodegraph.rs
src/core/src/ffi/cmd/compute.rs
src/core/src/signature.rs
src/core/src/lib.rs
... and 15 more

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[olgabot]

Exciting!! Thank you so much!

[luizirber]

I'm adding these docs and changes to #1221, which will be version 5 of the Nodegraph format (and incompatible with khmer).