investigations and fixes around new gather behavior.

[ctb]

Gather is exhibiting some changes after #942, and we investigated them in #976 and found some bugs and undocumented behavior changes.

• per change in number of matches reported by gather with default settings in 3.2.3 #976 (comment), have GatherMinHashes actually use threshold.
• fixed issue with loss of sensitivity when threshold-bp was not a multiple of scaled.
• found unintended behavior change with respect to meaning of threshold-bp

• replace raise Exception with assert, as this is "merely" debugging fodder.
• document gather threshold bp meaning in https://sourmash.readthedocs.io/en/latest/classifying-signatures.html#appendix-how-sourmash-gather-works

Standard 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 #1001 into master will decrease coverage by 0.16%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master    #1001      +/-   ##
==========================================
- Coverage   92.23%   92.06%   -0.17%     
==========================================
  Files          72       72              
  Lines        5393     5397       +4     
==========================================
- Hits         4974     4969       -5     
- Misses        419      428       +9     

Impacted Files	Coverage Δ
sourmash/cli/gather.py	100.00% <ø> (ø)
sourmash/sbt.py	87.62% <100.00%> (ø)
sourmash/sbtmh.py	92.66% <100.00%> (+0.13%)	⬆️
sourmash/search.py	93.63% <100.00%> (+0.11%)	⬆️
sourmash/sbt_storage.py	87.68% <0.00%> (-4.44%)	⬇️

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[ctb]

ready for review! I think this probably belongs in @taylorreiter or @luizirber basket.

[luizirber]

Code changes look good, will let @taylorreiter comment on expected behavior =]

[ctb]

On Wed, May 27, 2020 at 07:57:18AM -0700, Luiz Irber wrote: @luizirber approved this pull request. Code changes look good, will let @taylorreiter comment on expected behavior =]

OK :). Not a big fan of behavior changes, but I think it is more important to make it _explicit_ (which is what this does) than to revert to previously implicit behavior.

[ctb]

Unless @taylorreiter or others comment that they would like more time , I will merge tomorrow :)