Support quarto vignettes

.Rbuildignore

@@ -20,3 +20,4 @@
 ^CRAN-SUBMISSION$
 ^tools$
 ^\.lintr.R$
+^vignettes/\.quarto$

.github/workflows/R-CMD-check.yaml

@@ -44,6 +44,13 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tinytex: true 
+
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}

.github/workflows/netlify.yaml

@@ -16,6 +16,13 @@ jobs:
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tinytex: true 
+
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true

.github/workflows/pkgdown.yaml

@@ -24,9 +24,14 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v2
+     - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tinytex: true 
 
-      - uses: r-lib/actions/setup-tinytex@v2
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:

DESCRIPTION

@@ -54,14 +54,16 @@ Suggests:
     magick,
     methods,
     pkgload (>= 1.0.2),
+    quarto,
     rsconnect,
     rstudioapi,
     rticles,
     sass,
     testthat (>= 3.1.3),
     tools
 VignetteBuilder:
-    knitr
+    knitr,
+    quarto
 Config/Needs/website: usethis, servr
 Config/potools/style: explicit
 Config/testthat/edition: 3

NEWS.md

@@ -1,5 +1,6 @@
 # pkgdown (development version)
 
+* `build_articles()` and `build_article()` now support articles/vignettes written with quarto. Combining the disparate quarto and pkgdown templating systems is a delicate art, so while I've done my best to make it work, there may be some rough edges. So please file an issue you encounter quarto features that don't work quite right. Learn more in `vignette("quarto")`(#2210).
 * `preview_page()` has been deprecated (#2650).
 * `build_article()` now translates the "Abstract" title if it's used.
 * `build_*()` (apart from `build_site()`) functions no longer default to previewing in interactive sessions since they now all emit specific links to newly generated files.

R/build-article.R

@@ -28,6 +28,7 @@ build_article <- function(name,
   input <- pkg$vignettes$file_in[vig]
   output_file <- pkg$vignettes$file_out[vig]
   depth <- pkg$vignettes$depth[vig]
+  type <- pkg$vignettes$type[vig]
 
   input_path <- path_abs(input, pkg$src_path)
   output_path <- path_abs(output_file, pkg$dst_path)
@@ -36,10 +37,39 @@ build_article <- function(name,
     return(invisible())
   }
 
-  cli::cli_inform("Reading {src_path(input)}")
+  if (type == "rmd") {
+    build_rmarkdown_article(
+      pkg = pkg,
+      input_file = input,
+      input_path = input_path,
+      output_file = output_file,
+      output_path = output_path,
+      depth = depth,
+      seed = seed,
+      new_process = new_process,
+      pandoc_args = pandoc_args,
+      quiet = quiet
+    )  
+  } else {
+    build_quarto_articles(pkg = pkg, article = name)
+  }
+}
+
+build_rmarkdown_article <- function(pkg,
+                                    input_file,
+                                    input_path,
+                                    output_file,
+                                    output_path,
+                                    depth,
+                                    seed = NULL,
+                                    new_process = TRUE,
+                                    pandoc_args = character(),
+                                    quiet = TRUE,
+                                    call = caller_env() ) {
+  cli::cli_inform("Reading {src_path(input_file)}")
   digest <- file_digest(output_path)
 
-  data <- data_article(pkg, input)
+  data <- data_article(pkg, input_file, call = call)
   if (data$as_is) {
     if (identical(data$ext, "html")) {
       setup <- rmarkdown_setup_custom(pkg, input_path, depth = depth, data = data)
@@ -68,7 +98,7 @@ build_article <- function(name,
   if (new_process) {
     path <- withCallingHandlers(
       callr::r_safe(rmarkdown_render_with_seed, args = args, show = !quiet),
-      error = function(cnd) wrap_rmarkdown_error(cnd, input)
+      error = function(cnd) wrap_rmarkdown_error(cnd, input_file, call)
     )
   } else {
     path <- inject(rmarkdown_render_with_seed(!!!args))
@@ -93,9 +123,9 @@ build_article <- function(name,
   }
 
   invisible(path)
-
 }
 
+
 data_article <- function(pkg, input, call = caller_env()) {
   yaml <- rmarkdown::yaml_front_matter(path_abs(input, pkg$src_path))
 

R/build-articles.R

@@ -212,13 +212,14 @@ build_articles <- function(pkg = ".",
 
   build_articles_index(pkg)
   unwrap_purrr_error(purrr::walk(
-    pkg$vignettes$name,
+    pkg$vignettes$name[pkg$vignettes$type == "rmd"],
     build_article,
     pkg = pkg,
     lazy = lazy,
     seed = seed,
     quiet = quiet
   ))
+  build_quarto_articles(pkg, quiet = quiet)
 
   preview_site(pkg, "articles", preview = preview)
 }

R/build-quarto-articles.R

@@ -0,0 +1,141 @@
+build_quarto_articles <- function(pkg = ".", article = NULL, quiet = TRUE) {
+  check_required("quarto")
+  pkg <- as_pkgdown(pkg)
+
+  qmds <- pkg$vignettes[pkg$vignettes$type == "qmd", ]
+  if (!is.null(article)) {
+    qmds <- qmds[qmds$name == article, ]
+  }
+  if (nrow(qmds) == 0) {
+    return()
+  }
+
+  for (file in qmds$file_in) {
+    cli::cli_inform("Reading {src_path(file)}")
+  }
+  cli::cli_inform("Running {.code quarto render}")
+
+  old_digest <- purrr::map_chr(path(pkg$dst_path, qmds$file_out), file_digest)
+
+  # Override default quarto format
+  metadata_path <- withr::local_tempfile(
+    fileext = ".yml",
+    pattern = "pkgdown-quarto-metadata-"
+  )
+  write_yaml(quarto_format(pkg), metadata_path)
+
+  # If needed, temporarily make a quarto project so we can build entire dir
+  if (is.null(article)) {
+    project_path <- path(pkg$src_path, "vignettes", "_quarto.yaml")
+    if (!file_exists(project_path)) {
+      yaml::write_yaml(list(project = list(render = list("*.qmd"))), project_path)
+      withr::defer(file_delete(project_path))
+    }
+  }
+
+  if (is.null(article)) {
+    src_path <- path(pkg$src_path, "vignettes")
+  } else {
+    src_path <- path(pkg$src_path, qmds$file_in)
+  }
+
+  output_dir <- withr::local_tempdir("pkgdown-quarto-")
+  quarto::quarto_render(
+    src_path,
+    metadata_file = metadata_path,
+    execute_dir = output_dir,
+    quarto_args = c("--output-dir", output_dir),
+    quiet = quiet,
+    as_job = FALSE
+  )
+
+  # Read generated data from quarto template and render into pkgdown template
+  purrr::walk2(qmds$file_in, qmds$file_out, function(input_file, output_file) {
+    built_path <- path(output_dir, path_rel(output_file, "articles"))
+    if (path_ext(output_file) == "html") {
+      data <- data_quarto_article(pkg, built_path, input_file)
+      render_page(pkg, "quarto", data, output_file, quiet = TRUE)
+
+      update_html(path(pkg$dst_path, output_file), tweak_quarto_html)
+    } else {
+      file_copy(built_path, path(pkg$dst_path, output_file), overwrite = TRUE)
+    }
+  })
+
+  # Report on which files have changed
+  new_digest <- purrr::map_chr(path(pkg$dst_path, qmds$file_out), file_digest)
+  changed <- new_digest != old_digest
+  for (file in qmds$file_out[changed]) {
+    writing_file(path(pkg$dst_path, file), file)
+  }
+
+  # Copy resources
+  resources <- setdiff(
+    dir_ls(output_dir, recurse = TRUE, type = "file"),
+    path(output_dir, path_rel(qmds$file_out, "articles"))
+  )
+  file_copy_to(
+    src_paths = resources,
+    dst_paths = path(pkg$dst_path, "articles", path_rel(resources, output_dir)),
+    src_root = output_dir,
+    dst_root = pkg$dst_path,
+    src_label = NULL
+  )
+
+  invisible()
+}
+
+quarto_format <- function(pkg) {
+  list(
+    lang = pkg$lang,
+    format = list(
+      html = list(
+        template = system_file("quarto", "template.html", package = "pkgdown"),
+        minimal = TRUE,
+        theme = "none",
+        `html-math-method` = config_math_rendering(pkg),
+        `embed-resources` = FALSE,
+        `citations-hover` = TRUE,
+        `link-citations` = TRUE,
+        toc = FALSE # pkgdown generates with js
+      )
+    )
+  )
+}
+
+data_quarto_article <- function(pkg, path, input_path) { 
+  html <- xml2::read_html(path, encoding = "UTF-8")
+  meta_div <- xml2::xml_find_first(html, "//body/div[@class='meta']")
+
+  # Manually drop any jquery deps
+  head <- xpath_xml(html, "//head/script|//head/link")
+  head <- head[!grepl("jquery", xml2::xml_attr(head, "src"))]
+
+  list(
+    pagetitle = escape_html(xpath_text(html, "//head/title")),
+    toc = TRUE, 
+    source = repo_source(pkg, input_path),
+    includes = list(
+      head = xml2str(head),
+      before = xpath_contents(html, "//body/div[@class='includes-before']"),
+      after = xpath_contents(html, "//body/div[@class='includes-after']"),
+      style = xpath_text(html, "//head/style")
+    ),
+    meta = list(
+      title = xpath_contents(meta_div, "./h1"),
+      subtitle = xpath_contents(meta_div, "./p[@class='subtitle']"),
+      author = xpath_contents(meta_div, "./p[@class='author']"),
+      date = xpath_contents(meta_div, "./p[@class='date']"),
+      abstract = xpath_contents(meta_div, "./div[@class='abstract']")
+    ),
+    body = xpath_contents(html, "//main")
+  )
+}
+
+tweak_quarto_html <- function(html) { 
+  # If top-level headings use h1, move everything down one level
+  h1 <- xml2::xml_find_all(html, "//h1")
+  if (length(h1) > 1) {
+    tweak_section_levels(html)
+  }
+}

R/package.R

@@ -319,11 +319,12 @@ package_vignettes <- function(path = ".") {
   vig_path <- vig_path[!grepl("^_", path_file(vig_path))]
   vig_path <- vig_path[!grepl("^tutorials", path_dir(vig_path))]
 
-  yaml <- purrr::map(path(base, vig_path), rmarkdown::yaml_front_matter)
-  title <- purrr::map_chr(yaml, list("title", 1), .default = "UNKNOWN TITLE")
-  desc <- purrr::map_chr(yaml, list("description", 1), .default = NA_character_)
-  ext <- purrr::map_chr(yaml, c("pkgdown", "extension"), .default = "html")
-  title[ext == "pdf"] <- paste0(title[ext == "pdf"], " (PDF)")
+  type <- tolower(path_ext(vig_path))
+
+  meta <- purrr::map(path(base, vig_path), article_metadata)
+  title <- purrr::map_chr(meta, "title")
+  desc <- purrr::map_chr(meta, "desc")
+  ext <- purrr::map_chr(meta, "ext")
 
   # Vignettes will be written to /articles/ with path relative to vignettes/
   # *except* for vignettes in vignettes/articles, which are moved up a level
@@ -336,6 +337,7 @@ package_vignettes <- function(path = ".") {
 
   out <- tibble::tibble(
     name = as.character(path_ext_remove(vig_path)),
+    type = type,
     file_in = as.character(file_in),
     file_out = as.character(file_out),
     title = title,
@@ -345,6 +347,32 @@ package_vignettes <- function(path = ".") {
   out[order(path_file(out$file_out)), ]
 }
 
+article_metadata <- function(path) {
+  if (path_ext(path) == "qmd") {
+    inspect <- quarto::quarto_inspect(path)
+    meta <- inspect$formats[[1]]$metadata
+
+    out <- list(
+      title = meta$title %||% "UNKNOWN TITLE",
+      desc = meta$description %||% NA_character_,
+      ext = path_ext(inspect$formats[[1]]$pandoc$`output-file`) %||% "html"
+    )  
+  } else {
+    yaml <- rmarkdown::yaml_front_matter(path)
+    out <- list(
+      title = yaml$title[[1]] %||% "UNKNOWN TITLE",
+      desc = yaml$description[[1]] %||% NA_character_,
+      ext = yaml$pkgdown$extension %||% "html"
+    )
+  }
+
+  if (out$ext == "pdf") {
+    out$title <- paste0(out$title, " (PDF)")
+  }
+
+  out
+}
+
 find_template_config <- function(package,
                                  bs_version = NULL,
                                  error_call = caller_env()) {

R/render.R

@@ -23,7 +23,7 @@ render_page <- function(pkg = ".", name, data, path, depth = NULL, quiet = FALSE
   pkg <- as_pkgdown(pkg)
 
   if (is.null(depth)) {
-    depth <- length(strsplit(path, "/")[[1]]) - 1L
+    depth <- dir_depth(path)
   }
 
   html <- render_page_html(pkg, name = name, data = data, depth = depth)
@@ -64,7 +64,7 @@ render_page_html <- function(pkg, name, data = list(), depth = 0L) {
   rendered <- render_template(template, components)
 
   # Strip trailing whitespace
-  rendered <- gsub("\\s+\n", "\n", rendered, perl = TRUE)
+  rendered <- gsub(" +\n", "\n", rendered, perl = TRUE)
 
   xml2::read_html(rendered, encoding = "UTF-8")
 }
@@ -234,9 +234,7 @@ write_if_different <- function(pkg, contents, path, quiet = FALSE, check = TRUE)
   full_path <- path_abs(path, start = pkg$dst_path)
 
   if (check && !made_by_pkgdown(full_path)) {
-    if (!quiet) {
-      cli::cli_inform("Skipping {.file {path}}: not generated by pkgdown")
-    }
+    cli::cli_inform("Skipping {.file {path}}: not generated by pkgdown")
     return(FALSE)
   }
 

R/tweak-tags.R

@@ -156,7 +156,7 @@ tweak_tables <- function(html) {
 
 # from https://github.com/rstudio/bookdown/blob/ed31991df3bb826b453f9f50fb43c66508822a2d/R/bs4_book.R#L307
 tweak_footnotes <- function(html) {
-  container <- xml2::xml_find_all(html, ".//div[contains(@class, 'footnotes')]")
+  container <- xml2::xml_find_all(html, ".//div[contains(@class, 'footnotes')]|.//section[contains(@class, 'footnotes')]")
   if (length(container) != 1) {
     return()
   }