[EXP] add a prefetch linear search function to Index

[ctb]

NOTE: PR into #1370.

This PR adds:

• a --prefetch option (currently defaulting to True) to sourmash gather CLI
• a prefetch generator method on Index that does the linear search from [MRG] refactor gather functionality for speed & modularity; provide prefetch functionality. #1370/greyhound/etc.

See comment on #1370 for motivation.

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?

[ctb]

Fun fact!! When turning sourmash gather --prefetch on by default, almost all of the tests pass!

The two that don't pass are -

• test_gather_csv, because I don't properly track where the signature came from (ref Would a "Directory" Index be useful? #810 (comment))
• gather_query_downsample because, unlike in normal gather, I don't downsample the query appropriately with prefetch. This is actually questionable behavior to my thinking. I added a new test that checks for what I think is the right behavior, and left this one failing on this PR for now.

[ctb]

Legend has it that @luizirber will soon come place a comment on here about how prefetch(...) is Index.find with search_containment as the search function.

This appears to be accurate, with one exception: the find(...) function is currently not a generator, but prefetch is. I change find to a generator in 70168f1, and will refactor accordingly.

[luizirber]

Legend has it that @luizirber will soon come place a comment on here about how prefetch(...) is Index.find with search_containment as the search function.

This appears to be accurate, with one exception: the find(...) function is currently not a generator, but prefetch is. I change find to a generator in 70168f1, and will refactor accordingly.

I not sure they are the same same, but it sure feels like prefetch, Index.find, Index.filter and Index.select are very similar. Can we implement them in terms of each other in the base Index class? This way it is available for each implementation to override with a more efficient version, but we avoid having to implement all of them for each index implementation.

[ctb]

I not sure they are the same same, but it sure feels like prefetch, Index.find, Index.filter and Index.select are very similar. Can we implement them in terms of each other in the base Index class? This way it is available for each implementation to override with a more efficient version, but we avoid having to implement all of them for each index implementation.

absolutely agree (I assume you mean prefetch/find and filter/select).

[ctb]

merged into #1370.