Standardize CLI

[talonchandler]

Fixes #56 and #65.

This PR standardizes and simplifies the CLI:

• add -h shortcut for --help everywhere
• add shortcuts everywhere (e.g. -i == --input)
• standardize as much as possible to the form

  mantis COMMAND `
  -i INPUT_PATH_LIST/*/*/* `
  -c CONFIG_PATH `
  -o OUTPUT_PATH

• unify docstrings, example calls, argument names
• document CLI example calls on the README
• add tests for all CLI calls

[ieivanov]

A related issue that may be fixed here - I am finding that mantis run-acquisition --help takes ~15 seconds to return. Is that normal? Are we importing any large libraries at the top of the CLI call stack?

[talonchandler]

mantis run-acquisition --help takes ~15 seconds to return

~I couldn't find a simple solution, so I'm going to open a new issue and show some profiling results.~

I take it back...I found that run_acquisition was the slowest. Moving the imports inside the function made mantis run-acquisition -h run in ~1.5 seconds compared to the earlier ~5 seconds on my machine.

The other CLI calls take ~1.5.

[ieivanov]

Thanks for your work on this @talonchandler! @edyoshikun or @ziw-liu can we get one more review before merging this?

I changed the signature of run_acquisition as we discussed above and updated the readme. Otherwise, mostly minor changes.

[edyoshikun]

what's the best way to merge these changes to #55? There were some parsing.py changes there that probably have conflicts with this PR.

[talonchandler]

Thanks for the improvements, @ieivanov.

@edyoshikun I'll merge this to main then into #55. I'll handle the merge conflicts.