Merge branch 'main' into katex-update

DESCRIPTION

@@ -11,7 +11,8 @@ Authors@R: c(
     person("Olivier", "Roy", role = "aut"),
     person("Salim", "Brüggemann", role = "aut",
            comment = c(ORCID = "0000-0002-5329-5987")),
-    person("Posit Software, PBC", role = c("cph", "fnd"))
+    person("Posit Software, PBC", role = c("cph", "fnd"),
+           comment = c(ROR = "03wc8by49"))
   )
 Description: Generate an attractive and useful website from a source
     package.  'pkgdown' converts your documentation, vignettes, 'README',
@@ -73,5 +74,5 @@ Config/testthat/parallel: true
 Config/testthat/start-first: build-article, build-quarto-article, build-reference
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.2.9000
 SystemRequirements: pandoc

NEWS.md

@@ -4,7 +4,7 @@
 * Articles (i.e., Rmarkdown/Quarto documents in `vignettes/articles`, created by `usethis::use_article()` and available on pkgdown sites but not included in a built package) have improved test cases (thanks to @venpopov and @ethanbass).
 * pkgdown now uses the same Sass variables as bslib to set the navbar background color: `$navbar-bg` for the background color in light and dark mode, or `$navbar-light-bg` and `$navbar-dark-bg` for individually controlling light and dark mode background colors. `pkgdown-navbar-bg` and `$pkgdown-navbar-bg-dark` both still provide pkgdown-specific overrides (@gadenbuie, #2847).
 * Code repositories hosted on Codeberg are now supported in the `BugReports` and `URL` fields (@nfrerebeau, #2843).
-* Articles (i.e., vignettes in `vignettes/articles`, created by `usethis::use_article()` and available on pkgdown sites but not included in a built package) have improved test cases (thanks to @venpopov and @ethanbass).
+* Articles (i.e., Rmd/qmd files in `vignettes/articles`, created by `usethis::use_article()` and available on pkgdown sites but not included in a built package) have improved test cases (thanks to @venpopov and @ethanbass).
 * New `clean_site(force = TRUE)` for cleaning of `docs/` regardless of whether it was built by pkgdown (#2827).
 * Links to favicons in page headers were updated to reflect changes to https://realfavicongenerator.net/ (#2804). Favicons should be re-generated by manually removing the `pkgdown/favicon` directory and then running `pkgdown::build_favicons()`.
 * Reinstate Rd macro loading, which was accidentally disabled in v2.1.1 (#2782).

R/build-home-authors.R

@@ -84,10 +84,10 @@ data_home_sidebar_authors <- function(pkg = ".", call = caller_env()) {
   )
   data <- data_authors(pkg, roles)
   authors <- purrr::map_chr(data$main, author_desc, comment = FALSE)
-  
+
   before <- config_pluck_markdown_inline(pkg, "authors.sidebar.before", call = call)
   after <- config_pluck_markdown_inline(pkg, "authors.sidebar.after", call = call)
-  
+
   bullets <- c(before, authors, after)
   if (data$needs_page) {
     bullets <- c(bullets, a(tr_("More about authors..."), "authors.html"))
@@ -136,11 +136,15 @@ author_list <- function(x, authors_info = NULL, comment = FALSE, pkg = ".") {
   orcid <- purrr::pluck(x$comment, "ORCID")
   x$comment <- remove_orcid(x$comment)
 
+  ror <- purrr::pluck(x$comment, "ROR")
+  x$comment <- remove_ror(x$comment)
+
   list(
     name = name,
     roles = roles,
     comment = linkify(x$comment),
-    orcid = orcid_link(orcid)
+    orcid = orcid_link(orcid),
+    ror = ror_link(ror)
   )
 }
 
@@ -151,6 +155,9 @@ author_desc <- function(x, comment = TRUE) {
     if (!is.null(x$orcid)) {
       x$orcid
     },
+    if (!is.null(x$ror)) {
+      x$ror
+    },
     if (comment && !is.null(x$comment) && length(x$comment) != 0) {
       paste0("<br/>\n<small>(", linkify(x$comment), ")</small>")
     }
@@ -168,6 +175,17 @@ orcid_link <- function(orcid) {
   )
 }
 
+ror_link <- function(ror) {
+  if (is.null(ror)) {
+    return(NULL)
+  }
+
+  paste0(
+    "<a href='https://ror.org/", ror, "'>",
+    "<img src='https://raw.githubusercontent.com/ror-community/ror-logos/main/ror-icon-rgb.svg' class='ror' alt='ROR'></a>"
+  )
+}
+
 # Derived from:
 # db <- utils:::MARC_relator_db
 # db <- db[db$usage != "",]
@@ -300,3 +318,10 @@ remove_orcid <- function(x) {
   }
   out
 }
+remove_ror <- function(x) {
+  out <- x[names2(x) != "ROR"]
+  if (all(names(out) == "")) {
+    names(out) <- NULL
+  }
+  out
+}

R/build-home.R

@@ -119,10 +119,11 @@
 #' See `?build_home` and `?build_site` for details about changing the location
 #' of the authors information within the home sidebar and the site footer.
 #'
-#' ## Authors ORCID and bio
+#' ## Authors ORCID, ROR and bio
 #'
 #' Author ORCID identification numbers in the `DESCRIPTION` are linked using
-#' the ORCID logo:
+#' the ORCID logo,
+#' author ROR identification numbers are linked using the ROR logo:
 #'
 #' ```r
 #' Authors@R: c(
@@ -131,7 +132,9 @@
 #'     ),
 #'     person("Jay", "Hesselberth", role = "aut",
 #'       comment = c(ORCID = "0000-0002-6299-179X")
-#'     )
+#'     ),
+#'    person("Posit Software, PBC", role = c("cph", "fnd"),
+#'           comment = c(ROR = "03wc8by49"))
 #'   )
 #' ```
 #'

R/repo.R

@@ -65,15 +65,15 @@ package_repo <- function(pkg) {
   # Use metadata if available
   repo <- config_pluck_list(pkg, "repo")
   url <- config_pluck_list(pkg, "repo.url")
-  
+
 
   if (!is.null(url)) {
     return(repo)
   }
 
   # Otherwise try and guess from `BugReports` (1st priority) and `URL`s (2nd priority)
   urls <- c(
-    sub("/issues/?", "/", pkg$desc$get_field("BugReports", default = character())),
+    sub("(/-)?/issues/?", "/", pkg$desc$get_field("BugReports", default = character())),
     pkg$desc$get_urls()
   )
 
@@ -101,11 +101,12 @@ repo_meta_gh_like <- function(link, branch = NULL) {
   gh <- parse_github_like_url(link)
   branch <- branch %||% gha_current_branch()
   blob <- if (grepl("^https?://codeberg\\.", link)) "/src/branch/" else "/blob/"
+  issues <- if (grepl("^https?://gitlab\\.", link)) "/-/issues/" else "/issues/"
 
   repo_meta(
     paste0(gh$host, "/", gh$owner, "/", gh$repo, "/"),
     paste0(gh$host, "/", gh$owner, "/", gh$repo, blob, branch, "/"),
-    paste0(gh$host, "/", gh$owner, "/", gh$repo, "/issues/"),
+    paste0(gh$host, "/", gh$owner, "/", gh$repo, issues),
     paste0(gh$host, "/")
   )
 }
@@ -116,13 +117,13 @@ gha_current_branch <- function() {
   if (ref != "") {
     return(ref)
   }
-  
+
   # Set everywhere but might not be a branch
   ref <- Sys.getenv("GITHUB_REF_NAME")
   if (ref != "") {
     return(ref)
   }
-  
+
   "HEAD"
 }
 

inst/BS5/assets/pkgdown.scss

@@ -51,7 +51,7 @@ $pkgdown-navbar-bg-dark: if($navbar-dark-bg, $navbar-dark-bg, null) !default;
 }
 
 // make both the active nav and the hovered nav more clear by mixing the
-// background colour with the body and primary colours respectively 
+// background colour with the body and primary colours respectively
 .nav-item .nav-link {
   @include border-radius($border-radius);
 }
@@ -312,6 +312,11 @@ dt:target + dd {
   color: #A6CE39;
   margin-right: 4px;
 }
+// ror badge
+.ror {
+  height: 16px;
+  margin-right: 4px;
+}
 // activate font awesome
 .fab {
   font-family: "Font Awesome 5 Brands" !important;
@@ -372,7 +377,7 @@ a[href='#main'] {
 }
 .lifecycle-stable       { background-color: rgb(16, 128, 1);  color: var(--bs-white);}
 .lifecycle-superseded   { background-color: rgb(7, 64, 128);  color: var(--bs-white);}
-.lifecycle-experimental, 
+.lifecycle-experimental,
 .lifecycle-deprecated   { background-color: rgb(253, 128, 8); color: var(--bs-black);}
 
 /* Footnotes ---------------------------------------------------------------- */
@@ -452,7 +457,7 @@ pre, pre code {
 // Default dark mode styling does not look good for code
 [data-bs-theme="dark"] {
   pre, code {
-    background-color: RGBA(var(--bs-body-color-rgb), 0.1); 
+    background-color: RGBA(var(--bs-body-color-rgb), 0.1);
   }
   // don't double apply transparency
   pre code {
@@ -594,7 +599,7 @@ span.smallcaps {font-variant: small-caps;}
 ul.task-list{list-style: none;}
 ul.task-list li input[type="checkbox"] {
   width: 0.8em;
-  margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ 
+  margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */
   vertical-align: middle;
 }
 

inst/BS5/templates/content-authors.html

@@ -10,7 +10,7 @@ <h1>{{{pagetitle}}}</h1>
     <ul class="list-unstyled">
       {{#authors}}
       <li>
-        <p><strong>{{{name}}}</strong>. {{{roles}}}. {{{orcid}}}
+        <p><strong>{{{name}}}</strong>. {{{roles}}}. {{{orcid}}}{{{ror}}}
         {{#comment}}<br /><small>{{{.}}}</small>{{/comment}}</p>
       </li>
       {{/authors}}

inst/BS5/templates/content-citation-authors.html

@@ -11,7 +11,7 @@ <h2>{{#translate}}{{authors}}{{/translate}}</h2>
       <ul class="list-unstyled">
         {{#authors}}
         <li>
-          <p><strong>{{{name}}}</strong>. {{{roles}}}. {{{orcid}}}
+          <p><strong>{{{name}}}</strong>. {{{roles}}}. {{{orcid}}}{{{ror}}}
           {{#comment}}<br /><small>{{{.}}}</small>{{/comment}}</p>
         </li>
         {{/authors}}

inst/BS5/templates/head.html

@@ -5,7 +5,7 @@
 
 {{#has_favicons}}
 <!-- favicons -->
-<link rel="icon" type="image/png" sizes="48x48" href="{{#site}}{{root}}{{/site}}favicon-48x48.png">
+<link rel="icon" type="image/png" sizes="96x96" href="{{#site}}{{root}}{{/site}}favicon-96x96.png">
 <link rel="icon" type=”image/svg+xml” href="{{#site}}{{root}}{{/site}}favicon.svg">
 <link rel="apple-touch-icon" sizes="180x180" href="{{#site}}{{root}}{{/site}}apple-touch-icon.png">
 <link rel="icon" sizes="any" href="{{#site}}{{root}}{{/site}}favicon.ico" >

tests/testthat/_snaps/build-article.md

@@ -27,22 +27,6 @@
 
     <span class="co">## <span style="color: #BB0000;">X</span></span>
 
-# build_article yields useful error if pandoc fails
-
-    Code
-      build_article("test", pkg, pandoc_args = "--fail-if-warnings")
-    Message
-      Reading vignettes/test.Rmd
-    Condition
-      Error in `build_article()`:
-      ! Failed to render 'vignettes/test.Rmd'.
-      x [WARNING] This document format requires a nonempty <title> element.
-      x  Defaulting to 'test.knit' as the title.
-      x  To specify a title, use 'title' in metadata or --metadata title="...".
-      x Failing because there were warnings.
-      Caused by error:
-      ! pandoc document conversion failed with error 3
-
 # build_article yields useful error if R fails
 
     Code

tests/testthat/_snaps/build-home-authors.md

@@ -44,7 +44,7 @@
       <ul class='list-unstyled'>
       <li>BEFORE</li>
       <li>Jo Doe <br />
-      <small class = 'roles'> Author, maintainer </small>  </li>
+      <small class = 'roles'> Author, maintainer </small>   </li>
       <li>AFTER</li>
       </ul>
       </div>

tests/testthat/_snaps/build-home-index.md

@@ -64,7 +64,7 @@
       <h2 data-toc-skip>Developers</h2>
       <ul class='list-unstyled'>
       <li>Jo Doe <br />
-      <small class = 'roles'> Author, maintainer </small>  </li>
+      <small class = 'roles'> Author, maintainer </small>   </li>
       </ul>
       </div>
       
@@ -80,8 +80,8 @@
     <div class="developers">
     <h2 data-toc-skip>Developers</h2>
     <ul class="list-unstyled">
-    <li>Hadley Wickham <br><small class="roles"> Author, maintainer </small>  </li>
-    <li>RStudio <br><small class="roles"> Copyright holder, funder </small>  </li>
+    <li>Hadley Wickham <br><small class="roles"> Author, maintainer </small>   </li>
+    <li>RStudio <br><small class="roles"> Copyright holder, funder </small>   </li>
     <li><a href="authors.html">More about authors...</a></li>
     </ul>
     </div>

tests/testthat/test-build-article.R

@@ -176,11 +176,16 @@ test_that("build_article yields useful error if pandoc fails", {
   skip_if_no_pandoc("2.18")
 
   pkg <- local_pkgdown_site()
-  pkg <- pkg_add_file(pkg, "vignettes/test.Rmd", "Hi")
+  pkg <- pkg_add_file(pkg, "vignettes/test.Rmd", c(
+    "Some text.",
+    "",
+    "[^1]: Unreferenced footnote.",
+    ""
+  ))
 
-  expect_snapshot(
+  expect_error(
     build_article("test", pkg, pandoc_args = "--fail-if-warnings"),
-    error = TRUE
+    "Note with key .+ defined at .+ but not used"
   )
 })
 

tests/testthat/test-build-home-authors.R

@@ -56,6 +56,27 @@ test_that("ORCID can be identified & removed from all comment styles", {
   )
 })
 
+test_that("ROR can be identified & removed from all comment styles", {
+  desc <- desc::desc(text = c(
+    'Authors@R: c(',
+    '    person("no comment"),',
+    '    person("bare comment", comment = "comment"),',
+    '    person("ror only",   comment = c(ROR = "1")),',
+    '    person("both",         comment = c("comment", ROR = "2"))',
+    '  )'
+  ))
+  authors <- purrr::map(desc$get_authors(), author_list, list())
+  expect_equal(
+    purrr::map(authors, "ror"),
+    list(NULL, NULL, ror_link("1"), ror_link("2"))
+  )
+
+  expect_equal(
+    purrr::map(authors, "comment"),
+    list(character(), "comment", character(), "comment")
+  )
+})
+
 test_that("author comments linkified with escaped angle brackets (#2127)", {
   p <- list(name = "Jane Doe", roles = "rev", comment = "<https://x.org/>")
   expect_match(