Upcoming commands

[mortonjt]

Since we are going to be doing a refactor of the CLI anyways, it maybe worthwhile to think about what commands to have.

Right now, we have

rhapsody mmvec --help

Which is ok if mmvec is the only command - however in the near future, we'll be adding in multiple additional commands, namely

seq2seq: to explicitly handle sequence count inputs and sequence count output (which is the default now). May want to add overdispersion later seq2spectra: to handle count inputs and continuous (lognormal) outputs

If we go this route, it also makes sense to ditch the wrapper name and call this whole package mmvec. So this would now look like

mmvec seq2seq --help
mmvec seq2spectra --help

[mortonjt]

It'll probably be better to call this

mmvec single-omic --help
mmvec paired-omic --help

Thoughts on this will also be appreciated