[MRG] migrate command (update old indexes)

[luizirber]

This PR adds the migrate command to update old indexes to newer versions.

• If using an old database there will be a "WARNING" pointing how slow things are going to be. (Should we just stop running and throw an error instead?)
• Rewrote the metadata updates using a fill_up method (a BFS starting from the leaves).
• add another logging level, debug (and we should start using the logging module from stdlib...)
• add an extra argument to save: structure_only. If set, avoid re-saving the data and only updates the SBT JSON.
• Fix a bug with tree repair and min_n_below interactions.

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-io]

Codecov Report

Merging #494 into master will increase coverage by 0.17%.
The diff coverage is 93.18%.

@@            Coverage Diff             @@
##           master     #494      +/-   ##
==========================================
+ Coverage   90.51%   90.69%   +0.17%     
==========================================
  Files          33       33              
  Lines        4936     4999      +63     
  Branches       36       36              
==========================================
+ Hits         4468     4534      +66     
+ Misses        467      464       -3     
  Partials        1        1

Impacted Files	Coverage Δ
sourmash/__main__.py	95.83% <ø> (ø)	⬆️
sourmash/sbtmh.py	86.56% <100%> (+0.2%)	⬆️
sourmash/commands.py	91.58% <100%> (+0.08%)	⬆️
sourmash/logging.py	98% <71.42%> (-2%)	⬇️
sourmash/sbt.py	85.88% <94.28%> (+2.55%)	⬆️

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[luizirber]

Ready for review and merge @ctb

[ctb]

A few comments -

• there is no explicit test of the sourmash migrate command. I think we should have one!
• the warning message about using sourmash migrate is printed even when running sourmash migrate which seems odd
• the --output flag is odd. I would have thought that this would be the new name of the SBT, not the (I'm guessing here) size of the bloom filters in the new SBT.

We should also add explicit testing of loading old SBTs in here somewhere, but that could be a new issue that we handle separately.

[luizirber]

• Test added. It will probably need to be updated for each new version of the DB, but I guess this is fine (since new versions of DB might change internal details)
• added print_version_warning along the load() calls, defaults to True but we disable it for sourmash migrate
• of course it's odd, it's copy-pasta from another command =P. Removed.

On the explicit loading of older SBTs: despite having the _load_v{1,2} code, we have bigger problems (like v1 assuming the leaves were YAML signatures, which we removed support for loading when we adopted JSON). Not sure what is the best way: supporting it all adds a fairly large maintenance burden, but do we really have users with a v1 database around?