November 2023 spring cleaning about packagetemplate HOT 2 CLOSED

spring_clean <- function() {
  # internal helper function
  say <- function(x, crlf = FALSE) {
    eol <- ifelse(crlf, "\n\n", "\n")
    cat(paste0(x, eol))
  }

  # internal helper function
  files_with <- function(file_list, pattern, return_logicals = TRUE) {
    # index file_list with logical results of pattern search
    y <- unlist( # remove list returned by lapply below
      lapply(file_list, function(x) { # for each file in file_list
        x <- paste(readLines(x), collapse = " ") # get file contents
        grepl(pattern, x)
      })
    )
    if (return_logicals == FALSE) {
      y <- file_list[y]
    }
    y
  }



  package <- read.dcf("DESCRIPTION", "Package")
  yml <- yaml::read_yaml("_pkgdown.yml")
  webpage_url <- paste0("https://epiverse.github.io/", package)
  api_url <- paste0("https://api.github.com/repos/epiverse-trace/", package)

  # - [X] Verify that website URL is listed in `_pkgdown.yml`
  result <- yml$url == webpage_url
  result <- ifelse(result, "🟢", "❌")
  say(paste(result, "Website URL is listed in _pkgdown.yml"))
  # - [X] Verify pkgdown site is using epiversetheme
  result <- yml$template$package == "epiversetheme"
  result <- ifelse(result, "🟢", "❌")
  say(paste(result, "pkgdown site is using epiversetheme"))
  # - [ ] Add logo to `epiverse-trace/hex-stickers`
  # - [X] Use svg version of logo
  result <- file_test("-f", "man/figures/logo.svg")
  result <- ifelse(result, "🟢", "❌")
  say(paste(result, "svg version of logo used"))
  say(paste(result, "Logo properly detected by pkgdown & r-universe"))
  # - [ ] Verify logo is properly detected by pkgdown & r-universe
  #       (path and name need to be exactly
  #       `man/figures/logo.png` or `man/figures/logo.svg`)
  # - [X] Add a pkgdown reference index
  result <- !is.null(yml$reference)
  result <- ifelse(result, "🟢", "❌")
  say(paste(result, "Add a pkgdown reference index"))
  #       Use selectors (e.g., `starts_with()` or `contains()`) to select functions rather than an explicit list. This serves the double purpose of checking that functions follow a coherent naming scheme.
  # - [ ] Verify intro vignette appears under 'Get started'
  # - [ ] Verify vignettes are ordered correctly (if applicable)
  # - [X] Verify all images include helpful alt-text
  rmd_files <- list.files(pattern = "Rmd", recursive = TRUE)
  with_plot <- files_with(rmd_files, "plot\\(") # covers ggplot as well
  with_fig_alt <- files_with(rmd_files, "fig\\.alt")
  result <- rmd_files[xor(with_fig_alt, with_plot)]
  if (length(result) > 0) {
    say("❌ No alt-text in the following files")
    say(result)
    say("[Example: ```{r, fig.alt = 'Alt text here'}]")
  } else {
    say("🟢 All images include helpful alt-text")
  }





  ## Developer tools

  # - [ ] Update lintr, roxygen, usethis, testthat, devtools to latest version
  say("Updating lintr and devtools to the latest version")
  pak::pak(c("lintr", "devtools"), dependencies = TRUE)

  # - Copy from packagetemplate:
  say("Getting latest updates from packagetemplate")
  system("git clone https://github.com/epiverse-trace/packagetemplate")
  #   - [ ] [`.lintr`]
  say("Copying .lintr")
  system("mv -f packagetemplate/.lintr .")
  #   - [ ] [GitHub Actions worfklows]
  say("Copying Github Actions workflows")
  system("mv -f packagetemplate/.github/workflows/*.y* .github/workflows")
  #   - [ ] [`tools/`]
  say("Copying tools/ folder")
  system("rm -rf tools && mv packagetemplate/tools .")
  #   - [ ] [`tests/spelling.R`]
  say("Copying tests/spelling.R")
  system("mv -f packagetemplate/tests/spelling.R tests")
  #   - [ ] [`tests/testthat/helper-state.R`]
  #   - [ ] [`tests/testthat/setup-options.R`]
  say("Copying test/testthat/*.R")
  system("mv -f packagetemplate/tests/testthat/* tests/testthat/")
  system("rm -rf packagetemplate")
  # - [ ] Run `spelling::spell_check_package()`
  say("Spell checking package")
  spelling::spell_check_package()






  ## Misc good practice

  # - [ ] Change files ending in `.r` to `.R` in `R/` and/or `tests/testthat/`"
  say("Rename .r to
   .R ")
  system(
    'for file in $(find . -name "*.r"); do  mv "$file" "${file%.r}.R"; done'
  )

  # - [ ] Review usage of `# nolint` comments. New versions of lintr may have squashed previous bugs
  nolint_files <- list.files(pattern = "R$", recursive = TRUE) |>
    files_with("nolint", return_logicals = FALSE)
  if (nolint_files |> length() > 0) {
    say("❌ # nolint found in the following files")
    say(nolint_files)
    say("")
    say("New versions of lintr may have squashed previous bugs")
    say("Consider reviewing...")
  }

  # - [ ] Update year in license file
  year <- api_url |>
    readLines() |>
    jsonlite::fromJSON() |>
    (\(x) x$created_at)() |>
    substr(1, 4)
  readLines("LICENSE") |> # Update LICENSE
    paste(collapse = "\n") |>
    (\(x) gsub("YEAR:\\s*\\d{4}", paste("YEAR:", year), x))() |>
    writeLines(con = "LICENSE")
  say(paste("🟢 License file year updated to", year))






  ## Documentation

  # - [X] Use roxygen2 markdown syntax (`usethis::use_roxygen_md()`)
  say("Checking roxygen2 markdown syntax")
  urlchecker::use_roxygen_md()
  # - [ ] Add a related project section at the end of the `README`
  # - [X] Check that all URLs are working, up-to-date
  say("Checking URLs")
  urlchecker::url_check()
  # - [ ] Add package-level documentation page
  say("Checking package-level documentation page")
  urlchecker::use_package_doc()
  # - [ ] Move package-level imports to the package-level documentation
  # - [ ] Verify usage of all `@import` and `@importFrom` import functions
  # - [ ] Identify potential for [reuse in documentation]
  # - [X] Run `devtools::document()`
  say("Generating package documentation")
  devtools::document()






  ## `DESCRIPTION`

  # - [ ] Verify if any package in `Remotes` is still necessary
  # - [ ] Check that [package `Description`] is in line with the current scope
  # - [ ] Make sure links to GitHub repository and issue tracker are listed
  say("Checking GitHub links")
  usethis::use_github_links()
  # - [ ] Re-order and standardize `DESCRIPTION` with `desc::desc_normalize()`
  say("Standardize DESCRIPTION")
  desc::desc_normalize()
  # - [ ] Submit a PR adding yourself as author to packagetemplate



  ## Final `R CMD check`

  # - [ ] Run `devtools::check()` locally to catch `NOTE`s and `WARNING`s
  say("Running devtools::check()")
  devtools::check()

  ## GitHub

  # - [ ] Check if issues are still relevant. If not, please close them,
  #       ideally with a link to the commit fixing them or a comment
  #       explaining why they no longer apply.
  # - [ ] Check/close completed discussions you started
}