In jabenninghoff/rdev: R Development Tools

Test script to manually validate creating a new rdev package or R analysis package.

Setup

Load devtools. Load package manually using devtools::load_all(".") (command-shift-l).

# devtools already loaded
htmltools::tagList(
  xaringanExtra::use_clipboard(
    button_text = "<i class=\"fa fa-clipboard fa-2xl\"></i>",
    success_text = "<i class=\"fa fa-check fa-2xl\" style=\"color: #90BE6D\"></i>"
  ),
  rmarkdown::html_dependency_font_awesome()
)

Create GitHub Repository

Given:

rdev and dependencies are installed in the R site library (using setup-r)
Running in a session with no project open

When:

Creating a new GitHub repository with the following command:

rdev::create_github_repo("rdtest1", "rdev test package 1")

Then:

[ ] A new rdev package named "rdtest1" is created in the active GitHub account, downloaded to the local system, and populated with package files using usethis options in ~/.Rprofile
[ ] On macOS, the repository is opened in GitHub Desktop
[ ] On macOS, the repository settings are opened on github.com
[ ] Branch protection applied to the default branch:
[ ] Require a pull request before merging
[ ] Require status checks to pass before merging
[ ] Require branches to be up to date before merging
[ ] Status checks that are required:
- [ ] lint, GitHub Actions
- [ ] macos-latest (release), GitHub Actions
- [ ] missing-deps, GitHub Actions
- [ ] windows-latest (release), GitHub Actions
[ ] Require linear history
[ ] Code security and analysis:
[ ] Dependabot alerts
[ ] Dependabot security updates
[ ] The git repository will contain a single commit, 'Initial commit', with:
[ ] LICENSE: GitHub MIT License, with active GitHub user's name and current year in Copyright
[ ] .gitignore: GitHub R.gitignore
[ ] There will be 4 new files:
[ ] .Rbuildignore
[ ] DESCRIPTION
[ ] NAMESPACE
[ ] rdtest1.Rproj

Regression

Regression tests:

[ ] Confirm that running rdev::create_github_repo("rdtest1") errors when the "rdtest1" directory exists in usethis:::conspicuous_place()

rdev::create_github_repo("rdtest1")

Initialize rdev package

Given:

Running in an interactive session at the rdtest1 project root
Commands in 'Create GitHub Repository' have been run

When:

Following ?quickstart, without committing to git, initialize the rdev package by running init() in the newly created project:

rdev::init()

When prompted, select "Yes" and "implicit mode":

Initialize rdev package (run after create_github_repo)? (yes/No/cancel) y

...

This project contains a DESCRIPTION file.
Which files should renv use for dependency discovery in this project? 

1: Use only the DESCRIPTION file. (explicit mode)
2: Use all files in this project. (implicit mode)

Selection: 2

Then:

[ ] The 4 new files (.Rbuildignore, DESCRIPTION, NAMESPACE, rdtest1.Rproj) will be committed to GitHub with the message rdev::create_github_repo()

There will be 22 new or changed files (new unless otherwise noted):

[ ] .github/.gitignore
[ ] .github/workflows/lint.yaml
[ ] .github/workflows/missing-deps.yaml
[ ] .github/workflows/R-CMD-check.yaml
[ ] .gitignore: changed, add 'macOS, vim' section
[ ] .lintr
[ ] .Rbuildignore: changed, sorted
[ ] .Rprofile
[ ] DESCRIPTION: changed
[ ] License: MIT
[ ] Suggests: desc, devtools, fs, knitr, pkgload, rdev (>= 1.9.1), rmarkdown, testthat (>= 3.0.0), usethis
[ ] URL: GitHub pages, GitHub repo
[ ] BugReports: GitHub issues
[ ] Remotes: jabenninghoff/rdev
[ ] Config/testthat/edition: 3
[ ] LICENSE.md
[ ] man/rdtest1-package.Rd
[ ] NEWS.md
[ ] R/package.R
[ ] README.md
[ ] README.Rmd
[ ] renv.lock
[ ] renv/.gitignore
[ ] renv/activate.R
[ ] renv/settings.json
[ ] tests/testthat.R
[ ] tests/testthat/test-package.R
[ ] TODO.md

On GitHub:

[ ] GitHub Pages, enabled:
[ ] Branch: default, folder: /docs
[ ] Website (homepage) set to GitHub Pages URL

Task:

Following ?quickstart, manually update the Title and Description fields in the DESCRIPTION file (without committing):

desc::desc_set(Title = "Rdev Test Package 1")
desc::desc_set(Description = "Used in manual testing of the rdev package.")

Regression

Regression tests:

[ ] Confirm that .git/hooks/pre-commit is owner-executable (must be executable to work) and matches the pre-commit template:

dir .git/hooks/pre-commit

-rwxr--r--  1 agamemnon  staff  409 Jan 30 15:58 .git/hooks/pre-commit

cat .git/hooks/pre-commit

#!/bin/bash
# forked from https://github.com/r-lib/usethis/blob/main/inst/templates/readme-rmd-pre-commit.sh
README=($(git diff --cached --name-only | grep -Ei '^README\.[R]?md$'))
MSG="use 'git commit --no-verify' to override this check"

if [[ ${#README[@]} == 0 ]]; then
  exit 0
fi

if [[ README.Rmd -nt README.md ]]; then
  echo -e "README.md is out of date; please re-knit README.Rmd\n$MSG"
  exit 1
fi

Setup rdev

Given:

Running in an interactive session at the rdtest1 project root
Commands in 'Create GitHub Repository' have been run
Commands in 'Initialize rdev package' have been run

When:

Following ?quickstart, without committing to git, running setup_rdev() to configure the package as an rdev package:

rdev::setup_rdev()

When prompted, answer "Yes" to all questions:

Set up rdev package (run after init)? (yes/No/cancel) y
...
Do you want to proceed? [Y/n]: y
...
Are you sure you want to update the wordlist?
1: Yes
2: No

Selection: 1
...
Do you want to proceed? [Y/n]: y
...
Do you want to proceed? [Y/n]: y

Additionally, ci() will run successfully, generating the following R CMD check note:

> checking package subdirectories ... NOTE
  Problems with news in ‘NEWS.md’:
  No news entries found.

Then:

If using RStudio, there will be 5 files open:

[ ] _pkgdown.yml
[ ] TODO.md
[ ] NEWS.md
[ ] README.Rmd
[ ] DESCRIPTION

The following commits will be added to git:

[ ] rdev::use_rdev_package(): 22 new files or changed files from 'Initialize rdev package'
[ ] rdev::use_rdev_pkgdown(): 6 new or changed files:
[ ] .Rbuildignore: changed, added ^_pkgdown\.yml$, ^docs$, ^pkgdown$, sorted
[ ] .gitignore: changed, added docs
[ ] DESCRIPTION: added pkgdown
[ ] _pkgdown.yml: new
[ ] man/rdtest1-package.Rd: updated title and description
[ ] pkgdown/extra.css: new
[ ] rdev::use_spelling(): 5 new or changed files:
[ ] DESCRIPTION: added spelling, withr, Language
[ ] inst/WORDLIST: new, with the following words in the list:
- [ ] CMD
- [ ] Changelog
- [ ] ORCID
- [ ] Rdev
- [ ] rdev
- [ ] rdtest
- [ ] renv
[ ] tests/spelling.R: new, from rdev template
[ ] tests/testthat/test-package.R: deleted
[ ] tests/testthat/test-spelling.R: new, from rdev template
[ ] rdev::use_codecov(): 6 new or changed files:
[ ] .Rbuildignore: added codecov.yml
[ ] .github/workflows/test-coverage.yaml: new, added from rdev workflows
[ ] DESCRIPTION: added covr, DT
[ ] README.Rmd: added 'Codecov test coverage' badge
[ ] codecov.yml: new
[ ] renv.lock: added covr, DT, dependencies

Task:

Revert the changes to test use_analysis_package():

[ ] Undo and discard rdev::use_codecov()
[ ] Undo and discard rdev::use_spelling()
[ ] Undo and discard rdev::use_rdev_pkgdown()
[ ] Undo rdev::use_rdev_package() (without discarding the 22 files)
[ ] Run renv::clean() to remove unused packages
[ ] Restart R Session

Regression

Regression tests:

[ ] Confirm that there are no uncommitted changes in git

Set up analysis package

Given:

Running in an interactive session at the rdtest1 project root
Commands in 'Create GitHub Repository' have been run
Commands in 'Initialize rdev package' have been run

When:

Following ?quickstart, without committing to git, running setup_analysis() to configure the package as an analysis package:

rdev::setup_analysis()

When prompted, answer "Yes" to all questions:

Set up analysis package (run after init)? (yes/No/cancel) y
...
Do you want to proceed? [Y/n]: y
...
Do you want to proceed? [Y/n]: y
...
Are you sure you want to update the wordlist?
1: Yes
2: No

Selection: 1

Additionally, ci() will run successfully, generating the following R CMD check note:

> checking package subdirectories ... NOTE
  Problems with news in ‘NEWS.md’:
  No news entries found.

Then:

If using RStudio, there will be 4 files open:

[ ] TODO.md
[ ] NEWS.md
[ ] README.Rmd
[ ] DESCRIPTION

The following commits will be added to git:

[ ] rdev::use_rdev_package(): 22 new files or changed files from 'Initialize rdev package'
[ ] rdev::use_analysis_package(): 10 new or changed files:
[ ] .Rbuildignore: added analysis package generated files, sorted
[ ] .gitignore: added # analysis package generated files section
[ ] .nojekyll: new, empty file
[ ] DESCRIPTION: added dplyr, purrr, quarto to Suggests
[ ] README.Rmd: changed, with Notebooks section
[ ] _quarto.yml: new
[ ] analysis/_metadata.yml: new
[ ] analysis/assets/extra.css: new
[ ] changelog.qmd: new
[ ] index.qmd: new
[ ] man/rdtest1-package.Rd: updated title and description
[ ] renv.lock: updated with dplyr and dependencies
[ ] rdev::use_spelling(): 5 new or changed files:
[ ] DESCRIPTION: added spelling, withr, Language
[ ] inst/WORDLIST: new, with the following words in the list:
- [ ] CMD
- [ ] Changelog
- [ ] ORCID
- [ ] Rdev
- [ ] rdev
- [ ] rdtest
- [ ] renv
[ ] tests/spelling.R: new, from rdev template
[ ] tests/testthat/test-package.R: deleted
[ ] tests/testthat/test-spelling.R: new, from rdev template

Regression

Regression tests:

[ ] Confirm that there are no uncommitted changes in git

Build Quarto Site

Test the installation by the Quarto builder, which should throw an error:

build_quarto_site()

#> Error in build_analysis_site() : no *.Rmd or *.qmd files in analysis directory

Create an analysis notebook in RStudio using File > New File > R Markdown... > From Template > Analysis Notebook, save in analysis as test.Rmd, removing all library commands in the setup block except library(dplyr), remove order: in the header, and re-run the checks, which should complete successfully: