Intro to Github

[sarahcrisley]

Nice, simple breakdown of Github applications and terminology--very helpful! I also think it's super cool how Github can be used to share code linked to manuscripts (now if we could only finagle a way to get whole manuscripts open access on there, too!).

A few questions:

• Any recommendations for how best to organize your repositories? File structure, naming protocols, etc.
• I'm interested in transitioning all my R files onto Github. How did that process look for you all? Did you migrate things over, or just choose to start using git for new projects?

[ajrominger]

Great questions Sarah! I know some of this got covered in class, but I also wanted to write out a few thoughts:

• for naming and organization, I follow a pretty strict protocol aimed at making any repo be able to become an R package (I do that because R packages have really useful structure for staying organized, even if you're not releasing your code as a package); the protocol is:
  • repo name is characters only (no '_' or '-' or numbers)
  • sub folders in repo are:
    • data (where read-only data live)
    • R (where R functions--but not R scripts live)
    • man (where help documents about the functions in R live)
    • inst (where intermediate data sets and scripts live, e.g., i wrote a script to read in data from the data folder and then I wrote out some manipulated version of those data for later analysis...all those files live in inst)
    • manuscript a folder for the manuscript, written as a .Rmd
  • naming conventions for files within those sub-folders is a little less strict, but I generally like to use '_' between words in file names, and I name files that hold functions after the function name (e.g. if there's a function named myFun it would live in a file named myFun.R
• my personal journey with switching over to github:
  • first off, awesome that you're looking to do that too!
  • i definitely did not start with moving the "back-log" of code into github, but rather (just like you suggest) i made the switch by starting new projects with github first
  • additionally, if I had an existing project not on github, but I needed to make the code available to go with a publication, that was great motivation to move that code to github
  • finally for the back-log of code: as time permited (which it usually didn't) a project I found very useful to my own learning about R, packages, and github was to convert some of my favorite pieces of R code into a personal package of "helper functions" that is mostly intended for my own use, but hypothetically I could share with others; that's here

[sarahcrisley]

Hey Andy!

So sorry for the delay--looks like I've been slacking on checking my personal email these days! Thank you for answering my questions with such a thoughtful, detailed response. This is super helpful insight and I'm excited to get my GitHub phase rolling. Thanks again!

Sarah

On Wed, Oct 5, 2022 at 2:25 PM Andy Rominger @.***> wrote:

Great questions Sarah! I know some of this got covered in class, but I also wanted to write out a few thoughts:

• for naming and organization, I follow a pretty strict protocol aimed at making any repo be able to become an R package (I do that because R packages have really useful structure for staying organized, even if you're not releasing your code as a package); the protocol is:
  • repo name is characters only (no '_' or '-' or numbers)
  • sub folders in repo are:
    • data (where read-only data live)
    • R (where R functions--but not R scripts live)
    • man (where help documents about the functions in R live)
    • inst (where intermediate data sets and scripts live, e.g., i wrote a script to read in data from the data folder and then I wrote out some manipulated version of those data for later analysis...all those files live in inst)
    • manuscript a folder for the manuscript, written as a .Rmd
  • naming conventions for files within those sub-folders is a little less strict, but I generally like to use '_' between words in file names, and I name files that hold functions after the function name (e.g. if there's a function named myFun it would live in a file named myFun.R
• my personal journey with switching over to github:
  • first off, awesome that you're looking to do that too!
  • i definitely did not start with moving the "back-log" of code into github, but rather (just like you suggest) i made the switch by starting new projects with github first
  • additionally, if I had an existing project not on github, but I needed to make the code available to go with a publication, that was great motivation to move that code to github
  • finally for the back-log of code: as time permited (which it usually didn't) a project I found very useful to my own learning about R, packages, and github was to convert some of my favorite pieces of R code into a personal package of "helper functions" that is mostly intended for my own use, but hypothetically I could share with others; that's here https://github.com/ajrominger/socorro

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