MRG: when lingroups are provided, use them for csv_summary

[bluegenes]

Currently, when we generate a csv_summary with LINs, we get a summary at every single LIN rank, which is a lot of results and not very helpful. LINgroups are our way of linking the LINs (e.g. 14;1;0;0;0;0;0;0;0;0) to a known name/taxonomic group (e.g. "Phylotype I").

This PR changes the behavior of csv_summary when a lingroup file is provided, limiting summarized reporting to just the named lingroups. While the output is very similar to the lingroup output we already have, the most important difference is that the sample name is included in the output, meaning that we get intelligible results when running tax metagenome on more than one sample.

Prior tax metagenome behavior was to always generate a lingroup output file when a lingroups file is provided. Here, I disable that for multiple queries, since the results wouldn't make sense. I do not replace it with another default, but I did add a recommendation to the help + doc.

In the future, we could consider changing the default lingroup output to csv_summary, since it's actually useful for multiple files. Or, we could modify the lingroup output to include query information.

• Also fixes csv_summary format not created for multiple queries (tax metagenome) #3315

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 92.40%. Comparing base (5acf698) to head (e3c3bb6).
Report is 1 commits behind head on latest.

Additional details and impacted files

@@            Coverage Diff             @@
##           latest    #3311      +/-   ##
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+ Coverage   86.45%   92.40%   +5.94%     
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  Files         137      104      -33     
  Lines       16070    12925    -3145     
  Branches     2211     2219       +8     
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- Hits        13894    11943    -1951     
+ Misses       1869      675    -1194     
  Partials      307      307              

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python	92.40% <100.00%> (+<0.01%)	⬆️
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[bluegenes]

@sourmash-bio/devs ready for review

[ctb]

looks good - esp appreciate the documentation update.

there's some missing code coverage - is this just buggy codecov? I haven't dug in at all.

[ctb]

oh! I wanted to suggest that you put the suggested changes to behavior in the PR description into new issues, too; I think they require a major version bump?

[bluegenes]

looks good - esp appreciate the documentation update.

there's some missing code coverage - is this just buggy codecov? I haven't dug in at all.

looks like it was just buggy codecov!

[bluegenes]

oh! I wanted to suggest that you put the suggested changes to behavior in the PR description into new issues, too; I think they require a major version bump?

now in #3361