MRG: add plugin support for new command-line subcommands

[ctb]

Add command-line plug-in interface, per #1353.

This PR builds on #2428 to provide support for adding new sourmash subcommands, under sourmash scripts <cmd>.

The CLI plugin interface looks like this on the client side -

class cmd_somewhat:
    command = 'somewhat'
    description = "does a thing"

    def __init__(self, subparser):
        super().__init__(p)
        # add arguments etc here 
        debug_literal('RUNNING cmd_somewhat.__init__')
        subparser.add_argument('foo', type=int)

    def main(self, args):
        super().main(args)
        # what we actually run. 
        print('RUNNING cmd', self, args)
        print('XYZ somewhat', args.foo)
        print(f'2*{args.foo} is {2*args.foo}')

Adding this plugin enables:

% sourmash scripts  -h          

== This is sourmash version 4.6.1. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

usage:  scripts [-h]

optional arguments:
  -h, --help  show this help message and exit

extension commands:
  sourmash scripts somewhat --help - do a thing

and

% sourmash scripts somewhat 5 

== This is sourmash version 4.6.1. ==
== Please cite Brown and Irber (2016), doi:10.21105/joss.00027. ==

...
2*5 is 10

which is prety cool 🎉

Alternatives to script

could be sourmash ext or sourmash plugin?

[codecov]

Codecov Report

Merging #2438 (0813a01) into latest (59f48c1) will increase coverage by 7.85%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           latest    #2438      +/-   ##
==========================================
+ Coverage   84.72%   92.58%   +7.85%     
==========================================
  Files         132      104      -28     
  Lines       14731    12026    -2705     
  Branches     2503     2513      +10     
==========================================
- Hits        12481    11134    -1347     
+ Misses       1948      590    -1358     
  Partials      302      302              

Flag	Coverage Δ
python	92.58% <100.00%> (+0.05%)	⬆️
rust	?

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

Impacted Files	Coverage Δ
src/sourmash/__main__.py	100.00% <100.00%> (ø)
src/sourmash/cli/__init__.py	95.78% <100.00%> (+0.04%)	⬆️
src/sourmash/cli/info.py	100.00% <100.00%> (ø)
src/sourmash/cli/scripts/__init__.py	100.00% <100.00%> (ø)
src/sourmash/plugins.py	100.00% <100.00%> (ø)
src/core/src/index/revindex.rs
src/core/src/sketch/minhash.rs
src/core/src/ffi/cmd/compute.rs
src/core/src/signature.rs
src/core/src/encodings.rs
... and 24 more

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[ctb]

Ready for review!

[bluegenes]

Notes to self/questions for review: is scripts the right subcommand to use here?

I think you mentioned sourmash ext as an option somewhere. I really like that -- it's short and gets across the idea that the plugin is an "extension" beyond standard sourmash. But scripts is also good - maybe alias?

[ctb]

Notes to self/questions for review: is scripts the right subcommand to use here?

I think you mentioned sourmash ext as an option somewhere. I really like that -- it's short and gets across the idea that the plugin is an "extension" beyond standard sourmash. But scripts is also good - maybe alias?

added as an alias in 0813a01.

I think we should probably switch to it as the default, but I'm going to punt that to the next PR that will do more documenting and testing!

[bluegenes]

Lgtm!