jabenninghoff · jabenninghoff · Nov 25, 2023 · Nov 24, 2023 · Nov 24, 2023 · Nov 24, 2023
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: rdev
 Title: R Development Tools
-Version: 1.8.1
+Version: 1.8.2
 Authors@R:
     person("John", "Benninghoff", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-6230-4742"))

diff --git a/NAMESPACE b/NAMESPACE
@@ -33,6 +33,7 @@ export(use_codecov)
 export(use_lintr)
 export(use_package_r)
 export(use_rdev_package)
+export(use_rdev_pkgdown)
 export(use_rprofile)
 export(use_spelling)
 export(use_todo)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,9 @@
+# rdev 1.8.2
+
+* Added rendering fixes to `use_analysis_package()` (update: re-run `use_analysis_package()` and update notebooks from Analysis Notebook template)
+
+* Added function `use_rdev_pkgdown()`: add pkgdown with rdev customizations
+
 # rdev 1.8.1
 
 * Added support for [Visual Studio Code](https://code.visualstudio.com) to `setup-r`

diff --git a/R/setup.R b/R/setup.R
@@ -454,6 +454,10 @@ use_rdev_package <- function(quiet = TRUE) {
 #' When run, `use_analysis_package()`:
 #' 1. Creates analysis package directories
 #' 1. Adds exclusions to .gitignore and .Rbuildignore
+#' 1. Adds `extra.css` to `analysis/assets` and `pkgdown` (when `use_quarto` is `FALSE`) to fix
+#'    rendering of GitHub-style
+# nolint next: line_length_linter.
+#'    [task lists](https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/about-task-lists)
 #' 1. Adds `.nojekyll`, `_quarto.yml` and `index.qmd` from templates OR creates `_base.yml` in
 #'    `pkgdown` from the first `URL` in `DESCRIPTION`
 #' 1. Installs the `README.Rmd` template for analysis packages, and the `dplyr`
@@ -532,6 +536,8 @@ use_analysis_package <- function(use_quarto = TRUE, prompt = FALSE) {
   usethis::use_build_ignore(analysis_rbuildignore, escape = FALSE)
   sort_rbuildignore()
 
+  usethis::use_template("extra.css", save_as = "analysis/assets/extra.css", package = "rdev")
+
   urls <- desc::desc_get_urls()
   github_repo <- get_github_repo()
   if (use_quarto) {
@@ -548,8 +554,12 @@ use_analysis_package <- function(use_quarto = TRUE, prompt = FALSE) {
     usethis::use_template("index.qmd", package = "rdev", data = fields)
   } else {
     if (length(urls) >= 1 && !fs::file_exists("pkgdown/_base.yml")) {
-      yaml::write_yaml(list(url = urls[1], template = list(bootstrap = 5L)), "pkgdown/_base.yml")
+      yaml::write_yaml(
+        list(url = urls[1], template = list(bootstrap = 5L, bslib = list(preset = "bootstrap"))),
+        "pkgdown/_base.yml"
+      )
     }
+    usethis::use_template("extra.css", save_as = "pkgdown/extra.css", package = "rdev")
   }
 
   # always overwrite README.Rmd
@@ -581,3 +591,31 @@ use_analysis_package <- function(use_quarto = TRUE, prompt = FALSE) {
   )
   return(invisible(ret))
 }
+
+#' Use rdev pkgdown
+#'
+#' Add pkgdown with rdev customizations. Implemented as a wrapper for [usethis::use_pkgdown()].
+#'
+#' In addition to running [usethis::use_pkgdown()], `use_rdev_pkgdown` adds `extra.css` to
+#'   `pkgdown` to fix rendering of GitHub-style
+# nolint next: line_length_linter.
+#'   [task lists](https://docs.github.com/en/get-started/writing-on-github/working-with-advanced-formatting/about-task-lists),
+#'   and disables the [bslib::bs_theme()] `"shiny"` preset.
+#'
+#' @inheritParams usethis::use_pkgdown
+#'
+#' @export
+use_rdev_pkgdown <- function(config_file = "_pkgdown.yml", destdir = "docs") {
+  usethis::use_pkgdown(config_file = config_file, destdir = destdir)
+  fs::dir_create("pkgdown")
+  usethis::use_template("extra.css", save_as = "pkgdown/extra.css", package = "rdev")
+  pkg <- yaml::read_yaml(config_file)
+  pkg$template$bslib$preset <- "bootstrap"
+  # workaround for RStudio race condition
+  if (rlang::is_interactive()) {
+    writeLines(paste0("\nupdating ", config_file, "..."), sep = "")
+    Sys.sleep(1)
+    writeLines("done!")
+  }
+  yaml::write_yaml(pkg, config_file)
+}
diff --git a/README.md b/README.md
@@ -224,10 +224,10 @@ ci()
 #> * creating vignettes ... OK
 #> * checking for LF line-endings in source and make files and shell scripts
 #> * checking for empty or unneeded directories
-#> * building ‘rdev_1.8.1.tar.gz’
+#> * building ‘rdev_1.8.2.tar.gz’
 #> 
 #> ── R CMD check ─────────────────────────────────────────────────────────────────
-#> * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/RtmpK1M3iQ/filedb8a12319cdc/rdev.Rcheck’
+#> * using log directory ‘/private/var/folders/vn/cw5f9gws42v9m8mdsds_zbl00000gp/T/RtmpdCTAO3/file51204113e3f/rdev.Rcheck’
 #> * using R version 4.3.2 (2023-10-31)
 #> * using platform: aarch64-apple-darwin20 (64-bit)
 #> * R was compiled by
@@ -237,7 +237,7 @@ ci()
 #> * using session charset: UTF-8
 #> * using option ‘--no-manual’
 #> * checking for file ‘rdev/DESCRIPTION’ ... OK
-#> * this is package ‘rdev’ version ‘1.8.1’
+#> * this is package ‘rdev’ version ‘1.8.2’
 #> * package encoding: UTF-8
 #> * checking package namespace information ... OK
 #> * checking package dependencies ... OK
@@ -297,8 +297,8 @@ ci()
 #> * DONE
 #> 
 #> Status: OK
-#> ── R CMD check results ───────────────────────────────────────── rdev 1.8.1 ────
-#> Duration: 29.7s
+#> ── R CMD check results ───────────────────────────────────────── rdev 1.8.2 ────
+#> Duration: 32.4s
 #> 
 #> 0 errors ✔ | 0 warnings ✔ | 0 notes ✔
 ```
diff --git a/TODO.md b/TODO.md
@@ -2,56 +2,56 @@
 
 ## Content
 
-- [x] &nbsp;Add README.Rmd
-- [x] &nbsp;Update `DESCRIPTION` and use description data in `README.Rmd`
-- [x] &nbsp;Add ORCID
+- [x] Add README.Rmd
+- [x] Update `DESCRIPTION` and use description data in `README.Rmd`
+- [x] Add ORCID
 
 ## Package
 
-- [x] &nbsp;Write a utility function to sort `.Rbuildignore`
-- [x] &nbsp;Implement [pkgdown](https://pkgdown.r-lib.org)
-- [x] &nbsp;Add links / update [Rd formatting](https://roxygen2.r-lib.org/articles/rd-formatting.html) for all function documentation.
-- [x] &nbsp;Add dummy imports to silence R CMD check note per [tidyverse](https://github.com/tidyverse/tidyverse/blob/master/R/tidyverse.R)
-- [x] &nbsp;Migrate `build_analysis_site()` to rdev
-- [x] &nbsp;Switch from development version of `styler` (1.3.2.9000) when a new release becomes available
-- [x] &nbsp;~~Validate that `lint_all` works as expected within `ci`~~
-- [x] &nbsp;Add 'create package' workflow example to README, remove TODO section "Analysis package creation process"
-- [x] &nbsp;Move `_pkgdown.yml` to repository root to make projects discoverable by the [pgkdown](https://pkgdown.r-lib.org) GitHub [query](https://github.com/search?q=filename%3Apkgdown.yml+path%3A%2F&type=Code)
-- [x] &nbsp;Update `README.Rmd` template to dynamically generate list of notebooks in `analysis`
-- [x] &nbsp;Automate release process
-- [x] &nbsp;Automate creation of feature branches, including 'Bump version' using `desc::desc_bump_version("dev")`
-- [x] &nbsp;Add check to `stage_release()` to look for missing topics in `_pkgdown.yml` reference section
-- [x] &nbsp;Update `use_rdev_package()`
-- [x] &nbsp;Handle `.Rmd` files that already have an `html_document` section
-- [x] &nbsp;Move `rmd_metadata()` from README-analysis.Rmd to rdev package
-- [x] &nbsp;Add tests per comments in `R/` after reading package book, documentation
-- [x] &nbsp;Update Roxygen comments after reading package book, documentation, review and merge duplicate Roxygen docs
-- [x] &nbsp;Write a manual regression test script (notes with R commands) ~~as a vignette~~ to validate 'Creating Packages' ~~and 'GitHub Releases'~~
-- [x] &nbsp;Add messages, warnings to `build_analysis_site()` to report on progress
-- [x] &nbsp;Add function to spell check notebooks
-- [x] &nbsp;Automate branch protection
-- [x] &nbsp;Address issue <https://github.com/r-lib/usethis/issues/1568>, which has been closed
-- [x] &nbsp;Add dplyr when running `use_analysis_package()`
-- [x] &nbsp;~~Consider switching `getOption("pkgType")` from `source` to `both` per R [options](https://stat.ethz.ch/R-manual/R-devel/library/base/html/options.html)~~ per the [R macOS FAQ](https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#What-is-the-difference-between-the-CRAN-build-and-a-vanilla-build_003f), "Only the CRAN build is guaranteed to be compatible with the package binaries on CRAN (or Bioconductor)."
-- [x] &nbsp;Support creating repos in organizations
-- [x] &nbsp;~~Consider incorporating the GitHub description into `DESCRIPTION`~~
-- [x] &nbsp;Create a wrapper for `spelling` that includes notebooks in package spell checking, WORDLIST
-- [x] &nbsp;Add a `spell_check_test_notebooks()` function for CI spellchecks on notebooks
-- [x] &nbsp;Convert manual tests (`Setup.Rmd`) into an R Script that can be run from within the package created with `create_github_repo()`
-- [x] &nbsp;Add a function to add missing (notebook) dependencies to DESCRIPTION, see `renv::dependencies()` and `desc::desc_get_deps()`
-- [x] &nbsp;Add `check_renv()` to `ci()` and stop if `renv::status()` is not up to date
-- [x] &nbsp;Replace proof-docs with [urlchecker](https://urlchecker.r-lib.org), support checking GitHub Pages `docs` directory using `url_db_from_HTML_files` ~~(ask if a PR for this would be accepted)~~
-- [x] &nbsp;Move scripts from `tools` to `inst/bin` or similar, per [Stack Overflow](https://stackoverflow.com/questions/26104709/is-there-any-special-functionality-in-r-package-exec-or-tools-directories) and [R Packages](https://r-pkgs.org/inst.html#inst-other-langs)
-- [x] &nbsp;Switch from development versions of `styler` (1.3.2.9000) and `lintr` (2.0.1.9000) when a new release becomes available - both were needed to address bugs in the current release versions, 1.3.2 and 2.0.1.
-- [x] &nbsp;Add trailing slash to GitHub Pages URL
-- [x] &nbsp;Update `lint_all()` to lint all types, including `.Rpres`
-- [x] &nbsp;~~Add custom CSS files to [`_site.yml`](https://rmarkdown.rstudio.com/docs/reference/render_site.html) and analysis notebook templates to control font size, as described in this [article](https://medium.com/@HadrienD/how-to-customize-font-size-in-r-markdown-documents-f5adff36e2cc), or possibly using [`bs_theme()`](https://rstudio.github.io/bslib/articles/theming.html), since pkgdown customizes the default using [`build_bslib()`](https://github.com/r-lib/pkgdown/blob/main/R/theme.R)~~ (issue exists in unsupported Safari 14 but not Safari 15)
-- [ ] &nbsp;Follow up on `bslib` [breaking change](https://rstudio.github.io/bslib/news/index.html#bslib-060) defaulting to `preset="shiny"`
-- [ ] &nbsp;Investigate `&nbsp;` workaround for TODO lists
-- [ ] &nbsp;Replace `dev = TRUE` logic if <https://github.com/rstudio/renv/issues/1695> is accepted
-- [ ] &nbsp;Update errors and messages after reading Advanced R [Conditions](https://adv-r.hadley.nz/conditions.html) and re-reading the Tidyverse [Style Guide](https://style.tidyverse.org/index.html)
-- [ ] &nbsp;Establish default [knitr options](https://yihui.org/knitr/options/), including `knitr::opts_chunk$set(fig.align = "center"")`, add to analysis template, also review [settings](https://github.com/hadley/adv-r/blob/master/common.R) for *Advanced R*
-- [ ] &nbsp;Reduce the number of Imports, per R CMD check:
+- [x] Write a utility function to sort `.Rbuildignore`
+- [x] Implement [pkgdown](https://pkgdown.r-lib.org)
+- [x] Add links / update [Rd formatting](https://roxygen2.r-lib.org/articles/rd-formatting.html) for all function documentation.
+- [x] Add dummy imports to silence R CMD check note per [tidyverse](https://github.com/tidyverse/tidyverse/blob/master/R/tidyverse.R)
+- [x] Migrate `build_analysis_site()` to rdev
+- [x] Switch from development version of `styler` (1.3.2.9000) when a new release becomes available
+- [x] ~~Validate that `lint_all` works as expected within `ci`~~
+- [x] Add 'create package' workflow example to README, remove TODO section "Analysis package creation process"
+- [x] Move `_pkgdown.yml` to repository root to make projects discoverable by the [pgkdown](https://pkgdown.r-lib.org) GitHub [query](https://github.com/search?q=filename%3Apkgdown.yml+path%3A%2F&type=Code)
+- [x] Update `README.Rmd` template to dynamically generate list of notebooks in `analysis`
+- [x] Automate release process
+- [x] Automate creation of feature branches, including 'Bump version' using `desc::desc_bump_version("dev")`
+- [x] Add check to `stage_release()` to look for missing topics in `_pkgdown.yml` reference section
+- [x] Update `use_rdev_package()`
+- [x] Handle `.Rmd` files that already have an `html_document` section
+- [x] Move `rmd_metadata()` from README-analysis.Rmd to rdev package
+- [x] Add tests per comments in `R/` after reading package book, documentation
+- [x] Update Roxygen comments after reading package book, documentation, review and merge duplicate Roxygen docs
+- [x] Write a manual regression test script (notes with R commands) ~~as a vignette~~ to validate 'Creating Packages' ~~and 'GitHub Releases'~~
+- [x] Add messages, warnings to `build_analysis_site()` to report on progress
+- [x] Add function to spell check notebooks
+- [x] Automate branch protection
+- [x] Address issue <https://github.com/r-lib/usethis/issues/1568>, which has been closed
+- [x] Add dplyr when running `use_analysis_package()`
+- [x] ~~Consider switching `getOption("pkgType")` from `source` to `both` per R [options](https://stat.ethz.ch/R-manual/R-devel/library/base/html/options.html)~~ per the [R macOS FAQ](https://cran.r-project.org/bin/macosx/RMacOSX-FAQ.html#What-is-the-difference-between-the-CRAN-build-and-a-vanilla-build_003f), "Only the CRAN build is guaranteed to be compatible with the package binaries on CRAN (or Bioconductor)."
+- [x] Support creating repos in organizations
+- [x] ~~Consider incorporating the GitHub description into `DESCRIPTION`~~
+- [x] Create a wrapper for `spelling` that includes notebooks in package spell checking, WORDLIST
+- [x] Add a `spell_check_test_notebooks()` function for CI spellchecks on notebooks
+- [x] Convert manual tests (`Setup.Rmd`) into an R Script that can be run from within the package created with `create_github_repo()`
+- [x] Add a function to add missing (notebook) dependencies to DESCRIPTION, see `renv::dependencies()` and `desc::desc_get_deps()`
+- [x] Add `check_renv()` to `ci()` and stop if `renv::status()` is not up to date
+- [x] Replace proof-docs with [urlchecker](https://urlchecker.r-lib.org), support checking GitHub Pages `docs` directory using `url_db_from_HTML_files` ~~(ask if a PR for this would be accepted)~~
+- [x] Move scripts from `tools` to `inst/bin` or similar, per [Stack Overflow](https://stackoverflow.com/questions/26104709/is-there-any-special-functionality-in-r-package-exec-or-tools-directories) and [R Packages](https://r-pkgs.org/inst.html#inst-other-langs)
+- [x] Switch from development versions of `styler` (1.3.2.9000) and `lintr` (2.0.1.9000) when a new release becomes available - both were needed to address bugs in the current release versions, 1.3.2 and 2.0.1.
+- [x] Add trailing slash to GitHub Pages URL
+- [x] Update `lint_all()` to lint all types, including `.Rpres`
+- [x] ~~Add custom CSS files to [`_site.yml`](https://rmarkdown.rstudio.com/docs/reference/render_site.html) and analysis notebook templates to control font size, as described in this [article](https://medium.com/@HadrienD/how-to-customize-font-size-in-r-markdown-documents-f5adff36e2cc), or possibly using [`bs_theme()`](https://rstudio.github.io/bslib/articles/theming.html), since pkgdown customizes the default using [`build_bslib()`](https://github.com/r-lib/pkgdown/blob/main/R/theme.R)~~ (issue exists in unsupported Safari 14 but not Safari 15)
+- [ ] Remove `preset: bootstrap` if <https://github.com/r-lib/pkgdown/issues/2376> is accepted
+- [ ] Remove `pkgdown/extra.css` if <https://github.com/r-lib/pkgdown/issues/2377> is accepted
+- [ ] Replace `dev = TRUE` logic if <https://github.com/rstudio/renv/issues/1695> is accepted
+- [ ] Update errors and messages after reading Advanced R [Conditions](https://adv-r.hadley.nz/conditions.html) and re-reading the Tidyverse [Style Guide](https://style.tidyverse.org/index.html)
+- [ ] Establish default [knitr options](https://yihui.org/knitr/options/), including `knitr::opts_chunk$set(fig.align = "center"")`, add to analysis template, also review [settings](https://github.com/hadley/adv-r/blob/master/common.R) for *Advanced R*
+- [ ] Reduce the number of Imports, per R CMD check:
 
 ```
 > checking package dependencies ... NOTE
@@ -63,13 +63,13 @@
 
 ## GitHub
 
-- [x] &nbsp;Set up [GitHub Actions](https://usethis.r-lib.org/reference/github_actions.html)
-  - [x] &nbsp;Use [standard](https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml) `R CMD check`
-  - [x] &nbsp;Use [lintr](https://github.com/r-lib/actions/blob/master/examples/lint.yaml)
-- [x] &nbsp;Faster CI checks
-- [x] &nbsp;~~Switch to [full](https://github.com/r-lib/actions/blob/master/examples/check-full.yaml) `R CMD check` ?~~
-- [x] &nbsp;Update GitHub Actions from r-lib [examples](https://github.com/r-lib/actions/tree/master/examples)
-- [x] &nbsp;Run [test coverage](https://github.com/r-lib/actions/blob/master/examples/test-coverage.yaml)
-- [x] &nbsp;~~Skip CI checks for changes in only the `docs/` directory~~
-- [x] &nbsp;~~Add GitHub Action for html/link checking using something like [htmlproofer](https://github.com/gjtorikian/html-proofer)~~
-- [x] &nbsp;~~Autobuild `docs/` like [pkgdown](https://github.com/r-lib/actions/blob/master/examples/pkgdown.yaml) ?~~
+- [x] Set up [GitHub Actions](https://usethis.r-lib.org/reference/github_actions.html)
+  - [x] Use [standard](https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml) `R CMD check`
+  - [x] Use [lintr](https://github.com/r-lib/actions/blob/master/examples/lint.yaml)
+- [x] Faster CI checks
+- [x] ~~Switch to [full](https://github.com/r-lib/actions/blob/master/examples/check-full.yaml) `R CMD check` ?~~
+- [x] Update GitHub Actions from r-lib [examples](https://github.com/r-lib/actions/tree/master/examples)
+- [x] Run [test coverage](https://github.com/r-lib/actions/blob/master/examples/test-coverage.yaml)
+- [x] ~~Skip CI checks for changes in only the `docs/` directory~~
+- [x] ~~Add GitHub Action for html/link checking using something like [htmlproofer](https://github.com/gjtorikian/html-proofer)~~
+- [x] ~~Autobuild `docs/` like [pkgdown](https://github.com/r-lib/actions/blob/master/examples/pkgdown.yaml) ?~~
diff --git a/_pkgdown.yml b/_pkgdown.yml
@@ -38,6 +38,7 @@ reference:
     - use_lintr
     - use_package_r
     - use_rdev_package
+    - use_rdev_pkgdown
     - use_rprofile
     - use_spelling
     - use_todo