gwlilabmit/rendseq

Remove Command Line Interface

Closed this issue · 2 comments

miraep8 commented

Honestly, I think trying to support both might be confusing. I think having one well defined interface would be preferable! Then we can share scripts and jupyter notebooks that make use of the python interpreter!

julianstanley commented

Since it takes me an extra minute to open Jupyter, I appreciate the command line interface!

It also helps to be able to pipe wig output into rendseq

miraep8 commented

I am also open to keeping it. I guess my concerns are mostly:

  • I have talked to a couple people and having both seemed like a source of confusion. But this can be addressed by better documentation - ie a command line interface section and a notebook section.
    -I also worried a bit about maintence/making sure we keep both updated. (also for new contributors, I know Connie was a bit hesitant to make a command line interface). But we can have nice test cases (like the ones you wrote) which can catch if we do something that breaks the command line interfaces.
  • As they stand the command line interfaces only support partial functionality. But this concern can also be fixed by adding to them more!

So, sure - we can keep it! I guess I had originally written them as a convenience for myself, but if we want to keep it lets make it better! - ie document it/add more optional variables so that full functionality is supported. :) I think we already have an issue open to that effect (ie #4) but can add to that and make it a more general issue to address this.

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