[MRG] Add a MultiIndex class that wraps multiple Index classes.

[ctb]

This PR adds a MultiIndex class, which provides a wrapper for other Index classes. Each wrapped class should come with a paired location, which can be None; if set, the wrapper overrides the filename returned in search and gather with the paired location.

The PR also adds a filter method to LinearIndex and MultiIndex. This is a harbinger of selectors on scaled/num, #1072; I'm adding filter as an interim solution because I needed the functionality in sourmash_args and it made the code much cleaner.

Addresses several of the issues in DirectoryIndex issue, #810.

A side effect of switching to MultiIndex in various sourmash_args functions is that we can remove special-casing of SIGLIST in _load_databases and dependent functions. This further simplifies load_file_as_index and load_file_as_signatures. 👍

In particular, this approach provides source filename information for where matches are coming from; see this comment for detailed rationale. Could perhaps replace the SBT location attribute in #1373 with wrapping an SBT in one of these (which seems like a hack in the long term, but could work fine in the short term ;).

This wrapper approach may also provide a partial solution to lazy loading #1097, because it could support lazy loading of signatures by Index classes.

TODO:

• add a few tests that show that source filename in CSV output is correct 🎉

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 #1374 (d99828d) into latest (202bdc5) will increase coverage by 5.30%.
The diff coverage is 98.68%.

@@            Coverage Diff             @@
##           latest    #1374      +/-   ##
==========================================
+ Coverage   89.18%   94.49%   +5.30%     
==========================================
  Files         123       96      -27     
  Lines       18642    15176    -3466     
  Branches     1434     1447      +13     
==========================================
- Hits        16626    14340    -2286     
+ Misses       1780      603    -1177     
+ Partials      236      233       -3     

Flag	Coverage Δ
python	94.49% <98.68%> (+0.06%)	⬆️
rust	?

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

Impacted Files	Coverage Δ
src/sourmash/index.py	93.61% <94.91%> (+0.51%)	⬆️
src/sourmash/sourmash_args.py	92.93% <100.00%> (+0.49%)	⬆️
tests/test_index.py	100.00% <100.00%> (ø)
tests/test_sourmash.py	99.71% <100.00%> (+<0.01%)	⬆️
src/core/src/from.rs
src/core/src/encodings.rs
src/core/src/index/sbt/mod.rs
src/core/src/ffi/nodegraph.rs
src/core/src/sketch/nodegraph.rs
... and 22 more

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[ctb]

Ready for review @luizirber @bluegenes

[ctb]

OK, upgraded a bit after some ...excursions. Cleaner, better, more succinct.

[luizirber]

Anything else to add to this, @ctb? Otherwise, go for merging =]

[ctb]

thanks @luizirber - I'm doing some important downstream cleanup in #1406, and will fix any minor nits there.