add BiocStyle quarto engine

DESCRIPTION

@@ -18,12 +18,12 @@ Authors@R: c(
         )
 Imports: bookdown, knitr (>= 1.30), rmarkdown (>= 1.2), stats, utils, yaml,
     BiocManager
-Suggests: BiocGenerics, RUnit, htmltools
+Suggests: BiocGenerics, RUnit, htmltools, quarto
 biocViews: Software
 License: Artistic-2.0
 VignetteBuilder: knitr
+SystemRequirements: quarto
 Encoding: UTF-8
 URL: https://github.com/Bioconductor/BiocStyle
 BugReports: https://github.com/Bioconductor/BiocStyle/issues
-RoxygenNote: 6.1.0
-Date: 2025-08-01
+RoxygenNote: 7.3.2

R/utils-vignettes.R

@@ -0,0 +1,136 @@
+## BiocStyle vignette engine registration
+## Adapted from github.com/quarto-dev/quarto-r/blob/main/R/utils-vignettes.R
+register_vignette_engines <- function(pkg) {
+    vig_engine("html", quarto_format = "html")
+}
+
+vig_engine <- function(..., quarto_format) {
+    rmd_eng <- tools::vignetteEngine("rmarkdown", package = "knitr")
+    tools::vignetteEngine(
+        ...,
+        weave = vweave_quarto(quarto_format),
+        tangle = rmd_eng$tangle,
+        pattern = "[.]qmd$",
+        package = "BiocStyle",
+        aspell = rmd_eng$aspell
+    )
+}
+
+vweave_quarto <- function(format) {
+    meta <- get_meta(format)
+    function(file, driver, syntax, encoding, quiet = FALSE, ...) {
+        has_quarto_pkg <- nzchar(system.file(package = "quarto"))
+        has_quarto_bin <- has_quarto_pkg && !is.null(quarto::quarto_path())
+        # protect if Quarto is not installed
+        if (!has_quarto_bin) {
+            msg <- paste(
+                "Quarto is required to build Quarto vignettes but it is",
+                "not available. Install the 'quarto' R pacakge and the",
+                "Quarto binary and ensure it is on PATH."
+            )
+            if (is_R_CMD_check()) {
+                warning(msg, call. = FALSE)
+            } else {
+                stop(msg, call. = FALSE)
+            }
+            return(vweave_empty(file))
+        }
+
+        # Log debug information using the new configurable logging function
+        quarto:::quarto_log("R_LIBS: ", Sys.getenv("R_LIBS"))
+        quarto:::quarto_log(
+            ".libPaths(): ",
+            paste0(.libPaths(), collapse = ":")
+        )
+        quarto:::quarto_log(
+            "Packages: ",
+            paste0(dir(.libPaths()[1]), collapse = ",")
+        )
+
+        quarto::quarto_render(
+            file,
+            ...,
+            output_format = format,
+            metadata = meta
+        )
+    }
+}
+
+get_meta <- function(format) {
+    if (is.null(format)) {
+        return(NULL)
+    }
+    if (format == "html") {
+        return(get_meta_for_html())
+    }
+    if (format == "pdf") {
+        return(get_meta_for_pdf())
+    }
+}
+
+get_meta_for_pdf <- function() {
+    meta <- list()
+    meta$format$pdf <- list(
+        # don't try to install CTAN package on CRAN environment
+        `latex-auto-install` = !is_cran_check()
+    )
+    meta
+}
+
+get_meta_for_html <- function() {
+    css <- system.file(
+        "resources",
+        "html",
+        "biocstyle.css",
+        package = "BiocStyle"
+    )
+    scss <- system.file(
+        "resources",
+        "html",
+        "biocstyle.scss",
+        package = "BiocStyle"
+    )
+    meta <- list()
+    meta$format$html <-
+        list(
+            `embed-resources` = TRUE,
+            minimal = TRUE,
+            toc = TRUE,
+            `toc-float` = TRUE,
+            `toc-depth` = 3L,
+            `toc-location` = "left",
+            `number-sections` = TRUE,
+            theme = scss,
+            css = css
+        )
+    meta
+}
+
+is_R_CMD_check <- function() {
+    !is.na(Sys.getenv("_R_CHECK_PACKAGE_NAME_", NA)) ||
+        tolower(Sys.getenv("_R_CHECK_LICENSE_")) == "true"
+}
+
+# from knitr internal
+is_cran_check <- function() {
+    is_cran() && is_R_CMD_check()
+}
+
+is_cran <- function() {
+    !interactive() &&
+        !isTRUE(as.logical(Sys.getenv("NOT_CRAN", "false")))
+}
+
+# trick from knitr to avoid problem on R CMD check (e.g. when no Quarto
+# available) It will silently skip the vignette
+vweave_empty <- function(file, ..., .reason = "Quarto") {
+    out <- sprintf("%s.html", tools::file_path_sans_ext(basename(file)))
+    writeLines(
+        sprintf(
+            "The vignette could not be built because %s is not available.",
+            .reason
+        ),
+        out
+    )
+    out
+}

R/zzz.R

@@ -1,7 +1,8 @@
 resources <- bioconductor.sty <- bioconductor.css <- NULL
 
 # resolve paths once during package load
-.onLoad <- function(...) {
+.onLoad <- function(lib, pkg) {
+    register_vignette_engines(pkg)
     resources <<- system.file(package = "BiocStyle", "resources")
     bioconductor.sty <<- file.path(resources, "tex", "Bioconductor.sty")
     bioconductor.css <<- file.path(resources, "html", "bioconductor.css")