consider refactoring command-line interface code around plugin code

[ctb]

The CLI plugin system introduced in #2438 is (to my mind ;) pretty nice - maybe we could refactor the sourmash CLI code to look like this more generally?

class Command_XYZ(CommandLinePlugin):
    command = 'xyz'
    description = "does a thing"

    def __init__(self, subparser):
        super().__init__(subparser)
        # add argparse arguments here.
        debug_literal('RUNNING cmd_xyz.__init__')

    def main(self, args):
        # code that we actually run.
        super().main(args)
        print('RUNNING cmd', self, args)

[luizirber]

Can we expand the args in def main(self, args): to the actual args (sorta like https://github.com/sourmash-bio/sourmash/pull/245/files#diff-33c477dfa4d3640fd07b0474999840da51c478a0813345cef0518197f72d7525R21 ?)

It is still pretty hard to use the Python API interactively, it was painful to use #2433 in the browser... I think this can fit what I was trying in #245 in a more general way (where we can share CLI/API code more easily, and expose to plugins too)

[ctb]

I really like this idea!

But I'm not sure how to do it technically. main(self, args) takes the results of argparse.ArgumentParser.parse_args. Is the idea that we would do a click-style expansion of the args?

click example from genome-grist:

@click.command(context_settings={"ignore_unknown_options": True})
@click.argument("configfile")
@click.option("--no-use-conda", is_flag=True, default=False)
@click.option("--verbose", is_flag=True)
@click.option("--outdir", nargs=1)
@click.option("-h", "--help", nargs=0)
@click.argument("snakemake_args", nargs=-1)
def run(configfile, snakemake_args, no_use_conda, verbose, outdir, help):
    "execute genome-grist workflow (using snakemake underneath)"
    targets = [ arg for arg in snakemake_args if not arg.startswith('-') ]
...

I'm not sure how clean that would be, but I can try it out.

An alternative might be to add another method (execute? do? run?) to the class that would take the expanded arguments. But that seems like it would be uglier and require more manual work, be redundant, and cause errors. Hmm.

[ctb]

ref #1112