[MRG] add 'sourmash signature' signature manipulation utilities.

[ctb]

Provides merge, flatten, rename, intersect, extract, downsample, subtract, import, export, and overlap utilities via sourmash signature subcommands.

PR internal link: sourmash signature documentation updates.

Favorite internal review so far:

"it's grease for bioinformatics! (and all the functionality I never knew i needed in my life)"

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Also renames sourmash_lib to sourmash in most of the existing code, as minor cleanup.

Fixes #196 #239 #121 #241.

TODO:

• add at least minimal docs for the commands that exist
• add info or describe command (see code in Add "describe" to output kmer sizes, molecules, scaled, and num hashes for each signature #561)
• provide -o/--output to specify output
• add --ksize etc signature selection commands
• add extract command to extract one particular signature
• add downsample command (part of Add two utilities #149)
• add subtract command (part of Add two utilities #149)
• add basic tests for ksize/moltype
• add basic tests for --output
• define and test intersect and subtract behavior wrt --track-abundance
• figure out what to do about signatures calculated with --track-abundance, esp wrt mixtures of these signatures with non-track-abundance.
• add import and export (Convert mash JSON => sourmash signatures #121 Exporting mash hashes for interoperability marbl/Mash#27)
• adjust downsample to do conversions between num and scaled signatures (Add ability to adjust --num-hashes, --scaled on-the-fly in 'compare' and 'categorize' #560)
• add overlap (sourmash 'inspect' command #241)
• change merge, subtract, intersect to support multiple signatures in one file, & add documentation and tests for all functions that do support this (info, merge, intersect, subtract, flatten, downsample)

Upon merge:

• create low hanging fruit issues to add more tests for ksize/moltype selectors, --output, and signatures calculated with --track-abundance.
• review Python code in sig/__main__.py and extract ideas for new functions for the MinHash class - flatten, subtract, downsample conversion, etc, into new issues.

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 #587 into master will increase coverage by 0.79%.
The diff coverage is 95.34%.

@@            Coverage Diff             @@
##           master     #587      +/-   ##
==========================================
+ Coverage   88.64%   89.43%   +0.79%     
==========================================
  Files          25       27       +2     
  Lines        3786     4193     +407     
  Branches       37       37              
==========================================
+ Hits         3356     3750     +394     
- Misses        430      443      +13

Impacted Files	Coverage Δ
sourmash/lca/command_index.py	90.7% <100%> (+0.44%)	⬆️
sourmash/logging.py	96.07% <100%> (-1.93%)	⬇️
sourmash/__main__.py	96% <100%> (+0.16%)	⬆️
sourmash/lca/command_summarize.py	82.6% <100%> (+1.08%)	⬆️
sourmash/commands.py	89.33% <100%> (ø)	⬆️
sourmash/lca/command_rankinfo.py	91.66% <100%> (+1.87%)	⬆️
sourmash/sig/__init__.py	100% <100%> (ø)
sourmash/lca/command_compare_csv.py	93.5% <100%> (+1.29%)	⬆️
sourmash/lca/command_gather.py	84.75% <100%> (+1.21%)	⬆️
sourmash/lca/command_classify.py	86.36% <100%> (+1.13%)	⬆️
... and 8 more

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[ctb]

I think this is ready for a preliminary review by folks. @olgabot @taylorreiter @bluegenes any thoughts or comments welcome!

@luizirber while the tests aren't that comprehensive I think the basic command line API is OK, and as these commands are mostly wrappers around MinHash functionality, I'm not too concerned about the tests. I'm sure we'll add some as bugs are discovered, too :).

[luizirber]

I think this is a good place to put #121 too? Maybe not in this PR, but probably fits into sourmash signature

[ctb]

yes, #121 is an excellent addition - can provide import and export both! thx!

[ctb]

Hi @luizirber I think this is ready for code review!

Your opinion on sourmash sig info vs sourmash sig describe or about is solicited!

[ctb]

all tests passed!!!!

[bluegenes]

LGTM!