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JRaviLab / MolEvolvR

An R Package for characterizing proteins using molecular evolution and phylogeny
https://jravilab.github.io/MolEvolvR/
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Rename the listed function names in R/acc2lin.R #35

Closed Seyi007 closed 1 month ago

Seyi007 commented 1 month ago 
         [R/acc2lin.R](https://github.com/JRaviLab/MolEvolvR/blob/main/R/acc2lin.R)
Original Modified User Facing
sink.reset sinkReset
add_lins addLineage
acc2lin acc2Lineage
efetch_ipg efetchIPG
ipg2lin IPG2Lineage

Originally posted by @the-mayer in https://github.com/JRaviLab/MolEvolvR/issues/7#issuecomment-2394793279

All update should follow this format: Original Modified User Facing
original_function newFunction ✅

NOTE: Before beginning to work on a particular file, please check to see that @jananiravi has given the 👍 on the comment.

Please follow the contributing guidelines and create a new branch containing your changes. Commit your work, and submit a PR when ready for review.

Additionally, use the search in all files functionality in VS code, Rstudio, or any other text editor, and list all files the function is being called or used to be updated later.

awasyn commented 1 month ago

Can i work on this?

jananiravi commented 1 month ago

made minor changes. Yes, go for it, @awasyn!

awasyn commented 1 month ago

I would like to suggest that we deprecate the functions and display update message instead of simply renaming them. I am assuming that these are functions already in use by user. @jananiravi

jananiravi commented 1 month ago

This is a great suggestion in general, @awasyn! In this particular case, the repo is brand new and the only users are you (outreachy) and us! It's yet to go into widespread use. So for this instance, we plan to force-change the names and move on from there. In the future, once the package is in public use, depracation is the right way to go! cc: @the-mayer