[mat-2116] Rework CLI using Click, remove JSON requirements for use about beep HOT 8 CLOSED

please close if not useful or wrong place

from beep.

Totally agree, it would be nice to clean up the cli interface. Thanks for the suggestion!
The json format is a hold-over from our previous event based workflow so I think it's probably time to update them.
@moorepatrick Now that we are using Argo for workflow management would it be hard to change the commands for the container so that more cli compatible commands are used?

from beep.

@ardunn Click sounds like a pretty good option. We have used docopt in the past, but that tends to be a little clunky and click seems to have a simple interface that does not clutter up the code (or documentation).

from beep.

The workflows should not be impacted by this too much. They have actually mostly moved away from any lists in the input so having arguments instead would make things look a lot cleaner.

One thing to consider before we go too far down the path of a single CLI tool is how we plan to allow custom processing tasks.

from beep.

@moorepatrick are there clear custom processing cases where a single CLI tool would not work? It may help to enumerate some now so if we transfer over to Click we can write the code with those in mind.

from beep.

@ardunn We have not identified any specific use cases yet, but it probably deserves a full discussion.

from beep.

from #120

Problem

Not sure if this is an actual problem, since users of beep may just have one set of files they are working with, but when you are working with multiple input files, keeping track of what is going on with each file with the CLI + data-share directory is complicated...

Solution

Simply input and output files in the working directory according to whatever names the user wants (or sensible defaults in the cwd if no args passed), should be possible wth #107

from beep.

https://docs.google.com/document/d/17MdS8JfxcFBeJg6OjmWviCjqGsMs7uYXHP1KObNaCsA/edit?usp=sharing

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