Add subparser and conduct some basic refactors

bokulich-lab / mishmash

BSD 3-Clause "New" or "Revised" License

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Closed lina-kim closed 3 months ago

lina-kim commented 3 months ago

Closes #3 and #7.

Added subparser into CLI to logically separate the two commands get_metadata and get_accessions
Updated environment to resolve some security issues
Updated docs to reflect new function names.