[MRG] fix tax argument parsing

[bluegenes]

Most of the tax subcommands take multiple inputs via -g/--gather-csv and -t/--taxonomy-csv, but currently the later inputs override earlier inputs, e.g. -g gather1.csv -g gather2.csv will result in just gather2.csv being loaded. This PR fixes that by using argparse extend appropriately, and adds tests throughout.

This PR also fixes the --force argument so that it is properly passed into MultiLineageDB.load for taxonomy loading, and also properly used in gather loading.

Fixes #2213

Notes from testing

Testing the argparse action='extend' stuff systematically was tricky and annoying. I ended up adding a bunch of tests where I relied on two pieces of behavior -

• loading empty tax files was allowed with --force
• if argparse was incorrectly set up, it would fail to load the first set of provided taxonomy files per specifying multiple lineages for sourmash tax commands #2213.

So I would call something like sourmash tax prepare ... -t good_tax -t empty_tax --force.

If argparse was set up correctly, good_tax would be loaded, and empty_tax would be ignored.

If argparse was set up incorrectly, good_tax would be ignored, and only empty_tax would be received, but because it was empty, a later check (for non-empty taxonomies) would fail. Voila!

Finally, I verified that if I removed action='extend' from argparse options for the -g and -t arguments, at least one test failed. 🎉

TODO

• add action= 'extend' to appropriate args
• test annotate
• test prepare
• test grep
• test genome
• test metagenome

[codecov]

Codecov Report

Merging #2218 (92226e7) into latest (bc5ae03) will increase coverage by 7.31%.
The diff coverage is 90.00%.

@@            Coverage Diff             @@
##           latest    #2218      +/-   ##
==========================================
+ Coverage   84.76%   92.08%   +7.31%     
==========================================
  Files         131      100      -31     
  Lines       15619    11350    -4269     
  Branches     2236     2240       +4     
==========================================
- Hits        13240    10452    -2788     
+ Misses       2085      608    -1477     
+ Partials      294      290       -4     

Flag	Coverage Δ
python	92.08% <90.00%> (-0.03%)	⬇️
rust	?

Flags with carried forward coverage won't be shown. Click here to find out more.

Impacted Files	Coverage Δ
src/sourmash/cli/tax/annotate.py	100.00% <ø> (ø)
src/sourmash/cli/tax/grep.py	100.00% <ø> (ø)
src/sourmash/cli/tax/prepare.py	100.00% <ø> (ø)
src/sourmash/tax/__main__.py	92.63% <ø> (+2.32%)	⬆️
src/sourmash/tax/tax_utils.py	98.46% <83.33%> (+0.16%)	⬆️
src/sourmash/cli/tax/genome.py	90.90% <100.00%> (+0.58%)	⬆️
src/sourmash/cli/tax/metagenome.py	90.00% <100.00%> (+0.71%)	⬆️
src/sourmash/sbt_storage.py	85.76% <0.00%> (-3.39%)	⬇️
src/core/src/index/sbt/mhbt.rs
src/core/tests/test.rs
... and 31 more

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[ctb]

7a655cd implemented --force in taxonomy loading.

gotta add a few more tests and this will be fully baked.

[ctb]

This should be ready for review @bluegenes!

Note, I took it over from you so github won't care if you approve it, but that's ok, once you like it I'll merge it with admin superpower.

[bluegenes]

lgtm, thanks for taking over @ctb!

(gh won't let me approve, but ...I approve :)