Merge branch 'main' into translate-citation

NEWS.md

@@ -1,7 +1,7 @@
 # pkgdown (development version)
 
+* Fix parsing of github profiles and issues into links when present at the beginning of list items (@pearsonca, #2122)
 * Correct parse usage for S3 methods with non-syntactic class names (#2384).
-
 * Deprecated `build_favicon()` was removed (`build_favicons()` remains).
 * Use [cli](https://github.com/r-lib/cli) to provide interactive feedback. 
 * Preserve Markdown code blocks with class rmd from roxygen2 docs (@salim-b, #2298).
@@ -12,6 +12,7 @@
 * Set RNG seed for htmlwidgets IDs. This reduces noise in pkgdown reference HTML output when examples generate htmlwidgets (@salim-b, #2294).
 * Fix BS5 navbar template to get `navbar.type: dark` to work with bslib 0.6+ / Bootstrap 5.3+ (@tanho63, #2388)
 * Translates citation sections (@eliocamp, #2410).
+* Topic names that conflict with selector functions can now be listed as references in `_pkgdown.yml` (@dmurdoch, #2397).
 
 # pkgdown 2.0.7
 

R/build-articles.R

@@ -371,7 +371,8 @@ data_articles_index <- function(pkg = ".") {
 
   if (length(missing) > 0) {
     cli::cli_abort(
-      "{length(missing)} vignette{?s} missing from index: {.file {missing}}.",
+      "{length(missing)} vignette{?s} missing from index in \\
+      {pkgdown_config_href({pkg$src_path})}: {.val {missing}}.",
       call = caller_env()
     )
   }

R/build-favicons.R

@@ -32,7 +32,7 @@ build_favicons <- function(pkg = ".", overwrite = FALSE) {
   if (has_favicons(pkg) && !overwrite) {
     cli::cli_inform(c(
       "Favicons already exist in {.path pkgdown}",
-      "i" = "Set {.var overwrite = TRUE} to re-create."
+      "i" = "Set {.code overwrite = TRUE} to re-create."
     ))
     return(invisible())
   }
@@ -78,10 +78,7 @@ build_favicons <- function(pkg = ".", overwrite = FALSE) {
   result <- content$favicon_generation_result
 
   if (!identical(result$result$status, "success")) {
-    cli::cli_abort(c(
-        "API request failed.",
-        "i" = "{.href [Please submit a bug report](https://github.com/r-lib/pkgdown/issues)}"
-    ))
+    cli::cli_abort("API request failed.", .internal = TRUE)
   }
 
   tmp <- tempfile()

R/build-reference-index.R

@@ -1,4 +1,4 @@
-data_reference_index <- function(pkg = ".") {
+data_reference_index <- function(pkg = ".", error_call = caller_env()) {
   pkg <- as_pkgdown(pkg)
 
   meta <- pkg$meta[["reference"]] %||% default_reference_index(pkg)
@@ -13,7 +13,7 @@ data_reference_index <- function(pkg = ".") {
 
   has_icons <- purrr::some(rows, ~ .x$row_has_icons %||% FALSE)
 
-  check_missing_topics(rows, pkg)
+  check_missing_topics(rows, pkg, error_call = error_call)
   rows <- Filter(function(x) !x$is_internal, rows)
 
   print_yaml(list(
@@ -125,19 +125,19 @@ default_reference_index <- function(pkg = ".") {
   ))
 }
 
-check_missing_topics <- function(rows, pkg) {
+check_missing_topics <- function(rows, pkg, error_call = caller_env()) {
   # Cross-reference complete list of topics vs. topics found in index page
   all_topics <- rows %>% purrr::map("names") %>% unlist(use.names = FALSE)
   in_index <- pkg$topics$name %in% all_topics
 
   missing <- !in_index & !pkg$topics$internal
 
   if (any(missing)) {
-    topics <- paste0(pkg$topics$name[missing], collapse = ", ")
-    abort(c(
+    cli::cli_abort(c(
       "All topics must be included in reference index",
-      `x` = paste0("Missing topics: ", topics),
-      i = "Either add to _pkgdown.yml or use @keywords internal"
-    ))
+      "x" = "Missing topics: {pkg$topics$name[missing]}",
+      i = "Either add to {pkgdown_config_href({pkg$src_path})} or use @keywords internal"
+    ),
+    call = error_call)
   }
 }

R/build-reference.R

@@ -189,7 +189,8 @@ build_reference <- function(pkg = ".",
     topics <- purrr::transpose(pkg$topics)
   }
 
-  purrr::map(topics,
+  purrr::map(
+    topics,
     build_reference_topic,
     pkg = pkg,
     lazy = lazy,
@@ -269,8 +270,7 @@ build_reference_topic <- function(topic,
                                   pkg,
                                   lazy = TRUE,
                                   examples_env = globalenv(),
-                                  run_dont_run = FALSE
-                                  ) {
+                                  run_dont_run = FALSE ) {
 
   in_path <- path(pkg$src_path, "man", topic$file_in)
   out_path <- path(pkg$dst_path, "reference", topic$file_out)
@@ -297,12 +297,14 @@ build_reference_topic <- function(topic,
   if (data$has_deps) {
     deps <- bs_theme_deps_suppress(deps)
     deps <- htmltools::resolveDependencies(deps)
-    deps <- purrr::map(deps,
+    deps <- purrr::map(
+      deps,
       htmltools::copyDependencyToDir,
       outputDir = file.path(pkg$dst_path, "reference", "libs"),
       mustWork = FALSE
     )
-    deps <- purrr::map(deps,
+    deps <- purrr::map(
+      deps,
       htmltools::makeDependencyRelative,
       basepath = file.path(pkg$dst_path, "reference"),
       mustWork = FALSE
@@ -326,6 +328,7 @@ data_reference_topic <- function(topic,
                                  pkg,
                                  examples_env = globalenv(),
                                  run_dont_run = FALSE) {
+
   local_context_eval(pkg$figures, pkg$src_path)
   withr::local_options(list(downlit.rdname = get_rdname(topic)))
 

R/build.R

@@ -408,32 +408,32 @@ build_site_external <- function(pkg = ".",
     timeout = getOption('pkgdown.timeout', Inf)
   )
 
-  cli::cli_rule(paste0("Finished building pkgdown site for package ", cli::col_blue(pkg$package)))
+  cli::cli_rule("Finished building pkgdown site for package {.pkg {pkg$package}}")
 
   preview_site(pkg, preview = preview)
   invisible()
 }
 
 build_site_local <- function(pkg = ".",
-                       examples = TRUE,
-                       run_dont_run = FALSE,
-                       seed = 1014,
-                       lazy = FALSE,
-                       override = list(),
-                       preview = NA,
-                       devel = TRUE
-                       ) {
+                             examples = TRUE,
+                             run_dont_run = FALSE,
+                             seed = 1014,
+                             lazy = FALSE,
+                             override = list(),
+                             preview = NA,
+                             devel = TRUE) {
 
   pkg <- section_init(pkg, depth = 0, override = override)
 
-  cli::cli_rule(paste0("Building pkgdown site for package ", cli::col_blue(pkg$package)))
+  cli::cli_rule("Building pkgdown site for package {.pkg {pkg$package}}")
   cli::cli_inform("Reading from: {src_path(path_abs(pkg$src_path))}")
   cli::cli_inform("Writing to:   {dst_path(path_abs(pkg$dst_path))}")
 
   init_site(pkg)
 
   build_home(pkg, override = override, preview = FALSE)
-  build_reference(pkg,
+  build_reference(
+    pkg,
     lazy = lazy,
     examples = examples,
     run_dont_run = run_dont_run,
@@ -453,6 +453,6 @@ build_site_local <- function(pkg = ".",
     build_search(pkg, override = override)
   }
 
-  cli::cli_rule(paste0("Finished building pkgdown site for package ", cli::col_blue(pkg$package)))
+  cli::cli_rule("Finished building pkgdown site for package {.pkg {pkg$package}}")
   preview_site(pkg, preview = preview)
 }

R/check.R

@@ -12,6 +12,7 @@ check_pkgdown <- function(pkg = ".") {
   data_articles_index(pkg)
   data_reference_index(pkg)
 
-  cli::cli_alert_success("No problems found in {.file {pkgdown_config_relpath(pkg)}}")
+  cli::cli_inform(c(
+    "v" = "No problems found in {pkgdown_config_href({pkg$src_path})}"
+  ))
 }
-

R/package.R

@@ -129,6 +129,12 @@ pkgdown_config_path <- function(path) {
     )
   )
 }
+pkgdown_config_href <- function(path) {
+  cli::style_hyperlink(
+    text = "_pkgdown.yml",
+    url = paste0("file://", pkgdown_config_path(path))
+  )
+}
 
 read_meta <- function(path) {
   path <- pkgdown_config_path(path)

R/rd-example.R

@@ -13,8 +13,7 @@ rd2ex <- function(x, ...) {
 run_examples <- function(x,
                          topic = "unknown",
                          env = globalenv(),
-                         run_dont_run = FALSE
-                         ) {
+                         run_dont_run = FALSE) {
 
   if (!inherits(x, "tag")) {
     x <- rd_text(x)

R/repo.R

@@ -38,12 +38,12 @@ repo_auto_link <- function(pkg, text) {
 
   if (!is.null(url$user)) {
     user_link <- paste0("\\1<a href='", url$user, "\\2'>@\\2</a>")
-    text <- gsub("(\\s|^|\\()@([-\\w]+)", user_link, text, perl = TRUE)
+    text <- gsub("(p>|\\s|^|\\()@([-\\w]+)", user_link, text, perl = TRUE)
   }
 
   if (!is.null(url$issue)) {
     issue_link <- paste0("<a href='", url$issue, "\\2'>#\\2</a>")
-    text <- gsub("(\\(|\\s)#(\\d+)", paste0("\\1", issue_link), text, perl = TRUE)
+    text <- gsub("(p>|\\(|\\s)#(\\d+)", paste0("\\1", issue_link), text, perl = TRUE)
 
     if (!is.null(pkg$repo$jira_projects)) {
       issue_link <- paste0("<a href='", url$issue, "\\1\\2'>\\1\\2</a>")

R/topics.R

@@ -61,10 +61,11 @@ all_sign <- function(x, text) {
 }
 
 match_env <- function(topics) {
-  out <- env(empty_env(),
+  fns <- env(empty_env(),
     "-" = function(x) -x,
     "c" = function(...) c(...)
   )
+  out <- env(fns)
 
   topic_index <- seq_along(topics$name)
 
@@ -99,36 +100,36 @@ match_env <- function(topics) {
   is_public <- function(internal) {
     if (!internal) !topics$internal else rep(TRUE, nrow(topics))
   }
-  out$starts_with <- function(x, internal = FALSE) {
+  fns$starts_with <- function(x, internal = FALSE) {
     any_alias(~ grepl(paste0("^", x), .), .internal = internal)
   }
-  out$ends_with <- function(x, internal = FALSE) {
+  fns$ends_with <- function(x, internal = FALSE) {
     any_alias(~ grepl(paste0(x, "$"), .), .internal = internal)
   }
-  out$matches <- function(x, internal = FALSE) {
+  fns$matches <- function(x, internal = FALSE) {
     any_alias(~ grepl(x, .), .internal = internal)
   }
-  out$contains <- function(x, internal = FALSE) {
+  fns$contains <- function(x, internal = FALSE) {
     any_alias(~ grepl(x, ., fixed = TRUE), .internal = internal)
   }
-  out$has_keyword <- function(x) {
+  fns$has_keyword <- function(x) {
     which(purrr::map_lgl(topics$keywords, ~ any(. %in% x)))
   }
-  out$has_concept <- function(x, internal = FALSE) {
+  fns$has_concept <- function(x, internal = FALSE) {
     match <- topics$concepts %>%
       purrr::map(~ str_trim(.) == x) %>%
       purrr::map_lgl(any)
 
     which(match & is_public(internal))
   }
-  out$lacks_concepts <- function(x, internal = FALSE) {
+  fns$lacks_concepts <- function(x, internal = FALSE) {
     nomatch <- topics$concepts %>%
       purrr::map(~ match(str_trim(.), x, nomatch = FALSE)) %>%
       purrr::map_lgl(~ length(.) == 0L | all(. == 0L))
 
     which(nomatch & is_public(internal))
   }
-  out$lacks_concept <- out$lacks_concepts
+  fns$lacks_concept <- fns$lacks_concepts
   out
 }
 

README.Rmd

@@ -69,7 +69,7 @@ Then learn about the many new ways to customise your site in `vignette("customis
 
 ## In the wild
 
-At last count, pkgdown is used [by over 8,000 packages](https://github.com/search?q=path%3A_pkgdown.yml+language%3AYAML&type=code&l=YAML). Here are a few examples created by contributors to pkgdown:
+At last count, pkgdown is used [by over 11,000 packages](https://github.com/search?q=path%3A_pkgdown.yml+language%3AYAML&type=code&l=YAML). Here are a few examples created by contributors to pkgdown:
 
 * [bayesplot](http://mc-stan.org/bayesplot/index.html)
   ([source](https://github.com/stan-dev/bayesplot/tree/gh-pages)):

README.md

@@ -82,7 +82,7 @@ Then learn about the many new ways to customise your site in
 
 ## In the wild
 
-At last count, pkgdown is used [by over 8,000
+At last count, pkgdown is used [by over 11,000
 packages](https://github.com/search?q=path%3A_pkgdown.yml+language%3AYAML&type=code&l=YAML).
 Here are a few examples created by contributors to pkgdown:
 

man/rmd-fragments/footer-configuration.Rmd

@@ -24,7 +24,7 @@ The example below puts the authors' information on the right along with a legal
 footer:
   structure: 
     left: pkgdown
-    right: [authors, legal]
+    right: [developed_by, legal]
   components:
     legal: Provided without **any warranty**.
 ```

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

@@ -50,9 +50,9 @@
     Code
       data_reference_index(pkg)
     Condition
-      Error in `check_missing_topics()`:
+      Error:
       ! All topics must be included in reference index
-      x Missing topics: c, e, ?
+      x Missing topics: c, e, and ?
       i Either add to _pkgdown.yml or use @keywords internal
 
 # errors well when a content entry is empty
@@ -157,3 +157,31 @@
       has_icons: no
       
 
+# can use a selector name as a topic name
+
+    Code
+      data_reference_index(pkg)
+    Output
+      pagetitle: Function reference
+      rows:
+      - title: bla
+        slug: bla
+        desc: ~
+        is_internal: no
+      - topics:
+        - path: matches.html
+          title: matches
+          aliases: matches()
+          icon: ~
+        - path: A.html
+          title: A
+          aliases: A()
+          icon: ~
+        names:
+        - matches
+        - A
+        row_has_icons: no
+        is_internal: no
+      has_icons: no
+      
+

tests/testthat/_snaps/check.md

@@ -3,7 +3,7 @@
     Code
       check_pkgdown(pkg)
     Condition
-      Error in `check_missing_topics()`:
+      Error in `check_pkgdown()`:
       ! All topics must be included in reference index
       x Missing topics: ?
       i Either add to _pkgdown.yml or use @keywords internal
@@ -14,10 +14,12 @@
       check_pkgdown(pkg)
     Condition
       Error in `check_pkgdown()`:
-      ! 2 vignettes missing from index: 'articles/nested' and 'width'.
+      ! 2 vignettes missing from index in _pkgdown.yml: "articles/nested" and "width".
 
 # informs if everything is ok
 
     Code
       check_pkgdown(pkg)
+    Message
+      v No problems found in _pkgdown.yml
 

tests/testthat/assets/reference-selector/DESCRIPTION

@@ -0,0 +1,6 @@
+Package: testpackage
+Version: 1.0.0
+Title: A test package
+Description: A test package
+Authors@R: person("Hadley Wickham")
+RoxygenNote: 7.3.1

tests/testthat/assets/reference-selector/NAMESPACE

@@ -0,0 +1,4 @@
+# Generated by roxygen2: do not edit by hand
+
+export(A)
+export(matches)