[WIP] fix tax argument parsing

[bluegenes]

Fixes #2213

• [x] add action= 'extend' to appropriate args
• [ ] add some tests to make sure args are passed in appropriately

[codecov[bot]]

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%)	:arrow_down:
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%)	:arrow_up:
src/sourmash/tax/tax_utils.py	98.46% <83.33%> (+0.16%)	:arrow_up:
src/sourmash/cli/tax/genome.py	90.90% <100.00%> (+0.58%)	:arrow_up:
src/sourmash/cli/tax/metagenome.py	90.00% <100.00%> (+0.71%)	:arrow_up:
src/sourmash/sbt_storage.py	85.76% <0.00%> (-3.39%)	:arrow_down:
src/core/src/index/sbt/mhbt.rs
src/core/tests/test.rs
... and 31 more

:mega: We’re building smart automated test selection to slash your CI/CD build times. Learn more

[ctb]

7a655cd8 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.