[MRG] refactor & clean up database loading around MultiIndex class

[ctb]

This PR builds on #1374 to make database loading logic more generic. Specifically,

• move load_from_directory and load_from_file_list to MultiIndex class
• refactor sourmash_args._load_database accordingly

This results in substantial cleanup to sourmash_args, which is nice!

This is an intermediate step on the way to plugins, #1368 #1353.

This PR also:

• contains [MRG] expand signature selection and compatibility checking in database loading code #1420, which introduces expanded signature selection and compatibility checking for Index classes.
• fixes a bug in directory traversal that did not yield .sig.gz files appropriately
• removes LoadSingleSignature from sourmash categorize (refactor LoadSingleSignatures? #1077)
• refactors sourmash lca summarize/command_summarize.load_singletons_and_count to use MultiIndex.load_from_path(...) and MultiIndex.signatures_with_location(...) (Would a "Directory" Index be useful? #810)

notes

As currently written, there are some changes to exceptions that may not be acceptable for semantic versioning.

• load_file_as_index now raises ValueError instead of OSError. See test_api.py.
• load_signatures now raises ValueError instead of a general Exception for a parse error.

Fixes #1077
Fixes #810
Fixes #1376
Addresses #1072

TODO:

• docstrings!
• maybe further refactor out SIGLIST specific stuff? (punted to [MRG] expand signature selection and compatibility checking in database loading code #1420)
• consolidate compatibility checking etc. (punted to [MRG] expand signature selection and compatibility checking in database loading code #1420)
• test new MultiIndex load stuff directly (punted to Write additional unit/functional tests for MultiIndex #1408)
• improve debugging and exception reporting; maybe avoid overly broad try/except blocks 🙄 ...
• create a specific exception/exception hierarchy for collection loading functions? (punted to maybe create a new set of exceptions for collection loading functions #1417)
• add tests for LCA DB isfile code

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 #1406 (6d6eb42) into latest (ed3c809) will increase coverage by 5.23%.
The diff coverage is 94.11%.

@@            Coverage Diff             @@
##           latest    #1406      +/-   ##
==========================================
+ Coverage   89.27%   94.51%   +5.23%     
==========================================
  Files         123       96      -27     
  Lines       18790    15299    -3491     
  Branches     1447     1463      +16     
==========================================
- Hits        16775    14460    -2315     
+ Misses       1782      606    -1176     
  Partials      233      233              

Flag	Coverage Δ
python	94.51% <94.11%> (+0.02%)	⬆️
rust	?

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

Impacted Files	Coverage Δ
src/sourmash/logging.py	28.70% <28.57%> (-0.01%)	⬇️
src/sourmash/lca/lca_db.py	91.34% <66.66%> (-1.09%)	⬇️
src/sourmash/sbt.py	83.65% <75.00%> (-0.49%)	⬇️
src/sourmash/sourmash_args.py	95.95% <94.23%> (+3.02%)	⬆️
src/sourmash/index.py	90.76% <96.87%> (-2.85%)	⬇️
src/sourmash/commands.py	83.33% <100.00%> (+0.69%)	⬆️
src/sourmash/lca/command_summarize.py	80.95% <100.00%> (+0.15%)	⬆️
src/sourmash/signature.py	90.73% <100.00%> (+0.97%)	⬆️
tests/test_api.py	100.00% <100.00%> (ø)
tests/test_index.py	100.00% <100.00%> (ø)
... and 30 more

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[ctb]

Ready for review and merge @luizirber @bluegenes!

[ctb]

@bluegenes sorry I missed that you were reviewing this along with #1420 :). I resolved the issues you raised, let me know if there's more!

[ctb]

🎉