In r-lib/usethis: Automate Package and Project Setup

Contributing to someone else's package

So, you want to contribute to an R package? That's fantastic!

Here we walk through the process of making a so-called pull request to the praise package. This package is designed to help package developers "build friendly R packages that praise their users if they have done something good, or they just need it to feel better." You can use praise to construct encouraging feedback by sampling from its collection of positive adjectives, adverbs, verbs, smileys, and exclamations:

library(praise)

template <- "${EXCLAMATION} - your pull request is ${adjective}!"

praise(template)
#> [1] "YEE-HAW - your pull request is groovy!"

We are going to propose a new adjective: "formidable".

What's a pull request?

A pull request is how you propose a change to a GitHub repository. Think of it as a request for the maintainer to pull your changes into their repo.

The pr_*() family of functions is designed to make working with GitHub pull requests as painless as possible, for both contributors and package maintainers. They are designed to support the Git and GitHub workflows recommended in Happy Git and GitHub for the useR.

A pull request (PR) involves two players, a contributor and a reviewer. To make it more clear who runs which code, the code chunks in this article are color coded: code executed by the contributor appears in chunks with light gray background and code executed by the reviewer appears in chunks with beige background.

# contributor code

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Set up advice

This article assumes that you have already done the Git and GitHub parts of the setup vignette and that you have configured a GitHub personal access token, as described in Managing Git(Hub) Credentials. A good way to check that you are ready to use the pr_* family of functions is to run git_sitrep(), which prints info about your current Git, gert, and GitHub setup.

Specifically, the pr_*() functions make use of:

The GitHub API, which requires a personal access token (PAT).
- create_github_token() helps you set one up.
Your preferred Git transport protocol: "https" or "ssh".
- If usethis can't figure this out, it might ask you. You can set the usethis.protocol option to proactively address this.
gert, an R package which does Git operations from R. The gert package, in turn, relies on the credentials package to obtain your Git credentials.
- If you use the "https" protocol, your GitHub PAT is the only credential you need. Which is a good reason to choose "https"!

Attach usethis

All the code below assumes you've attached usethis in your R session:

library(usethis)

Fork and clone

The first step is to fork the source repository, to get your own copy on GitHub, and then clone that, to get your own local copy. There are many ways to accomplish these two steps, but here we demonstrate usethis::create_from_github():

create_from_github("rladies/praise")

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What this does:

Forks the praise repo, owned by rladies on GitHub, into your GitHub account.
Clones your praise repo into a folder named "praise" on your desktop (or similar).
- origin remote is set to your praise repo.
Does additional Git setup:
- upstream remote is set to the praise repo owned by rladies.
- master branch is set to track upstream/master, so you can pull upstream changes in the future.
Opens a new instance of RStudio in the praise project, if you're working in RStudio. Otherwise, switches your current R session to that project.

Arguments you might like to know about:

Specify fork = TRUE or fork = FALSE if you don't want to defer to the default behaviour.
Use destdir to put praise in a specific location on your computer. You can set the usethis.destdir option if you always want usethis to put new projects in a specific directory.

Branch, then make your change

We start the process of contributing to the package with pr_init(), which creates a branch in our repository for the pull request. It is a good idea to make your pull requests from a feature branch, not from the repo's default branch, which is master here (another common choice is main). We'll call this branch "formidable".

pr_init(branch = "formidable")

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This creates a local branch called formidable and we switch to it (or "check it out"). Now you can work locally, making changes to files and committing them to Git.

Let's go ahead and make the change, which is adding the word "formidable" to the R/adjective.R file in the package. Below is the diff and the commit associated with this change.

#| fig-alt: Screenshot of the RStudio Git pane showing the file 
#|     R/adjective.R staged for a commit. The preview of the file
#|     highlights the addition of the line "formidabel", with no comma
#|     at the end of the line. The Commit message says 
#|     "Add 'formidable' to adjectives".
knitr::include_graphics("img/pr-functions-diff.png", dpi = 300)

You might spot that we made two mistakes here:

We intended to add "formidable", but added "formidabel" instead.
We forgot a comma at the end of the line.

Let's assume we didn't actually catch these mistakes, and didn't build and check the package, which would have revealed the missing comma. We all make mistakes.

Submit pull request

pr_push() pushes the local change to your copy of praise on GitHub and puts you in position to make your pull request.

pr_push()

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This launches a browser window at the URL specified in the last message, which looks like the following.

#| fig-alt: A screenshot showing the diff on GitHub, with the old 
#|     version of the file on the left, and the new version 
#|     containing the newly added line 'formidabel', with no comma, 
#|     on the right. There is a green button that says "Create Pull Request".
knitr::include_graphics("img/pr-functions-pull-request.png", dpi = 300)

Click "Create pull request" to make the PR. After clicking you will be able to choose between draft PR and actual PR (If opening a draft PR, mark it as ready for review once you're done, e.g. after a few more commits and one new call to pr_push()).

GitHub will ping the package maintainer and they will review our pull request. We can view this pull request in the browser with pr_view(). And anyone can follow along with this PR rladies/praise#90.

pr_view(90)

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Review of the pull request

If we're lucky, and our pull request is perfect, the maintainer will accept it, a.k.a. merge it. However, in this case, the PR still needs some work. So the package maintainer leaves us comments requesting changes.

#| fig-alt: A screenshot of the comments section on the pull request. 
#|     A comment from a collaborator on the new line says "Did 
#|     you mean to add 'formidable'? And can you please add a comma 
#|     at the end? Thanks!"
knitr::include_graphics("img/pr-functions-comments.png", dpi = 300)

Being somewhat new to all this, we try to address one of these comments (fix spelling) and neglect the other (forget to add the comma). We make another change and commit it.

#| fig-alt: A screenshot of the Rstudio Git pane, showing the changed line 
#|     with "formidabel" changed to "formidable". The file R/adjective.R
#|     is staged for a commit, with the commit message "Fix Spelling!"
knitr::include_graphics("img/pr-functions-address-comments.png", dpi = 300)

Run pr_push() again to update the branch in our fork, which is automatically reflected in the PR.

pr_push()

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Now the reviewer gets another chance to review our changes. At this point they might choose to just make the necessary changes and push their commits into our pull request to finish things up.

To do so, the reviewer fetches the PR to their local machine with pr_fetch().

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Fetching the PR creates a local branch for them called mine-cetinkaya-rundel-formidable, which is a text string comprised of the GitHub username of the contributor and the name of the branch they had created for this PR. pr_fetch() also then sets an upstream tracking branch for the local branch that got created and switches to that branch so the reviewer can make their changes on the correct branch.

Once the reviewer makes the necessary changes, such as adding the missing comma, they run pr_push() to push their changes into our PR.

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Merge and finish

Finally, the reviewer merges our pull request on GitHub. Locally, they can run pr_finish() to switch back to the default branch (usually named main or master), pull, delete the local branch created during the process of interacting with our PR, and remove the associated remote.

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Since the reviewer has contributed some code to our pull request, we can get that code back to our computer with pr_pull(). This is optional here, since the full PR has already been incorporated into the default branch of the source repo (usually named main or master). But pr_pull() can be useful in PRs if there are a few rounds of alternating contributions from you and the maintainer.

pr_pull()

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Finally, we can also conclude the PR process on our end with pr_finish().

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Remember you can see how this whole PR unfolded at rladies/praise#90.

Other helpful functions

There are a few other functions in the pr_*() family that we didn't encounter in this PR scenario:

pr_merge_main() is used for getting changes that have occurred in the main line of development while we have been working on this PR. If you're working in a fork, this does git pull upstream master. If you're making a PR from an internal branch, this does git pull origin master. This can be useful to execute in your PR branch, if there are big changes in the project and your PR has become un-mergeable. This is also useful to execute whenever you return to the default branch (usually named main or master) and, indeed, pr_pause() includes this. This makes sure that your copy of the package is up-to-date with the source repo.
pr_pause() makes sure you're synced with the PR, switches back to the default branch, and calls pr_merge_main() to keep you up-to-date with the source repo. This is likely something a package maintainer reviewing numerous PRs will need to use, as they switch back and forth between reviewing/extending PRs and the main line of development on the default branch.
pr_resume() helps you resume work on a PR after you've spent some time with another branch checked out. If you give it no arguments, it will present an interactive choice of local branches and indicates which, if any, are associated with a PR.