[MRG] add --include-db-pattern and --exclude-db-pattern to search/gather

[ctb]

This PR adds --include-db-pattern and --exclude-db-pattern to sourmash search, gather, prefetch, compare, sig cat, sig extract, and sig rename using the manifest column-filtering code introduced in #1864.

Fixes #1865

Misc thoughts:

• in general the loading and filtering code in commands.py is getting kinda ugly, seems like there might be some room for significant refactoring...

TODO:

• add to compare
• add to sig cat, sig extract, and sig rename
• tests for --picklist incompat
• refactor/cleanup/centralize code
• question: what happens when no manifests are available?

[codecov]

Codecov Report

Merging #1871 (2e3fbdd) into latest (dff5309) will increase coverage by 8.02%.
The diff coverage is 98.76%.

@@            Coverage Diff             @@
##           latest    #1871      +/-   ##
==========================================
+ Coverage   82.52%   90.55%   +8.02%     
==========================================
  Files         121       91      -30     
  Lines       13061     8903    -4158     
  Branches     1751     1756       +5     
==========================================
- Hits        10779     8062    -2717     
+ Misses       2016      578    -1438     
+ Partials      266      263       -3     

Flag	Coverage Δ
python	90.55% <98.76%> (+0.09%)	⬆️
rust	?

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

Impacted Files	Coverage Δ
src/sourmash/cli/sig/grep.py	100.00% <ø> (ø)
src/sourmash/commands.py	88.50% <83.33%> (+0.06%)	⬆️
src/sourmash/cli/compare.py	100.00% <100.00%> (ø)
src/sourmash/cli/gather.py	100.00% <100.00%> (ø)
src/sourmash/cli/prefetch.py	100.00% <100.00%> (ø)
src/sourmash/cli/search.py	100.00% <100.00%> (ø)
src/sourmash/cli/sig/cat.py	100.00% <100.00%> (ø)
src/sourmash/cli/sig/extract.py	100.00% <100.00%> (ø)
src/sourmash/cli/sig/rename.py	100.00% <100.00%> (ø)
src/sourmash/cli/utils.py	100.00% <100.00%> (ø)
... and 36 more

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[ctb]

I think this may be ready for review @bluegenes

[bluegenes]

wow, so clean and powerful 🎉

some minor comments and questions, otherwise lgtm!

[ctb]

will merge upon tests passing, after a quick re-review of the changes I just made :)