Open RiesBen opened 1 month ago
Hello! Thank you for your review and comments! We will complete all of these that are feasible to completed. We started a issue checklist with all the reviewer comments, so we can address them and write our teams notes here #101. Feel free to review this checklist also.
@RiesBen Hello! I hope you are doing well. We are working to finish this, have made a lot of progress, and are getting close to completing it. I do have the following question (s):
For this comment "Documentation: Repository Doc strings - API Reference Docs missing? (can be generated with sphinx-apidoc)":
The user's main functions existed but are _not labeled as functions but data structures_ for the software, and they cover all the possible combinations of variables that the user can enter, checking them and providing very informative error outputs. The main functions are (i.e., data structures) .
I added all the _additional utilities_, which are not intended to be used for the direct application of this software. Is this what you were suggesting here or did you only want the main user function (i.e., data structures in the above)?
It would be much appreciated if you could clarify this so I can make sure it is what you are suggesting Can you or let me know if adding the additional utilities what you were thinking or simply keeping the _data structure_s (i.e., main functions)?
Thank you again for your time on your review and your comments that made this software package better!
Hi @bc118 , a right, this is the section I was searching for! cool, that you added the additional utilities! :) I think both in something like API reference or so would be the correct section, no? Why is it actually Datastructure? Isn't this more a code structure or API reference section?
Hi! Ah, yes. In the docs titles/labeling, we have tried to keep it consistent across the MoSDeF software family (mbuild, foyer, gmso, forcefield-utilities, and MoSDeF-GOMC, etc.) and Data structures was what we have been using for this section. I was not around for the original naming of the sections, but I suspect it means how they need to structure the input data and what to expect the output or attributes in the classes.
I also added a few other features (force to k0=0 for OPLS form or a constant) and a lot more examples.
JOSS Review: https://github.com/openjournals/joss-reviews/issues/6970
Hi I looked through you submission. In general the repository looks good to me! I installed the package and tested the unit tests. For the submission I have the following comments & suggestions:
sphinx-apidoc
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