start outputting zip collections instead of .sig files?

[ctb]

from @bluegenes in #1349 (comment) -

• Future thoughts: Are you set on zipfile generation being external? If not --
• Zipped output from search or gather(when outputting matches/unmatched) could be useful?
• If sketching a bunch of sigs, could we write directly to a zip file? Not sure I would actually do this for non --singleton cases as it would eliminate parallelization, but just throwing it out there.

I think we could adjust or extend save_signatures(...) to create a .zip file when .zip is given as the output filename. Could do something similar with .sbt.zip, .lca.json, and other, perhaps?

see also #1349 (comment)

[ctb]

trying this out in #1370.

thoughts -

• could use a helper class to allow/enable progressive output of signatures where possible
• output to .gz by convention? or by default (e.g. in directories)?
• can we somehow make valid JSON with progressive output to a single file?
• support .zip output? can we make that progressive, too?

[ctb]

see b1d54df for creation of helper class, sourmash_args.SaveMatchingSignatures.

[ctb]

reference to explore streaming JSON output - https://medium.com/galvanize/streaming-structured-json-18da4edd4f20

maybe we should adjust JSON signature format to support a collection of individual records, rather than a list?

[ctb]

closed by #1493.