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neksa / mutagene

Python library and package for mutational analysis
https://www.ncbi.nlm.nih.gov/projects/mutagene/
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Pypi #6

Closed carolinecunningham closed 5 years ago

carolinecunningham commented 5 years ago

documentation for motif sub package started (in docs folder) & fixed parsers to be more clear (w/in cli folder)

neksa commented 5 years ago

I see there are a lot of commits with just "Update motif_doc.rst". You don't have to commit every time you change a file.

neksa commented 5 years ago

You have not applied changes from the pypi branch before creating a pull request, so there are conflicts.

neksa commented 5 years ago

I don't think we agreed that genome and input should be positional arguments

carolinecunningham commented 5 years ago

They aren't positional args in my most recent code (exact same as what you have).

I made them positional before we discussed them, and then I reverted them back to what you had originally, so maybe you are seeing my earlier changes?

On Thu, Jun 27, 2019 at 11:13 AM Alexander Goncearenco < notifications@github.com> wrote:

I don't think we agreed that genome and input should be positional arguments

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neksa commented 5 years ago

The output is in TSV format https://en.wikipedia.org/wiki/Tab-separated_values

neksa commented 5 years ago

I will not be able to react on every commit, it will just paralyze me. :) I will be going through pull request in the end of the week, reviewing one commit at a time carefully. I also suggest synchronizing with the branch before pull request and making as few commits as needed.

Also, we may need integration tests before changing the command line interface behavior. Every change in command line interface that affects behavior means that we will need to redo the tutorial and videos and bump a version number to make clear that it is not backwards compatible. Visual/text changes are fine.