diff --git a/.air.toml b/.air.toml
new file mode 100644
index 0000000000..6e3adb0f8e
--- /dev/null
+++ b/.air.toml
@@ -0,0 +1,8 @@
+[format]
+line-width = 80
+indent-width = 2
+indent-style = "space"
+line-ending = "auto"
+persistent-line-breaks = true
+exclude = []
+default-exclude = true
\ No newline at end of file
diff --git a/.vscode/extensions.json b/.vscode/extensions.json
index 08e494f308..4888f46730 100644
--- a/.vscode/extensions.json
+++ b/.vscode/extensions.json
@@ -3,6 +3,7 @@
     "denoland.vscode-deno",
     "esbenp.prettier-vscode",
     "sumneko.lua",
-    "nvarner.typst-lsp"
+    "nvarner.typst-lsp",
+    "Posit.air-vscode"
   ]
 }
diff --git a/.vscode/settings.json b/.vscode/settings.json
index 985c5a0003..1802fcff71 100644
--- a/.vscode/settings.json
+++ b/.vscode/settings.json
@@ -3,8 +3,12 @@
     "editor.defaultFormatter": "denoland.vscode-deno"
   },
   "[r]": {
-    "editor.formatOnSave": false,
-    "editor.defaultFormatter": "REditorSupport.r"
+    "editor.formatOnSave": true,
+    "editor.defaultFormatter": "Posit.air-vscode"
+  },
+  "[quarto]": {
+    "editor.formatOnSave": true,
+    "editor.defaultFormatter": "quarto.quarto"
   },
   "[html]": {
     "editor.formatOnSave": false
@@ -16,5 +20,7 @@
   "deno.lint": true,
   "deno.unstable": true,
   "deno.importMap": "./src/import_map.json",
-  "deno.disablePaths": ["tests/integration/playwright/"]
+  "deno.disablePaths": ["tests/integration/playwright/"],
+  // opt-out lintr as we use air formatter
+  "r.lsp.diagnostics": false
 }
diff --git a/src/resources/capabilities/knitr.R b/src/resources/capabilities/knitr.R
index 89499aa533..3d82a8a910 100644
--- a/src/resources/capabilities/knitr.R
+++ b/src/resources/capabilities/knitr.R
@@ -23,4 +23,4 @@ if (requireNamespace("rmarkdown", quietly = TRUE)) {
   cat("null")
 }
 cat("\n")
-cat("--- YAML_END ---\n")
\ No newline at end of file
+cat("--- YAML_END ---\n")
diff --git a/src/resources/rmd/execute.R b/src/resources/rmd/execute.R
index 42c2f47946..51b61f8257 100644
--- a/src/resources/rmd/execute.R
+++ b/src/resources/rmd/execute.R
@@ -6,10 +6,21 @@
 # requiring backticks (because we'll use it in inline code that is itself wrapped in backticks)
 
 # execute rmarkdown::render
-execute <- function(input, format, tempDir, libDir, dependencies, cwd, params, resourceDir, handledLanguages, markdown) {
-
+execute <- function(
+  input,
+  format,
+  tempDir,
+  libDir,
+  dependencies,
+  cwd,
+  params,
+  resourceDir,
+  handledLanguages,
+  markdown
+) {
   # calculate knit_root_dir (before we setwd below)
-  knit_root_dir <- if (!is.null(cwd)) tools::file_path_as_absolute(cwd) else NULL
+  knit_root_dir <- if (!is.null(cwd)) tools::file_path_as_absolute(cwd) else
+    NULL
 
   # change to input dir and make input relative (matches
   # behavior/expectations of rmarkdown::render code)
@@ -19,7 +30,7 @@ execute <- function(input, format, tempDir, libDir, dependencies, cwd, params, r
 
   # rmd input filename
   rmd_input <- paste0(xfun::sans_ext(input), ".rmarkdown")
-      
+
   # swap out the input by reading then writing content.
   # This handles `\r\n` EOL on windows in `markdown` string
   # by spliting in lines
@@ -28,7 +39,7 @@ execute <- function(input, format, tempDir, libDir, dependencies, cwd, params, r
     rmd_input
   )
   input <- rmd_input
-      
+
   # remove the rmd input on exit
   rmd_input_path <- rmarkdown:::abs_path(rmd_input)
   on.exit(unlink(rmd_input_path), add = TRUE)
@@ -40,17 +51,17 @@ execute <- function(input, format, tempDir, libDir, dependencies, cwd, params, r
   #  if (!tolower(xfun::file_ext(input)) %in% c("r", "rmd", "rmarkdown")) {
   #    # rmd input filename
   #    rmd_input <- paste0(xfun::sans_ext(input), ".Rmd")
-  #    
+  #
   #    # swap out the input
   #    write(markdown, rmd_input)
   #    input <- rmd_input
-  #    
+  #
   #    # remove the rmd input on exit
   #    rmd_input_path <- rmarkdown:::abs_path(rmd_input)
   #    on.exit(unlink(rmd_input_path))
   #  }
   #}
-  
+
   # pass through ojs chunks
   knitr::knit_engines$set(ojs = function(options) {
     knitr:::one_string(c(
@@ -86,11 +97,13 @@ execute <- function(input, format, tempDir, libDir, dependencies, cwd, params, r
   # set some default DT options for dashboards (if not otherwise specified)
   if (is_dashboard_output(format)) {
     if (is.na(getOption("DT.options", NA))) {
-      options(DT.options = list(
-        bPaginate = FALSE, 
-        dom = "ifrt", 
-        language = list(info = "Showing _TOTAL_ entries")
-      ))
+      options(
+        DT.options = list(
+          bPaginate = FALSE,
+          dom = "ifrt",
+          language = list(info = "Showing _TOTAL_ entries")
+        )
+      )
     }
   }
 
@@ -109,7 +122,7 @@ execute <- function(input, format, tempDir, libDir, dependencies, cwd, params, r
       code <- readLines(file.path(resourceDir, "rmd", "ojs.R"))
       rmarkdown::shiny_prerendered_chunk("server-extras", code, TRUE)
     }
-    
+
     # This truly awful hack ensures that rmarkdown doesn't tell us we're
     # producing HTML widgets when targeting a non-html format (doing this
     # is triggered by the "prefer-html" options)
@@ -117,7 +130,7 @@ execute <- function(input, format, tempDir, libDir, dependencies, cwd, params, r
       render_env <- parent.env(parent.frame())
       render_env$front_matter$always_allow_html <- TRUE
     }
-    
+
     # return no new pandoc args
     NULL
   }
@@ -126,8 +139,8 @@ execute <- function(input, format, tempDir, libDir, dependencies, cwd, params, r
   df_print <- format$execute$`df-print`
   if (
     df_print == "paged" &&
-    !is_pandoc_html_format(format) &&
-    !is_html_prefered(format)
+      !is_pandoc_html_format(format) &&
+      !is_html_prefered(format)
   ) {
     df_print <- "kable"
   }
@@ -168,7 +181,11 @@ execute <- function(input, format, tempDir, libDir, dependencies, cwd, params, r
     } else if (inherits(v, "AsIs")) {
       v
     } else if (is.character(v)) {
-      gsub(pattern="(\\[|\\]|[`*_{}()>#+-.!])", x=v, replacement="\\\\\\1")
+      gsub(
+        pattern = "(\\[|\\]|[`*_{}()>#+-.!])",
+        x = v,
+        replacement = "\\\\\\1"
+      )
     } else {
       v
     }
@@ -182,7 +199,7 @@ execute <- function(input, format, tempDir, libDir, dependencies, cwd, params, r
     run_pandoc = FALSE,
     envir = env
   )
-  knit_meta <-  attr(render_output, "knit_meta")
+  knit_meta <- attr(render_output, "knit_meta")
   files_dir <- attr(render_output, "files_dir")
   intermediates_dir <- attr(render_output, "intermediates_dir")
 
@@ -191,35 +208,40 @@ execute <- function(input, format, tempDir, libDir, dependencies, cwd, params, r
   preserved <- extract_preserve_chunks(output_file, format)
 
   # include supporting files
-  supporting <- if (!is.null(intermediates_dir) && file_test("-d", intermediates_dir))
-    rmarkdown:::abs_path(intermediates_dir)
-  else
-    character()
+  supporting <- if (
+    !is.null(intermediates_dir) && file_test("-d", intermediates_dir)
+  )
+    rmarkdown:::abs_path(intermediates_dir) else character()
 
   # ammend knit_meta with paged table if df_print == "paged"
   if (df_print == "paged") {
-    knit_meta <- append(knit_meta, list(rmarkdown::html_dependency_pagedtable()))
+    knit_meta <- append(
+      knit_meta,
+      list(rmarkdown::html_dependency_pagedtable())
+    )
   }
 
-  # see if we are going to resolve knit_meta now or later 
+  # see if we are going to resolve knit_meta now or later
   if (dependencies) {
     engineDependencies <- NULL
     includes <- pandoc_includes(
-      input, 
+      input,
       format,
-      output_file, 
-      ifelse(!is.null(libDir), libDir, files_dir), 
-      knit_meta, 
+      output_file,
+      ifelse(!is.null(libDir), libDir, files_dir),
+      knit_meta,
       tempDir
     )
   } else {
     includes <- NULL
-    engineDependencies = list(knitr = I(list(jsonlite::serializeJSON(knit_meta))))
+    engineDependencies = list(
+      knitr = I(list(jsonlite::serializeJSON(knit_meta)))
+    )
   }
 
   # include postprocessing if required
   if (!is.null(preserved)) {
-    preserve <- split(unname(preserved),names(preserved))
+    preserve <- split(unname(preserved), names(preserved))
   } else {
     preserve <- NA
   }
@@ -232,7 +254,7 @@ execute <- function(input, format, tempDir, libDir, dependencies, cwd, params, r
   # results
   list(
     engine = "knitr",
-    markdown = paste(markdown, collapse="\n"),
+    markdown = paste(markdown, collapse = "\n"),
     supporting = I(supporting),
     filters = I("rmarkdown/pagebreak.lua"),
     includes = includes,
@@ -260,14 +282,12 @@ pandoc_options <- function(format) {
 
 # knitr options for format
 knitr_options <- function(format, resourceDir, handledLanguages) {
-
   # may need some knit hooks
   knit_hooks <- list()
 
   # opt_knit for compatibility w/ rmarkdown::render
   to <- format$pandoc$to
-  if (identical(to, "pdf"))
-    to <- "latex"
+  if (identical(to, "pdf")) to <- "latex"
   opts_knit <- list(
     quarto.version = 1,
     rmarkdown.pandoc.from = format$pandoc$from,
@@ -304,15 +324,13 @@ knitr_options <- function(format, resourceDir, handledLanguages) {
     opts_chunk$results <- "asis"
   }
 
-
   # add screenshot force if prefer-html specified
   if (is_html_prefered(format)) {
     opts_chunk$screenshot.force <- FALSE
   }
 
-
   # add fig.retina if requested
-  if (opts_chunk$dev == "retina"){
+  if (opts_chunk$dev == "retina") {
     opts_chunk$dev <- "png"
     opts_chunk$fig.retina = 2
   }
@@ -361,7 +379,7 @@ knitr_options_with_cache <- function(input, format, opts) {
       }
       cache <- TRUE
     }
- 
+
     # set the glocal cache option
     opts$opts_chunk$cache <- isTRUE(cache)
 
@@ -386,9 +404,15 @@ knitr_cache_dir <- function(input, format) {
 }
 
 # produce pandoc format (e.g. includes from knit_meta)
-pandoc_includes <- function(input, format, output, files_dir, knit_meta, tempDir) {
-
-  # get dependencies from render 
+pandoc_includes <- function(
+  input,
+  format,
+  output,
+  files_dir,
+  knit_meta,
+  tempDir
+) {
+  # get dependencies from render
   dependencies <- dependencies_from_render(input, files_dir, knit_meta, format)
 
   # embed shiny_prerendered dependencies
@@ -397,7 +421,8 @@ pandoc_includes <- function(input, format, output, files_dir, knit_meta, tempDir
       output,
       dependencies$shiny,
       files_dir,
-      dirname(input))
+      dirname(input)
+    )
   }
 
   # apply any required patches
@@ -409,7 +434,6 @@ pandoc_includes <- function(input, format, output, files_dir, knit_meta, tempDir
 
 # get dependencies implied by the result of render (e.g. html dependencies)
 dependencies_from_render <- function(input, files_dir, knit_meta, format) {
-
   # check for runtime
   front_matter <- rmarkdown::yaml_front_matter(input)
   runtime <- front_matter$runtime
@@ -431,7 +455,7 @@ dependencies_from_render <- function(input, files_dir, knit_meta, format) {
     resolver <- function(deps) {
       dependencies$shiny <<- list(
         deps = deps,
-        packages =  rmarkdown:::get_loaded_packages()
+        packages = rmarkdown:::get_loaded_packages()
       )
       list()
     }
@@ -450,17 +474,30 @@ dependencies_from_render <- function(input, files_dir, knit_meta, format) {
       list() # format deps
     )
 
-    
-    # We explicitly will inject dependencies for bslib (bootstrap and supporting 
-    # js / css) so we block those dependencies from making their way into the 
+    # We explicitly will inject dependencies for bslib (bootstrap and supporting
+    # js / css) so we block those dependencies from making their way into the
     # document
     filteredDependencies = c("bootstrap")
     if (is_dashboard_output(format)) {
-      bslibDepNames <- c("bootstrap", "bslib-webComponents-js", "bslib-tag-require", "bslib-card-js", "bslib-card-styles", "htmltools-fill", "bslib-value_box-styles", "bs3compat", "bslib-sidebar-js", "bslib-sidebar-styles", "bslib-page_fillable-styles", "bslib-page_navbar-styles", "bslib-component-js", "bslib-component-css")
+      bslibDepNames <- c(
+        "bootstrap",
+        "bslib-webComponents-js",
+        "bslib-tag-require",
+        "bslib-card-js",
+        "bslib-card-styles",
+        "htmltools-fill",
+        "bslib-value_box-styles",
+        "bs3compat",
+        "bslib-sidebar-js",
+        "bslib-sidebar-styles",
+        "bslib-page_fillable-styles",
+        "bslib-page_navbar-styles",
+        "bslib-component-js",
+        "bslib-component-css"
+      )
       append(filteredDependencies, bslibDepNames)
     }
-    
-    
+
     # filter out bootstrap
     extras$dependencies <- Filter(
       function(dependency) !(dependency$name %in% filteredDependencies),
@@ -475,24 +512,29 @@ dependencies_from_render <- function(input, files_dir, knit_meta, format) {
     # extract static ojs definitions for HTML only (not prefer-html)
     if (is_pandoc_html_format(format)) {
       ojs_defines <- rmarkdown:::flatten_dependencies(
-        knit_meta, function(dep) inherits(dep, "ojs-define")
+        knit_meta,
+        function(dep) inherits(dep, "ojs-define")
       )
       ojs_define_str <- knitr:::one_string(unlist(ojs_defines))
       if (ojs_define_str != "") {
-        dependencies$includes$in_header <- knitr:::one_string(c(dependencies$includes$in_header, ojs_define_str))
+        dependencies$includes$in_header <- knitr:::one_string(c(
+          dependencies$includes$in_header,
+          ojs_define_str
+        ))
       }
     }
   } else if (
     is_pandoc_latex_output(format) &&
-    rmarkdown:::has_latex_dependencies(knit_meta)
+      rmarkdown:::has_latex_dependencies(knit_meta)
   ) {
     latex_dependencies <- rmarkdown:::flatten_latex_dependencies(knit_meta)
-    dependencies$includes$in_header <- rmarkdown:::latex_dependencies_as_string(latex_dependencies)
+    dependencies$includes$in_header <- rmarkdown:::latex_dependencies_as_string(
+      latex_dependencies
+    )
   }
 
   # return dependencies
   dependencies
-
 }
 
 # return the html dependencies as an HTML string suitable for inclusion
@@ -501,19 +543,33 @@ html_dependencies_as_string <- function(dependencies, files_dir) {
   if (!rmarkdown:::dir_exists(files_dir)) {
     dir.create(files_dir, showWarnings = FALSE, recursive = TRUE)
   }
-  dependencies <- lapply(dependencies, htmltools::copyDependencyToDir, files_dir)
+  dependencies <- lapply(
+    dependencies,
+    htmltools::copyDependencyToDir,
+    files_dir
+  )
   dependencies <- lapply(dependencies, function(dependency) {
     dir <- dependency$src$file
     if (!is.null(dir)) {
-      dependency$src$file <- gsub("\\\\", "/", paste(files_dir, basename(dir), sep = "/"))
+      dependency$src$file <- gsub(
+        "\\\\",
+        "/",
+        paste(files_dir, basename(dir), sep = "/")
+      )
     }
     dependency
   })
-  return(htmltools::renderDependencies(dependencies, "file", encodeFunc = identity))
+  return(htmltools::renderDependencies(
+    dependencies,
+    "file",
+    encodeFunc = identity
+  ))
 }
 
 is_shiny_prerendered <- function(runtime, server = NULL) {
-  if (identical(runtime, "shinyrmd") || identical(runtime, "shiny_prerendered")) {
+  if (
+    identical(runtime, "shinyrmd") || identical(runtime, "shiny_prerendered")
+  ) {
     TRUE
   } else if (identical(server, "shiny")) {
     TRUE
@@ -537,7 +593,7 @@ create_pandoc_includes <- function(includes, tempDir) {
   write_includes("in_header", "include-in-header")
   write_includes("before_body", "include-before-body")
   write_includes("after_body", "include-after-body")
-  
+
   pandoc
 }
 
@@ -597,16 +653,14 @@ is_pandoc_markdown_output <- function(format) {
   is_pandoc_to_format(format, markdown_formats)
 }
 
-# should be equivalent of TS function: 
+# should be equivalent of TS function:
 # isHtmlCompatible() in src/config/format.ts
 is_html_prefered <- function(format) {
   # `prefer-html: true` can be set in markdown format that supports HTML outputs
-  (
-    is_pandoc_markdown_output(format) &&
-    isTRUE(format$render$`prefer-html`)
-  ) ||
-  # this could happen when using embed shortcode which convert to ipynb output format.
-  is_pandoc_ipynb_output(format)
+  (is_pandoc_markdown_output(format) &&
+    isTRUE(format$render$`prefer-html`)) ||
+    # this could happen when using embed shortcode which convert to ipynb output format.
+    is_pandoc_ipynb_output(format)
 }
 
 is_dashboard_output <- function(format) {
@@ -622,7 +676,6 @@ apply_patches <- function(format, includes) {
 
 # patch to ensure that htmlwidgets size correctly when slide changes
 apply_slides_patch <- function(includes) {
-
   slides_js <- '
 <script>
   // htmlwidgets need to know to resize themselves when slides are shown/hidden.
@@ -668,26 +721,32 @@ apply_slides_patch <- function(includes) {
 
 apply_responsive_patch <- function(format) {
   if (isTRUE(format$metadata[["fig-responsive"]])) {
-
     # tweak sizing for htmlwidget figures (use 100% to be responsive)
     if (requireNamespace("htmlwidgets", quietly = TRUE)) {
-      htmlwidgets_resolveSizing <- htmlwidgets:::resolveSizing 
+      htmlwidgets_resolveSizing <- htmlwidgets:::resolveSizing
       resolveSizing <- function(x, sp, standalone, knitrOptions = NULL) {
-          # default sizing resolution
-          sizing <- htmlwidgets_resolveSizing(x, sp, standalone, knitrOptions)
-            
-          # if this is a knitr figure then set width to 100% and height
-          # to an appropriately proportioned value based on the assumption
-          # that the display width will be ~650px
-          if (isTRUE(sp$knitr$figure) && is.numeric(sizing$height) && is.numeric(sizing$width)) {
-            sizing$height <- paste0(as.integer(sizing$height / sizing$width * 650), "px")
-            sizing$width <- "100%"
-          }
-          
-          # return sizing
-          sizing
+        # default sizing resolution
+        sizing <- htmlwidgets_resolveSizing(x, sp, standalone, knitrOptions)
+
+        # if this is a knitr figure then set width to 100% and height
+        # to an appropriately proportioned value based on the assumption
+        # that the display width will be ~650px
+        if (
+          isTRUE(sp$knitr$figure) &&
+            is.numeric(sizing$height) &&
+            is.numeric(sizing$width)
+        ) {
+          sizing$height <- paste0(
+            as.integer(sizing$height / sizing$width * 650),
+            "px"
+          )
+          sizing$width <- "100%"
         }
 
+        # return sizing
+        sizing
+      }
+
       assignInNamespace("resolveSizing", resolveSizing, ns = "htmlwidgets")
     }
   }
@@ -698,14 +757,14 @@ apply_responsive_patch <- function(format) {
   if (is.null(x)) y else x
 }
 
-# from rmarkdown 
+# from rmarkdown
 # https://github.com/rstudio/rmarkdown/blob/0951a2fea7e317f77d27969c25f3194ead38805e/R/util.R#L318-L331
 has_crop_tools <- function(warn = TRUE) {
   if (packageVersion("knitr") >= "1.44") {
     return(knitr:::has_crop_tools(warn))
   }
   # for older version we do inline the function from rmarkdown
-  # but it does not have the knitr improvment for windows 
+  # but it does not have the knitr improvment for windows
   # https://github.com/yihui/knitr/issues/2246
   tools <- c(
     pdfcrop = unname(rmarkdown:::find_program("pdfcrop")),
@@ -714,9 +773,10 @@ has_crop_tools <- function(warn = TRUE) {
   missing <- tools[tools == ""]
   if (length(missing) == 0) return(TRUE)
   x <- paste0(names(missing), collapse = ", ")
-  if (warn) warning(
-    sprintf("\nTool(s) not installed or not in PATH: %s", x),
-    "\n-> As a result, figure cropping will be disabled."
-  )
+  if (warn)
+    warning(
+      sprintf("\nTool(s) not installed or not in PATH: %s", x),
+      "\n-> As a result, figure cropping will be disabled."
+    )
   FALSE
-}
\ No newline at end of file
+}
diff --git a/src/resources/rmd/hooks.R b/src/resources/rmd/hooks.R
index 1b0c7e8e75..f696c5c573 100644
--- a/src/resources/rmd/hooks.R
+++ b/src/resources/rmd/hooks.R
@@ -3,8 +3,8 @@
 
 # inline knitr:::merge_list()
 merge_list <- function(x, y) {
-    x[names(y)] <- y
-    x
+  x[names(y)] <- y
+  x
 }
 
 # inline from knitr:::create_fence() from version 1.38
@@ -19,8 +19,13 @@ create_fence <- function(x, char = "`") {
 # convert some engine names to language names
 eng2lang <- function(x) {
   d <- c(
-    asy = "cpp", mysql = "sql", node = "javascript", 
-    psql = "sql", rscript = "r", rcpp = "cpp", tikz = "tex"
+    asy = "cpp",
+    mysql = "sql",
+    node = "javascript",
+    psql = "sql",
+    rscript = "r",
+    rcpp = "cpp",
+    tikz = "tex"
   )
   x <- tolower(x)
   if (x %in% names(d)) d[x] else x
@@ -28,10 +33,9 @@ eng2lang <- function(x) {
 
 
 knitr_hooks <- function(format, resourceDir, handledLanguages) {
-
   knit_hooks <- list()
   opts_hooks <- list()
-  
+
   # options in yaml (save last yaml.code for source hook)
   lastYamlCode <- NULL
   opts_hooks[["code"]] <- function(options) {
@@ -41,10 +45,9 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
       lastYamlCode <<- options[["yaml.code"]]
     }
     options
-  } 
-
+  }
 
-   # force eval to 'FALSE' for all chunks if execute: enabled: false
+  # force eval to 'FALSE' for all chunks if execute: enabled: false
   executeEnabled <- format$execute[["enabled"]]
   if (!is.null(executeEnabled) && executeEnabled == FALSE) {
     opts_hooks[["eval"]] <- function(options) {
@@ -90,42 +93,51 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
       options[["results"]] <- "asis"
     } else {
       if (identical(options[["results"]], "hide")) {
-         options[["results"]] <- "markup"
+        options[["results"]] <- "markup"
       }
       if (identical(options[["fig.show"]], "hide")) {
-         options[["fig.show"]] <- "asis"
+        options[["fig.show"]] <- "asis"
       }
     }
-    options[["message"]] <- ifelse(!isFALSE(output), knitr::opts_chunk$get("message"), FALSE)
-    options[["warning"]] <- ifelse(!isFALSE(output), knitr::opts_chunk$get("warning"), FALSE)
+    options[["message"]] <- ifelse(
+      !isFALSE(output),
+      knitr::opts_chunk$get("message"),
+      FALSE
+    )
+    options[["warning"]] <- ifelse(
+      !isFALSE(output),
+      knitr::opts_chunk$get("warning"),
+      FALSE
+    )
     options
   }
 
   # automatically set gifski hook for fig.animate
   opts_hooks[["fig.show"]] <- function(options) {
-    
     # get current value of fig.show
     fig.show <- options[["fig.show"]]
-    
+
     # use gifski as default animation hook for non-latex output
     if (identical(fig.show, "animate")) {
-      if (!is_pandoc_latex_output(format) && is.null(options[["animation.hook"]])) {
+      if (
+        !is_pandoc_latex_output(format) && is.null(options[["animation.hook"]])
+      ) {
         options[["animation.hook"]] <- "gifski"
       }
-      
-    # fig.show "asis" -> "hold" for fig: labeled chunks
+
+      # fig.show "asis" -> "hold" for fig: labeled chunks
     } else if (identical(fig.show, "asis")) {
       if (is_figure_label(output_label(options))) {
         options[["fig.show"]] <- "hold"
       }
     }
-    
+
     # return options
     options
   }
 
   # coalesce echos so that all code is displayed for renderings: [light, dark]
-  opts_hooks[["renderings"]] <- function(options){
+  opts_hooks[["renderings"]] <- function(options) {
     options$fig.show = 'hold'
     options
   }
@@ -137,7 +149,7 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
         options[["comment"]] <- "##"
       }
     }
-   
+
     # return options
     options
   }
@@ -147,8 +159,7 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
     opts_hooks[[option]] <<- function(options) {
       if (identical(options[[option]], FALSE)) {
         options[[option]] <- TRUE
-        for (hide in hidden)
-          options[[paste0(hide,".hidden")]] <- TRUE
+        for (hide in hidden) options[[paste0(hide, ".hidden")]] <- TRUE
       }
       options
     }
@@ -171,14 +182,16 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
   }
   delegating_output_hook = function(type, classes) {
     delegating_hook(type, function(x, options) {
-      if (identical(options[["results"]], "asis") ||
-          isTRUE(options[["collapse"]])) {
+      if (
+        identical(options[["results"]], "asis") ||
+          isTRUE(options[["collapse"]])
+      ) {
         x
       } else {
         # prefix for classes
         classes <- c("cell-output", paste0("cell-output-", classes))
         # add .hidden class if keep-hidden hook injected an option
-        if (isTRUE(options[[paste0(type,".hidden")]]))
+        if (isTRUE(options[[paste0(type, ".hidden")]]))
           classes <- c(classes, "hidden")
         output_div(x, NULL, classes)
       }
@@ -187,14 +200,16 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
 
   # entire chunk
   knit_hooks$chunk <- delegating_hook("chunk", function(x, options) {
-
     # Do nothing more for some specific chunk content -----
 
     # Quarto language handler
-    if (any(as.logical(lapply(handledLanguages, function(lang) {
-      prefix <- paste0("```{", lang, "}")
-      startsWith(x, prefix)
-    }))) && endsWith(x, "```")) {
+    if (
+      any(as.logical(lapply(handledLanguages, function(lang) {
+        prefix <- paste0("```{", lang, "}")
+        startsWith(x, prefix)
+      }))) &&
+        endsWith(x, "```")
+    ) {
       return(x)
     }
 
@@ -211,7 +226,7 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
     # For any other, adding a cell output div -----
 
     # read some options
-    
+
     label <- output_label(options)
     fig.cap <- options[["fig.cap"]]
     cell.cap <- NULL
@@ -222,7 +237,7 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
     if (isTRUE(format$render$`notebook-preserve-cells`) && !is.null(label)) {
       cellId <- paste0("cell-", label)
     }
-    
+
     # fixup duplicate figure labels
     placeholder <- output_label_placeholder(options)
     if (!is.null(placeholder)) {
@@ -236,7 +251,7 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
     # caption output
     if (!is.null(fig.cap) && !is.null(fig.subcap)) {
       cell.cap <- paste0("\n", fig.cap, "\n")
-    }  else {
+    } else {
       label <- NULL
     }
 
@@ -244,18 +259,17 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
     fig.sep <- options[["fig.sep"]]
     fig.ncol <- options[["fig.ncol"]]
     if (!is.null(fig.sep)) {
-      
       # recycle fig.sep
       fig.num <- options[["fig.num"]] %||% 1L
       fig.sep <- rep_len(fig.sep, fig.num)
-      
+
       # recyle out.width
-      out.width <- options[["out.width"]] 
+      out.width <- options[["out.width"]]
       if (is.null(out.width)) {
         out.width <- 1
-      } 
+      }
       out.width <- rep_len(out.width, fig.num)
-      
+
       # build fig.layout
       fig.layout <- list()
       fig.row <- c()
@@ -270,12 +284,12 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
         fig.layout[[length(fig.layout) + 1]] <- fig.row
       }
       options[["layout"]] <- fig.layout
-      
-    # populate layout-ncol from fig.ncol
+
+      # populate layout-ncol from fig.ncol
     } else if (!is.null(fig.ncol)) {
       options[["layout-ncol"]] = fig.ncol
     }
-    
+
     # alias fig.align to layout-align
     fig.align = options[["fig.align"]]
     if (!is.null(fig.align) && !identical(fig.align, "default")) {
@@ -289,7 +303,13 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
     }
 
     # forward selected attributes
-    forward <- c("layout", "layout-nrow", "layout-ncol", "layout-align", "layout-valign")
+    forward <- c(
+      "layout",
+      "layout-nrow",
+      "layout-ncol",
+      "layout-align",
+      "layout-valign"
+    )
     forwardAttr <- character()
     for (attr in forward) {
       value = options[[attr]]
@@ -307,16 +327,21 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
 
     # forward any other unknown attributes
     # From knitr 1.44, knitr:::opts_chunk_attr and knitr::opts_chunk$get()
-    # should cover all options and knitr will only normalize 
-    # to their . version the known knitr options. 
+    # should cover all options and knitr will only normalize
+    # to their . version the known knitr options.
     # Other options (like quarto specific ones) will keep there original values
     # with - separator.
-    knitr_default_opts <- unique(c(names(knitr:::opts_chunk_attr), names(knitr::opts_chunk$get())))
-    # quarto options common with knitr and that will be normalized to .
+    knitr_default_opts <- unique(c(
+      names(knitr:::opts_chunk_attr),
+      names(knitr::opts_chunk$get())
+    ))
+    # quarto options common with knitr and that will be normalized to
+    # fmt: skip
     quarto_knitr_opts <- c(
       "fig.cap", "fig.subcap", "fig.scap", "fig.link", "fig.alt",
       "fig.align", "fig.env", "fig.pos", "fig.num", "out.width"
     )
+    # fmt: skip
     quarto_opts <- c(
       "label", "lst-cap", "lst-label", "classes", "panel", "column",
       "tbl-column", "tbl-cap-location", "cap-location", "code-fold",
@@ -332,6 +357,7 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
       "output.hidden", "warning.hidden", "message.hidden"
     )
     # Other knitr option possibly not in knitr_default_opts
+    # fmt: skip
     other_opts <- c(
       "eval", "yaml.code", "code", "file", "params.src", "original.params.src",
       "fenced.echo", "chunk.echo", "lang", "out.width.px", "out.height.px",
@@ -339,27 +365,35 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
       "class.warning", "class.error", "attr.source", "attr.output",
       "attr.message", "attr.warning", "attr.error", "connection", "hash"
     )
-    known_opts <- c(knitr_default_opts, quarto_knitr_opts, quarto_opts, other_opts)
+    known_opts <- c(
+      knitr_default_opts,
+      quarto_knitr_opts,
+      quarto_opts,
+      other_opts
+    )
     unknown_opts <- setdiff(names(options), known_opts)
     unknown_opts <- Filter(Negate(is.null), unknown_opts)
     unknown_opts <- Filter(function(opt) !startsWith(opt, "."), unknown_opts)
     # json encode if necessary
-    unknown_values <- lapply(options[unknown_opts],
-                             function(value) {
-                               if (!is.character(value) || length(value) > 1) {
-                                 value <- jsonlite::toJSON(value, auto_unbox = TRUE)
-                               } 
-                               # will be enclosed in single quotes so escape
-                               gsub("'", "\\\'", value, fixed = TRUE)
-                            })
+    unknown_values <- lapply(
+      options[unknown_opts],
+      function(value) {
+        if (!is.character(value) || length(value) > 1) {
+          value <- jsonlite::toJSON(value, auto_unbox = TRUE)
+        }
+        # will be enclosed in single quotes so escape
+        gsub("'", "\\\'", value, fixed = TRUE)
+      }
+    )
     # append to forward list
-    forwardAttr <- c(forwardAttr, 
-                     sprintf("%s='%s'", unknown_opts, unknown_values))
+    forwardAttr <- c(
+      forwardAttr,
+      sprintf("%s='%s'", unknown_opts, unknown_values)
+    )
     if (length(forwardAttr) > 0)
-      forwardAttr <- paste0(" ", paste(forwardAttr, collapse = " "))
-    else
+      forwardAttr <- paste0(" ", paste(forwardAttr, collapse = " ")) else
       forwardAttr <- ""
-   
+
     # handle classes
     classes <- c("cell", options[["classes"]])
     if (is.character(options[["panel"]]))
@@ -377,23 +411,35 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
     if (is.character(options[["cap-location"]]))
       classes <- c(classes, paste0("caption-", options[["cap-location"]]))
     if (is.character(options[["fig-cap-location"]])) {
-      classes <- c(classes, paste0("fig-cap-location-", options[["fig-cap-location"]]))
+      classes <- c(
+        classes,
+        paste0("fig-cap-location-", options[["fig-cap-location"]])
+      )
     } else if (is.character(options[["fig.cap-location"]])) {
       # knitr < 1.44 compatibility where fig- -> fig.
-      classes <- c(classes, paste0("fig-cap-location-", options[["fig.cap-location"]]))
+      classes <- c(
+        classes,
+        paste0("fig-cap-location-", options[["fig.cap-location"]])
+      )
     }
     if (is.character(options[["tbl-cap-location"]]))
-      classes <- c(classes, paste0("tbl-cap-location-", options[["tbl-cap-location"]]))
+      classes <- c(
+        classes,
+        paste0("tbl-cap-location-", options[["tbl-cap-location"]])
+      )
 
     if (isTRUE(options[["include.hidden"]])) {
       classes <- c(classes, "hidden")
     }
-    classes <- sapply(classes, function(clz) ifelse(startsWith(clz, "."), clz, paste0(".", clz)))
+    classes <- sapply(
+      classes,
+      function(clz) ifelse(startsWith(clz, "."), clz, paste0(".", clz))
+    )
 
     # allow table label through
     if (is_table_label(options[["label"]])) {
       label <- options[["label"]]
-    } 
+    }
 
     if (is.null(label) && !is.null(cellId)) {
       label <- cellId
@@ -403,27 +449,34 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
       label <- paste0(label, " ")
     }
 
-    # if there is a label, additional classes, a forwardAttr, or a cell.cap 
+    # if there is a label, additional classes, a forwardAttr, or a cell.cap
     # then the user is deemed to have implicitly overridden results = "asis"
     # (as those features don't work w/o an enclosing div)
-    needCell <- isTRUE(nzchar(label)) || 
-                length(classes) > 1 ||
-                isTRUE(nzchar(forwardAttr)) ||
-                isTRUE(nzchar(cell.cap))
+    needCell <- isTRUE(nzchar(label)) ||
+      length(classes) > 1 ||
+      isTRUE(nzchar(forwardAttr)) ||
+      isTRUE(nzchar(cell.cap))
     if (identical(options[["results"]], "asis") && !needCell) {
       x
     } else {
       # Newline first and after to ensure Pandoc Fenced Div is correctly parsed
       paste0(
         "\n",
-        options[["indent"]], "::: {", 
-        labelId(label), paste(classes, collapse = " ") ,forwardAttr, "}\n", x, "\n", cell.cap ,
-        options[["indent"]], ":::\n"
+        options[["indent"]],
+        "::: {",
+        labelId(label),
+        paste(classes, collapse = " "),
+        forwardAttr,
+        "}\n",
+        x,
+        "\n",
+        cell.cap,
+        options[["indent"]],
+        ":::\n"
       )
     }
   })
   knit_hooks$source <- function(x, options) {
-
     # How knitr handles the prompt option for R chunks
     x <- knitr:::hilight_source(x, "markdown", options)
     x <- knitr:::one_string(c('', x))
@@ -433,7 +486,7 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
     id <- NULL
 
     # leave some specific engine alone
-    if (! options[["engine"]] %in% c("verbatim", "embed")) {
+    if (!options[["engine"]] %in% c("verbatim", "embed")) {
       # Add classes and attributes required for quarto specific features
       class <- paste(class, "cell-code")
       if (isTRUE(options[["source.hidden"]])) {
@@ -446,12 +499,16 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
         }
       }
       if (identical(options[["code-overflow"]], "wrap"))
-        class <- paste(class, "code-overflow-wrap")
-      else if (identical(options[["code-overflow"]], "scroll"))
+        class <- paste(class, "code-overflow-wrap") else if (
+        identical(options[["code-overflow"]], "scroll")
+      )
         class <- paste(class, "code-overflow-scroll")
       fold <- options[["code-fold"]]
       if (!is.null(fold)) {
-        attr <- paste(attr, paste0('code-fold="', tolower(as.character(fold)), '"'))
+        attr <- paste(
+          attr,
+          paste0('code-fold="', tolower(as.character(fold)), '"')
+        )
       }
       fold <- options[["code-summary"]]
       if (!is.null(fold)) {
@@ -459,7 +516,10 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
       }
       lineNumbers <- options[["code-line-numbers"]]
       if (!is.null(lineNumbers)) {
-        attr <- paste(attr, paste0('code-line-numbers="', tolower(as.character(lineNumbers)), '"'))
+        attr <- paste(
+          attr,
+          paste0('code-line-numbers="', tolower(as.character(lineNumbers)), '"')
+        )
       }
     }
 
@@ -470,7 +530,10 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
       lang <- NULL
       yamlCode <- lastYamlCode
       if (!is.null(yamlCode)) {
-        yamlCode <- Filter(function(line) !grepl("\\|\\s+echo:\\s+fenced\\s*$", line), yamlCode)
+        yamlCode <- Filter(
+          function(line) !grepl("\\|\\s+echo:\\s+fenced\\s*$", line),
+          yamlCode
+        )
         yamlCode <- paste(yamlCode, collapse = "\n")
         if (!nzchar(yamlCode)) {
           x <- trimws(x, "left")
@@ -479,7 +542,17 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
         x <- trimws(x, "left")
       }
       ticks <- create_fence(x, "`")
-      x <- paste0("\n", ticks, "{{", options[["original.params.src"]], "}}\n", yamlCode, x, "\n", ticks)
+      x <- paste0(
+        "\n",
+        ticks,
+        "{{",
+        options[["original.params.src"]],
+        "}}\n",
+        yamlCode,
+        x,
+        "\n",
+        ticks
+      )
     } else {
       # If requested, preserve the code yaml and emit it into the code blocks
       if (isTRUE(format$render$`produce-source-notebook`)) {
@@ -503,14 +576,13 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
     )
 
     paste0("\n\n", ticks, attrs, x, "\n", ticks, "\n\n")
-   
   }
   knit_hooks$output <- delegating_output_hook("output", c("stdout"))
   knit_hooks$warning <- delegating_output_hook("warning", c("stderr"))
   knit_hooks$message <- delegating_output_hook("message", c("stderr"))
   knit_hooks$plot <- knitr_plot_hook(format)
   knit_hooks$error <- delegating_output_hook("error", c("error"))
-  
+
   list(
     knit = knit_hooks,
     opts = opts_hooks
@@ -518,13 +590,11 @@ knitr_hooks <- function(format, resourceDir, handledLanguages) {
 }
 
 knitr_plot_hook <- function(format) {
-
   htmlOutput <- knitr:::is_html_output(format$pandoc$to)
   latexOutput <- is_pandoc_latex_output(format)
   defaultFigPos <- format$render[["fig-pos"]]
 
   function(x, options) {
-    
     # are we using animation (if we are then ignore all but the last fig)
     fig.num <- options[["fig.num"]] %||% 1L
     fig.cur = options$fig.cur %||% 1L
@@ -532,21 +602,20 @@ knitr_plot_hook <- function(format) {
     animate = fig.num > 1 && options$fig.show == 'animate' && !tikz
     if (animate) {
       if (fig.cur < fig.num) {
-        return ('')
-      } else  {
-        # if it's the gifski hook then call it directly (it will call 
+        return('')
+      } else {
+        # if it's the gifski hook then call it directly (it will call
         # this function back with the composed animated gif)
         hook <- knitr:::hook_animation(options)
         if (identical(hook, knitr:::hook_gifski)) {
-          return (hook(x, options))
+          return(hook(x, options))
         }
       }
     }
-  
+
     # classes
     classes <- paste0("cell-output-display")
-    if (isTRUE(options[["plot.hidden"]]))
-      classes <- c(classes, "hidden")
+    if (isTRUE(options[["plot.hidden"]])) classes <- c(classes, "hidden")
 
     # label
     placeholder <- output_label_placeholder(options)
@@ -556,7 +625,7 @@ knitr_plot_hook <- function(format) {
       ""
     )
     attr <- label
-    
+
     # knitr::fix_options will convert out.width and out.height to their
     # latex equivalents, reverse this transformation so our figure layout
     # code can deal directly with percentages
@@ -572,21 +641,23 @@ knitr_plot_hook <- function(format) {
     if (!identical(fig.env, "figure")) {
       keyvalue <- c(keyvalue, sprintf("fig-env='%s'", fig.env))
     }
-    fig.pos <- options[['fig.pos']] 
+    fig.pos <- options[['fig.pos']]
     if (nzchar(fig.pos)) {
       keyvalue <- c(keyvalue, sprintf("fig-pos='%s'", fig.pos))
-    # if we are echoing code, there is no default fig-pos, and
-    # we are not using a layout then automatically set fig-pos to 'H'
-    } else if (latexOutput &&
-               isTRUE(options[["echo"]]) &&
-               length(names(options)[startsWith(names(options), "layout")]) == 0 &&
-               is.null(defaultFigPos)) {
+      # if we are echoing code, there is no default fig-pos, and
+      # we are not using a layout then automatically set fig-pos to 'H'
+    } else if (
+      latexOutput &&
+        isTRUE(options[["echo"]]) &&
+        length(names(options)[startsWith(names(options), "layout")]) == 0 &&
+        is.null(defaultFigPos)
+    ) {
       keyvalue <- c(keyvalue, "fig-pos='H'")
     }
     fig.alt <- options[["fig.alt"]]
     escapeAttr <- function(x) gsub("'", "\\'", x, fixed = TRUE)
     if (!is.null(fig.alt) && nzchar(fig.alt)) {
-       keyvalue <- c(keyvalue, sprintf("fig-alt='%s'", escapeAttr(fig.alt)))
+      keyvalue <- c(keyvalue, sprintf("fig-alt='%s'", escapeAttr(fig.alt)))
     }
     fig.scap <- options[['fig.scap']]
     if (!is.null(fig.scap)) {
@@ -600,7 +671,7 @@ knitr_plot_hook <- function(format) {
     if (!is.null(resize.height)) {
       keyvalue <- c(keyvalue, sprintf("resize.height='%s'", resize.height))
     }
-    
+
     # add keyvalue
     keyvalue <- paste(
       c(
@@ -622,74 +693,68 @@ knitr_plot_hook <- function(format) {
 
     # special handling for animations
     if (animate) {
-      
       # get the caption (then remove it so the hook doesn't include it)
       caption <- figure_cap(options)
       options[["fig.cap"]] <- NULL
       options[["fig.subcap"]] <- NULL
-      
+
       # check for latex
       if (is_pandoc_latex_output(format)) {
-        
         # include dependency on animate package
         knitr::knit_meta_add(list(
           rmarkdown::latex_dependency("animate")
         ))
-        
+
         latexOutput <- paste(
           "```{=latex}",
           latex_animation(x, options),
           "```",
           sep = "\n"
         )
-        
+
         # add the caption if we have one
         if (nzchar(caption)) {
           latexOutput <- paste0(latexOutput, "\n\n", caption, "\n")
         }
-        
+
         # enclose in output div
         output_div(latexOutput, label, classes)
-        
-      # otherwise assume html
+
+        # otherwise assume html
       } else {
         # render the animation
         hook <- knitr:::hook_animation(options)
         htmlOutput <- hook(x, options)
         htmlOutput <- htmlPreserve(htmlOutput)
-        
+
         # add the caption if we have one
         if (nzchar(caption)) {
           htmlOutput <- paste0(htmlOutput, "\n\n", caption, "\n")
         }
-        
+
         # enclose in output div
         output_div(htmlOutput, label, classes)
       }
-     
     } else {
-      
       # generate markdown for image
       md <- sprintf("![%s](%s)%s", figure_cap(options), x, attr)
-      
+
       # enclose in link if requested
       link <- options[["fig.link"]]
       if (!is.null(link)) {
         md <- sprintf("[%s](%s)", md, link)
       }
-      
+
       # result = "asis" specific
       if (identical(options[["results"]], "asis")) return(md)
-      
-      # enclose in output div 
+
+      # enclose in output div
       output_div(md, NULL, classes)
     }
-
   }
 }
 
 knitr_options_hook <- function(options) {
-
   if (!knitr_has_yaml_chunk_options()) {
     # partition yaml options
     results <- partition_yaml_options(options$engine, options$code)
@@ -707,14 +772,13 @@ knitr_options_hook <- function(options) {
       options <- merge_list(options, results$yaml)
       # set code
       options$code <- results$code
-    } 
+    }
     options[["yaml.code"]] <- results$yamlSource
-    
   } else {
     # from knitr 1.44 onwards the normalization is done at parsing time by knitr
     # for all known options c(names(opts_chunk_attr), names(opts_chunk$get()))
     # so normalization here should not be necessary anymore at some point
-    # TODO: remove normalization here in a few years 
+    # TODO: remove normalization here in a few years
     #       when 1.44 is widely used version
     options <- normalize_options(options)
   }
@@ -729,33 +793,31 @@ knitr_options_hook <- function(options) {
   if (!is.null(options[["fig-dpi"]])) {
     options[["dpi"]] <- options[["fig-dpi"]]
   }
-  
-  # if there are line annotations in the code then we need to 
+
+  # if there are line annotations in the code then we need to
   # force disable messages/warnings
   comment_chars <- engine_comment_chars(options$engine)
-  pattern <- paste0(".*\\Q", comment_chars[[1]], "\\E\\s*",
-                    "<[0-9]+>\\s*")
+  pattern <- paste0(".*\\Q", comment_chars[[1]], "\\E\\s*", "<[0-9]+>\\s*")
   if (length(comment_chars) > 1) {
     pattern <- paste0(pattern, ".*\\Q", comment_chars[[2]], "\\E\\s*")
   }
   pattern <- paste0(pattern, "$")
   if (any(grepl(pattern, options$code))) {
     options$warning <- FALSE
-    options$results <- "hold" 
+    options$results <- "hold"
   }
 
-
-  # fig.subcap: TRUE means fig.subcap: "" (more natural way 
+  # fig.subcap: TRUE means fig.subcap: "" (more natural way
   # to specify that empty subcaps are okay)
   if (isTRUE(options[["fig.subcap"]])) {
     options[["fig.subcap"]] <- ""
   }
-  
-  # return options  
+
+  # return options
   options
 }
 
-# convert any option with e.g. fig- into fig. 
+# convert any option with e.g. fig- into fig.
 # we do this so that all downstream code can consume a single
 # variation of these functions. We support both syntaxes because
 # quarto/pandoc generally uses - as a delimeter everywhere,
@@ -765,13 +827,13 @@ knitr_options_hook <- function(options) {
 # from knitr 1.44 onwards the normalization is done at parsing time by knitr
 # for all known options c(names(opts_chunk_attr), names(opts_chunk$get()))
 # so normalization here should not be necessary anymore at some point
-# TODO: remove normalization here in a few years 
+# TODO: remove normalization here in a few years
 #       when 1.44 is widely used version
 normalize_options <- function(options) {
   # TODO: knitr 1.44 store all known options as it does the normalization
   #       they are in `c(names(opts_chunk_attr), names(opts_chunk$get()))`
   knitr_options_dashed <- c(
-    # Text output 
+    # Text output
     "strip-white",
     "class-output",
     "class-message",
@@ -867,15 +929,14 @@ partition_yaml_options <- function(engine, code) {
   comment_chars <- engine_comment_chars(engine)
   comment_start <- paste0(comment_chars[[1]], "| ")
   comment_end <- ifelse(length(comment_chars) > 1, comment_chars[[2]], "")
-  
+
   # check for option comments
   match_start <- startsWith(code, comment_start)
   match_end <- endsWith(trimws(code, "right"), comment_end)
   matched_lines <- match_start & match_end
-  
+
   # has to have at least one matched line at the beginning
   if (isTRUE(matched_lines[[1]])) {
-    
     # divide into yaml and code
     if (all(matched_lines)) {
       yamlSource <- code
@@ -883,30 +944,36 @@ partition_yaml_options <- function(engine, code) {
     } else {
       last_match <- which.min(matched_lines) - 1
       yamlSource <- code[1:last_match]
-      code <- code[(last_match+1):length(code)]
+      code <- code[(last_match + 1):length(code)]
     }
-    
+
     # trim right
     if (any(match_end)) {
       yamlSource <- trimws(yamlSource, "right")
     }
-  
+
     # extract yaml from comments, then parse it
-    yaml <- substr(yamlSource, 
-                   nchar(comment_start) + 1, 
-                   nchar(yamlSource) - nchar(comment_end))
+    yaml <- substr(
+      yamlSource,
+      nchar(comment_start) + 1,
+      nchar(yamlSource) - nchar(comment_end)
+    )
     yaml_options <- yaml::yaml.load(yaml, eval.expr = TRUE)
     if (!is.list(yaml_options) || length(names(yaml_options)) == 0) {
-      warning("Invalid YAML option format in chunk: \n", paste(yaml, collapse = "\n"), "\n")
+      warning(
+        "Invalid YAML option format in chunk: \n",
+        paste(yaml, collapse = "\n"),
+        "\n"
+      )
       yaml_options <- list()
     }
-    
+
     # extract code
     if (length(code) > 0 && knitr:::is_blank(code[[1]])) {
       code <- code[-1]
       yamlSource <- c(yamlSource, "")
     }
-    
+
     list(
       yaml = yaml_options,
       yamlSource = yamlSource,
@@ -930,8 +997,8 @@ engine_comment_chars <- function(engine) {
     matlab = "%",
     csharp = "//",
     fsharp = "//",
-    c = c("/*",  "*/"),
-    css = c("/*",  "*/"),
+    c = c("/*", "*/"),
+    css = c("/*", "*/"),
     sas = c("*", ";"),
     powershell = "#",
     bash = "#",
@@ -988,10 +1055,7 @@ output_div <- function(x, label, classes, attr = NULL) {
 }
 
 labelId <- function(label) {
-  if (!is.null(label) && !startsWith(label, "#"))
-    paste0("#", label)
-  else
-    label
+  if (!is.null(label) && !startsWith(label, "#")) paste0("#", label) else label
 }
 
 figure_cap <- function(options) {
@@ -999,12 +1063,8 @@ figure_cap <- function(options) {
   if (is.null(output_label) || is_figure_label(output_label)) {
     fig.cap <- options[["fig.cap"]]
     fig.subcap <- options[["fig.subcap"]]
-    if (length(fig.subcap) != 0)
-      fig.subcap
-    else if (length(fig.cap) != 0)
-      fig.cap
-    else
-      ""
+    if (length(fig.subcap) != 0) fig.subcap else if (length(fig.cap) != 0)
+      fig.cap else ""
   } else {
     ""
   }
@@ -1023,10 +1083,7 @@ output_label <- function(options) {
 output_label_placeholder <- function(options) {
   kPlaceholder <- "D08295A6-16DC-499D-85A8-8BA656E013A2"
   label <- output_label(options)
-  if (is_figure_label(label))
-    paste0(label, kPlaceholder)
-  else
-    NULL
+  if (is_figure_label(label)) paste0(label, kPlaceholder) else NULL
 }
 
 is_figure_label <- function(label) {
@@ -1052,10 +1109,7 @@ block_attr <- function(id = NULL, lang = NULL, class = NULL, attr = NULL) {
   }
   attributes <- c(id, lang, class, attr)
   attributes <- paste(attributes[!is.null(attributes)], collapse = " ")
-  if (nzchar(attributes))
-    paste0("{", attributes, "}")
-  else
-    ""
+  if (nzchar(attributes)) paste0("{", attributes, "}") else ""
 }
 
 block_class <- function(x) {
@@ -1066,7 +1120,10 @@ latex_sizes_to_percent <- function(options) {
   #  \linewidth
   width <- options[["out.width"]]
   if (!is.null(width)) {
-    latex_width <- regmatches(width, regexec("^([0-9\\.]+)\\\\linewidth$", width))
+    latex_width <- regmatches(
+      width,
+      regexec("^([0-9\\.]+)\\\\linewidth$", width)
+    )
     if (length(latex_width[[1]]) > 1) {
       width <- paste0(as.numeric(latex_width[[1]][[2]]) * 100, "%")
       options[["out.width"]] <- width
@@ -1075,7 +1132,10 @@ latex_sizes_to_percent <- function(options) {
   # \textheight
   height <- options[["out.height"]]
   if (!is.null(height)) {
-    latex_height <- regmatches(height, regexec("^([0-9\\.]+)\\\\textheight$", height))
+    latex_height <- regmatches(
+      height,
+      regexec("^([0-9\\.]+)\\\\textheight$", height)
+    )
     if (length(latex_height[[1]]) > 1) {
       height <- paste0(as.numeric(latex_height[[1]][[2]]) * 100, "%")
       options[["out.height"]] <- height
@@ -1087,23 +1147,33 @@ latex_sizes_to_percent <- function(options) {
 # ported from:
 # https://github.com/yihui/knitr/blob/f8f90baad99d873202b8dc8042eab7a88fac232f/R/hooks-latex.R#L151-L171
 latex_animation <- function(x, options) {
-  
   fig.num = options$fig.num %||% 1L
-  
+
   ow = options$out.width
   # maxwidth does not work with animations
   if (identical(ow, '\\maxwidth')) ow = NULL
   if (is.numeric(ow)) ow = paste0(ow, 'px')
-  size = paste(c(sprintf('width=%s', ow),
-                 sprintf('height=%s', options$out.height),
-                 options$out.extra), collapse = ',')
-  
+  size = paste(
+    c(
+      sprintf('width=%s', ow),
+      sprintf('height=%s', options$out.height),
+      options$out.extra
+    ),
+    collapse = ','
+  )
+
   aniopts = options$aniopts
   aniopts = if (is.na(aniopts)) NULL else gsub(';', ',', aniopts)
   size = paste(c(size, sprintf('%s', aniopts)), collapse = ',')
   if (nzchar(size)) size = sprintf('[%s]', size)
-  sprintf('\\animategraphics%s{%s}{%s}{%s}{%s}', size, 1 / options$interval,
-          sub(sprintf('%d$', fig.num), '', xfun::sans_ext(x)), 1L, fig.num)
+  sprintf(
+    '\\animategraphics%s{%s}{%s}{%s}{%s}',
+    size,
+    1 / options$interval,
+    sub(sprintf('%d$', fig.num), '', xfun::sans_ext(x)),
+    1L,
+    fig.num
+  )
 }
 
 is_ipynb_output <- function(to) {
diff --git a/src/resources/rmd/ojs.R b/src/resources/rmd/ojs.R
index 775515248f..5f022f8856 100644
--- a/src/resources/rmd/ojs.R
+++ b/src/resources/rmd/ojs.R
@@ -5,20 +5,33 @@ ojs_define <- function(..., .session = shiny::getDefaultReactiveDomain()) {
   if (is.null(nm)) {
     nm <- rep_len("", length(vars))
   }
-  mapply(function(q, nm, val) {
-    # Infer name, if possible
-    if (nm == "") {
-      tryCatch({
-        nm <- rlang::as_name(q)
-      }, error = function(e) {
-        code <- paste(collapse = "\n", deparse(rlang::f_rhs(q)))
-        stop("ojs_define() could not create a name for the argument: ", code)
-      })
-    }
-    .session$output[[nm]] <- val
-    outputOptions(.session$output, nm, suspendWhenHidden = FALSE)
-    .session$sendCustomMessage("ojs-export", list(name = nm))
-    NULL
-  }, quos, nm, vars, SIMPLIFY = FALSE, USE.NAMES = FALSE)
+  mapply(
+    function(q, nm, val) {
+      # Infer name, if possible
+      if (nm == "") {
+        tryCatch(
+          {
+            nm <- rlang::as_name(q)
+          },
+          error = function(e) {
+            code <- paste(collapse = "\n", deparse(rlang::f_rhs(q)))
+            stop(
+              "ojs_define() could not create a name for the argument: ",
+              code
+            )
+          }
+        )
+      }
+      .session$output[[nm]] <- val
+      outputOptions(.session$output, nm, suspendWhenHidden = FALSE)
+      .session$sendCustomMessage("ojs-export", list(name = nm))
+      NULL
+    },
+    quos,
+    nm,
+    vars,
+    SIMPLIFY = FALSE,
+    USE.NAMES = FALSE
+  )
   invisible()
 }
diff --git a/src/resources/rmd/ojs_static.R b/src/resources/rmd/ojs_static.R
index 8ddae38631..14f1d65137 100644
--- a/src/resources/rmd/ojs_static.R
+++ b/src/resources/rmd/ojs_static.R
@@ -2,7 +2,8 @@ ojs_define <- function(...) {
   # validate that we aren't in a cached chunk
   cache <- knitr:::opts_current$get("cache")
   if (is.numeric(cache) && cache > 0) {
-    stop("ojs_define() cannot be cached\n",
+    stop(
+      "ojs_define() cannot be cached\n",
       "Add cache: false to this cell's options to disable caching",
       call. = FALSE
     )
@@ -14,25 +15,37 @@ ojs_define <- function(...) {
     nm <- rep_len("", length(vars))
   }
   contents <- jsonlite::toJSON(
-    list(contents = I(mapply(
-      function(q, nm, val) {
-        # Infer name, if possible
-        if (nm == "") {
-          tryCatch(
-            {
-              nm <- rlang::as_name(q)
-            },
-            error = function(e) {
-              code <- paste(collapse = "\n", deparse(rlang::f_rhs(q)))
-              stop("ojs_define() could not create a name for the argument: ", code)
-            }
-          )
-        }
-        list(name = nm, value = val)
-      }, quos, nm, vars,
-      SIMPLIFY = FALSE, USE.NAMES = FALSE
-    ))),
-    dataframe = "columns", null = "null", na = "null", auto_unbox = TRUE
+    list(
+      contents = I(mapply(
+        function(q, nm, val) {
+          # Infer name, if possible
+          if (nm == "") {
+            tryCatch(
+              {
+                nm <- rlang::as_name(q)
+              },
+              error = function(e) {
+                code <- paste(collapse = "\n", deparse(rlang::f_rhs(q)))
+                stop(
+                  "ojs_define() could not create a name for the argument: ",
+                  code
+                )
+              }
+            )
+          }
+          list(name = nm, value = val)
+        },
+        quos,
+        nm,
+        vars,
+        SIMPLIFY = FALSE,
+        USE.NAMES = FALSE
+      ))
+    ),
+    dataframe = "columns",
+    null = "null",
+    na = "null",
+    auto_unbox = TRUE
   )
   script_string <- c(
     "<script type=\"ojs-define\">",
diff --git a/src/resources/rmd/patch.R b/src/resources/rmd/patch.R
index addf5c8af0..1794293ec2 100644
--- a/src/resources/rmd/patch.R
+++ b/src/resources/rmd/patch.R
@@ -13,11 +13,12 @@ htmlPreserve <- function(x) {
   x <- paste(x, collapse = "\n")
   if (nzchar(x)) {
     # use fenced code block if there are embedded newlines
-    if (grepl("\n", x, fixed = TRUE))
+    if (grepl("\n", x, fixed = TRUE)) {
       sprintf("\n```{=html}\n%s\n```\n", x)
-    # otherwise use inline span
-    else
+    } else {
+      # otherwise use inline span
       sprintf("`%s`{=html}", x)
+    }
   } else {
     x
   }
@@ -27,7 +28,12 @@ assignInNamespace("htmlPreserve", htmlPreserve, ns = "htmltools")
 if (!knitr_has_yaml_chunk_options()) {
   # override parse_block to assign chunk labels from yaml options
   knitr_parse_block <- knitr:::parse_block
-  parse_block = function(code, header, params.src, markdown_mode = out_format('markdown')) {
+  parse_block = function(
+    code,
+    header,
+    params.src,
+    markdown_mode = out_format('markdown')
+  ) {
     originalParamsSrc <- params.src
     engine = sub('^([a-zA-Z0-9_]+).*$', '\\1', params.src)
     partitioned <- partition_yaml_options(engine, code)
@@ -37,42 +43,51 @@ if (!knitr_has_yaml_chunk_options()) {
     if (startsWith(params$label, unnamed_label)) {
       label <- partitioned$yaml[["label"]] %||% partitioned$yaml[["id"]]
       if (!is.null(label)) {
-        params.src <- sub("^[a-zA-Z0-9_]+ *[ ,]?", 
-                          paste0(engine, " ", label, ", "), 
-                          params.src)
+        params.src <- sub(
+          "^[a-zA-Z0-9_]+ *[ ,]?",
+          paste0(engine, " ", label, ", "),
+          params.src
+        )
       }
-    } 
-    
+    }
+
     # strip trailing comma and whitespace
     params.src <- sub("\\s*,?\\s*$", "", params.src)
-    
+
     # look for other options to forward. note that ideally we could extract *all*
     # parameters and then pass partitioned$code below, however we can construct
     # cases where deparsed versions of the options include a newline, which causes
     # an error. we'll wait and see if this capability is incorporated natively
     # into knitr parse_block -- if it's not then we can pursue more robust versions
-    # of textual option forwarding that don't run into newlines 
+    # of textual option forwarding that don't run into newlines
     extra_opts <- list()
     for (opt in c("ref.label", "ref-label")) {
       if (!is.null(partitioned$yaml[[opt]])) {
         value <- partitioned$yaml[[opt]]
         opt <- sub("-", ".", opt)
-        extra_opts[[opt]] <- paste(gsub("\n", " ", deparse(value, 
-                                                           width.cutoff = 500, 
-                                                           nlines = 1), fixed = TRUE), 
-                                   collapse = " ") 
+        extra_opts[[opt]] <- paste(
+          gsub(
+            "\n",
+            " ",
+            deparse(value, width.cutoff = 500, nlines = 1),
+            fixed = TRUE
+          ),
+          collapse = " "
+        )
       }
     }
     if (length(extra_opts) > 0) {
-      extra_opts <- paste(paste0(names(extra_opts), "=", as.character(extra_opts), ", "), 
-                          collapse = "")
+      extra_opts <- paste(
+        paste0(names(extra_opts), "=", as.character(extra_opts), ", "),
+        collapse = ""
+      )
       params.src <- paste0(params.src, ", ", sub(",\\s*$", "", extra_opts))
     }
-    
+
     # proceed
     block <- knitr_parse_block(code, header, params.src, markdown_mode)
     block[["params"]][["original.params.src"]] <- originalParamsSrc
-    block[["params"]][["chunk.echo"]] <- isTRUE(params[["echo"]]) || 
+    block[["params"]][["chunk.echo"]] <- isTRUE(params[["echo"]]) ||
       isTRUE(partitioned$yaml[["echo"]])
     block
   }
@@ -82,7 +97,6 @@ if (!knitr_has_yaml_chunk_options()) {
 # override wrapping behavior for knitr_asis output (including htmlwidgets)
 # to provide for enclosing output div and support for figure captions
 wrap_asis_output <- function(options, x) {
-
   # if the options are empty then this is inline output, return unmodified
   if (length(options) == 0) {
     return(x)
@@ -97,22 +111,24 @@ wrap_asis_output <- function(options, x) {
   }
   classes <- paste0("cell-output-display")
   attrs <- NULL
-  if (isTRUE(options[["output.hidden"]]))
-    classes <- paste0(classes, " .hidden")
+  if (isTRUE(options[["output.hidden"]])) classes <- paste0(classes, " .hidden")
 
   if (identical(options[["html-table-processing"]], "none")) {
     attrs <- paste(attrs, "html-table-processing=none")
   }
-  
+
   # if this is an html table then wrap it further in ```{=html}
   # (necessary b/c we no longer do this by overriding kable_html,
   # which is in turn necessary to allow kableExtra to parse
   # the return value of kable_html as valid xml)
-  if (grepl("^<\\w+[ >]", x) && grepl("<\\/\\w+>\\s*$", x) && 
-      !grepl('^<div class="kable-table">', x)) {
+  if (
+    grepl("^<\\w+[ >]", x) &&
+      grepl("<\\/\\w+>\\s*$", x) &&
+      !grepl('^<div class="kable-table">', x)
+  ) {
     x <- paste0("`````{=html}\n", x, "\n`````")
   }
-  
+
   # If asis output, don't include the output div
   if (identical(options[["results"]], "asis")) return(x)
 
@@ -128,14 +144,15 @@ add_html_caption <- function(options, x, ...) {
 }
 assignInNamespace("add_html_caption", add_html_caption, ns = "knitr")
 
-# wrap was renamed to sew in 1.32.8. 
+# wrap was renamed to sew in 1.32.8.
 if (utils::packageVersion("knitr") >= "1.32.8") {
   knitr_sew <- knitr:::sew
   sew <- function(x, options = list(), ...) {
-
     # some sew s3 methods take the default chunk options
-    if (missing(options) && 
-        inherits(x, c("knit_image_paths", "html_screenshot", "knit_embed_url"))) {
+    if (
+      missing(options) &&
+        inherits(x, c("knit_image_paths", "html_screenshot", "knit_embed_url"))
+    ) {
       options <- knitr::opts_chunk$get()
     }
 
@@ -144,7 +161,7 @@ if (utils::packageVersion("knitr") >= "1.32.8") {
     } else if (inherits(x, "knit_asis")) {
       # delegate
       is_html_widget <- inherits(x, "knit_asis_htmlwidget")
-      # knit_asis method checks on missing options which 
+      # knit_asis method checks on missing options which
       # it gets in knitr because UseMethod() is called in generic
       # but here we pass our default empty list options
       x <- if (missing(options)) {
@@ -160,9 +177,9 @@ if (utils::packageVersion("knitr") >= "1.32.8") {
       } else {
         wrap_asis_output(options, x)
       }
-    
-    # this used to be completely generic, however R 3.4 wasn't able to
-    # dispatch correctly via UseMethod so we do manual binding
+
+      # this used to be completely generic, however R 3.4 wasn't able to
+      # dispatch correctly via UseMethod so we do manual binding
     } else if (inherits(x, "character")) {
       knitr:::sew.character(x, options, ...)
     } else if (inherits(x, "html_screenshot")) {
@@ -189,11 +206,10 @@ if (utils::packageVersion("knitr") >= "1.32.8") {
       knitr_sew(x, options, ...)
     }
   }
-  assignInNamespace("sew", sew, ns = "knitr")  
+  assignInNamespace("sew", sew, ns = "knitr")
 } else {
   knitr_wrap <- knitr:::wrap
   wrap <- function(x, options = list(), ...) {
-    
     if (inherits(x, "knit_image_paths")) {
       knitr:::wrap.knit_image_paths(x, options, ...)
     } else if (inherits(x, "knit_asis")) {
@@ -208,9 +224,9 @@ if (utils::packageVersion("knitr") >= "1.32.8") {
       } else {
         wrap_asis_output(options, x)
       }
-    
-    # this used to be completely generic, however R 3.4 wasn't able to
-    # dispatch correctly via UseMethod so we do manual binding
+
+      # this used to be completely generic, however R 3.4 wasn't able to
+      # dispatch correctly via UseMethod so we do manual binding
     } else if (inherits(x, "character")) {
       knitr:::wrap.character(x, options, ...)
     } else if (inherits(x, "html_screenshot")) {
@@ -235,7 +251,7 @@ if (utils::packageVersion("knitr") >= "1.32.8") {
       knitr_wrap(x, options, ...)
     }
   }
-  assignInNamespace("wrap", wrap, ns = "knitr")  
+  assignInNamespace("wrap", wrap, ns = "knitr")
 }
 
 
@@ -251,7 +267,7 @@ kable_html <- function(...) {
 
 # kableExtra::kable_styling parses/post-processes the output of kable_html
 # as xml. e.g. see https://github.com/haozhu233/kableExtra/blob/a6af5c067c2b4ca8317736f4a3e6c0f7db508fef/R/kable_styling.R#L216
-# this means that we can't simply inject pandoc RawBlock delimiters into 
+# this means that we can't simply inject pandoc RawBlock delimiters into
 # the return value of kable_html, as it will cause the xml parser to fail,
 # e.g. see https://github.com/quarto-dev/quarto-cli/issues/75. As a result
 # we no longer do this processing (see commented out assignInNamespace below)
@@ -262,8 +278,6 @@ kable_html <- function(...) {
 
 # assignInNamespace("kable_html", kable_html, ns = "knitr")
 
-
-
 # patch knitr:::valid_path to remove # prefix and colons from file names
 knitr_valid_path <- knitr:::valid_path
 valid_path = function(prefix, label) {
@@ -278,10 +292,12 @@ assignInNamespace("valid_path", valid_path, ns = "knitr")
 # it was added in 1.46 but we need to support older version too
 # https://github.com/quarto-dev/quarto-cli/pull/7799
 # FIXME: can be cleaned when knitr 1.45 is considered too old
-if (knitr_has_yaml_chunk_options() && utils::packageVersion("knitr") <= "1.45") {
+if (
+  knitr_has_yaml_chunk_options() && utils::packageVersion("knitr") <= "1.45"
+) {
   knitr_comment_chars <- knitr:::comment_chars
   knitr_comment_chars$ojs <- "//"
   knitr_comment_chars$mermaid <- "%%"
   knitr_comment_chars$dot <- "//"
   assignInNamespace("comment_chars", knitr_comment_chars, ns = "knitr")
-}
\ No newline at end of file
+}
diff --git a/src/resources/rmd/rmd.R b/src/resources/rmd/rmd.R
index 726f6abfed..751a90f0e4 100755
--- a/src/resources/rmd/rmd.R
+++ b/src/resources/rmd/rmd.R
@@ -3,14 +3,14 @@
 
 # main
 .main <- function() {
-
   # execute knitr::spin
   spin <- function(input) {
-
     if (utils::packageVersion("knitr") < "1.44") {
       stop(
         "knitr >= 1.44 is required for rendering with Quarto from `.R` files. ",
-        "Please update knitr.", call. = FALSE)
+        "Please update knitr.",
+        call. = FALSE
+      )
     }
 
     # read file
@@ -18,37 +18,49 @@
 
     # spin and return
     knitr::spin(text = text, knit = FALSE, format = "qmd")
-
   }
 
   # dependencies (convert knit_meta to includes)
-  dependencies <- function(input, format, output, tempDir, libDir, data, quiet) {
-    
+  dependencies <- function(
+    input,
+    format,
+    output,
+    tempDir,
+    libDir,
+    data,
+    quiet
+  ) {
     # unserialize knit_meta
     knit_meta <- lapply(data, jsonlite::unserializeJSON)
 
     # determine files_dir
-    files_dir <- if (!is.null(libDir)) libDir else rmarkdown:::knitr_files_dir(output)
+    files_dir <- if (!is.null(libDir)) libDir else
+      rmarkdown:::knitr_files_dir(output)
 
     # yield pandoc format
     list(
-      includes = pandoc_includes(input, format, output, files_dir, knit_meta, tempDir)
+      includes = pandoc_includes(
+        input,
+        format,
+        output,
+        files_dir,
+        knit_meta,
+        tempDir
+      )
     )
   }
 
   # postprocess (restore preserved)
   postprocess <- function(input, format, output, preserved_chunks) {
-
     # check for html output
-    isHTML <-  knitr::is_html_output(
-      format$pandoc$to, 
+    isHTML <- knitr::is_html_output(
+      format$pandoc$to,
       c("markdown", "epub", "gfm", "commonmark", "commonmark_x", "markua")
     )
 
     # bail if we don't have any perserved chunks and aren't doing code linking
     code_link <- isHTML && isTRUE(format$render$`code-link`)
-    if (length(preserved_chunks) == 0 && code_link == FALSE)
-      return()
+    if (length(preserved_chunks) == 0 && code_link == FALSE) return()
 
     # change to input dir and make input relative
     oldwd <- setwd(dirname(rmarkdown:::abs_path(input)))
@@ -60,11 +72,11 @@
     if (!is.null(r_options)) {
       do.call(options, r_options)
     }
-    
+
     # read output and initialize output_res to no-op
     output_str <- xfun::read_utf8(output)
     output_res <- output_str
-    
+
     # perform code linking if requested
     if (isTRUE(code_link)) {
       has_annotations <- function(input) {
@@ -83,7 +95,7 @@
 
           # Update the chunk mapt to mark lines that are
           # within a code chunk
-            for (x in seq_along(chunkStarts)) {
+          for (x in seq_along(chunkStarts)) {
             start <- chunkStarts[x]
             end <- chunkEnds[x]
             for (y in start:end) {
@@ -105,23 +117,36 @@
       }
 
       if (!has_annotations(input)) {
-        if (requireNamespace("downlit", quietly = TRUE) && requireNamespace("xml2", quietly = TRUE)) {
+        if (
+          requireNamespace("downlit", quietly = TRUE) &&
+            requireNamespace("xml2", quietly = TRUE)
+        ) {
           # run downlit
           downlit::downlit_html_path(output, output)
 
           # fix xml2 induced whitespace problems that break revealjs columns
           # (b/c they depend on inline-block behavior) then reset output_res
           downlit_output <- paste(xfun::read_utf8(output), collapse = "\n")
-          downlit_output <- gsub('(</div>)\n(<div class="column")', "\\1\\2", downlit_output)
+          downlit_output <- gsub(
+            '(</div>)\n(<div class="column")',
+            "\\1\\2",
+            downlit_output
+          )
           output_res <- strsplit(downlit_output, "\n", fixed = TRUE)[[1]]
         } else {
-          warning("The downlit and xml2 packages are required for code linking", call. = FALSE)
+          warning(
+            "The downlit and xml2 packages are required for code linking",
+            call. = FALSE
+          )
         }
       } else {
-        warning("Since code annotations are present, code-linking has been disabled", call. = FALSE)
+        warning(
+          "Since code annotations are present, code-linking has been disabled",
+          call. = FALSE
+        )
       }
     }
-   
+
     # restore preserved chunks if requested
     if (length(preserved_chunks) > 0) {
       # convert preserved chunks to named character vector
@@ -129,38 +154,45 @@
       preserved_chunks <- as.character(preserved_chunks)
       names(preserved_chunks) <- names
 
-
       if (isHTML) {
         # Pandoc adds an empty <p></p> around the IDs of preserved chunks, and we
         # need to remove these empty tags, otherwise we may have invalid HTML like
         # <p><div>...</div></p>. For the reason of the second gsub(), see
         # https://github.com/rstudio/rmarkdown/issues/133.
         for (i in names(preserved_chunks)) {
-          output_res <- gsub(paste0("<p>", i, "</p>"), i, output_res,
-                            fixed = TRUE, useBytes = TRUE)
-          output_res <- gsub(paste0(' id="[^"]*?', i, '[^"]*?" '), ' ', output_res,
-                            useBytes = TRUE)
+          output_res <- gsub(
+            paste0("<p>", i, "</p>"),
+            i,
+            output_res,
+            fixed = TRUE,
+            useBytes = TRUE
+          )
+          output_res <- gsub(
+            paste0(' id="[^"]*?', i, '[^"]*?" '),
+            ' ',
+            output_res,
+            useBytes = TRUE
+          )
         }
-        output_res <- htmltools::restorePreserveChunks(output_res, preserved_chunks)
-
+        output_res <- htmltools::restorePreserveChunks(
+          output_res,
+          preserved_chunks
+        )
       } else {
-
         output_res <- knitr::restore_raw_output(output_str, preserved_chunks)
       }
     }
-    
+
     # re-write output if necessary
     if (!identical(output_str, output_res)) {
-      xfun::write_utf8(output_res, output)  
+      xfun::write_utf8(output_res, output)
     }
   }
 
   run <- function(input, port, host) {
     shiny_args <- list()
-    if (!is.null(port))
-      shiny_args$port <- port
-    if (!is.null(host))
-      shiny_args$host <- host
+    if (!is.null(port)) shiny_args$port <- port
+    if (!is.null(host)) shiny_args$host <- host
 
     # we already ran quarto render before the call to run
     Sys.setenv(RMARKDOWN_RUN_PRERENDER = "0")
@@ -193,31 +225,52 @@
 
   # print execute-debug message ("spin" and "run" don't pass format option)
   debug <- (!request$action %in% c("spin", "run")) &&
-            isTRUE(params$format$execute[["debug"]])
-  if (debug)
-    message("[knitr engine]: ", request$action)
+    isTRUE(params$format$execute[["debug"]])
+  if (debug) message("[knitr engine]: ", request$action)
 
   # dispatch request
   if (request$action == "spin") {
     result <- spin(params$input)
     result <- paste(result, collapse = '\n')
   } else if (request$action == "execute") {
-    result <- execute(params$input, params$format, params$tempDir,  params$libDir, params$dependencies, params$cwd, params$params, params$resourceDir, params$handledLanguages, params$markdown)
+    result <- execute(
+      params$input,
+      params$format,
+      params$tempDir,
+      params$libDir,
+      params$dependencies,
+      params$cwd,
+      params$params,
+      params$resourceDir,
+      params$handledLanguages,
+      params$markdown
+    )
   } else if (request$action == "dependencies") {
-    result <- dependencies(params$input, params$format, params$output, params$tempDir, params$libDir, params$dependencies, params$quiet)
+    result <- dependencies(
+      params$input,
+      params$format,
+      params$output,
+      params$tempDir,
+      params$libDir,
+      params$dependencies,
+      params$quiet
+    )
   } else if (request$action == "postprocess") {
-    result <- postprocess(params$input, params$format, params$output, params$preserve)
+    result <- postprocess(
+      params$input,
+      params$format,
+      params$output,
+      params$preserve
+    )
   } else if (request$action == "run") {
     result <- run(params$input, params$port, params$host)
   }
 
   # write results
-  if (debug)
-    message("[knitr engine]: writing results")
+  if (debug) message("[knitr engine]: writing results")
   resultJson <- jsonlite::toJSON(auto_unbox = TRUE, result)
   xfun:::write_utf8(paste(resultJson, collapse = "\n"), request[["results"]])
-  if (debug)
-    message("[knitr engine]: exiting")
+  if (debug) message("[knitr engine]: exiting")
 }
 
 if (!rmarkdown::pandoc_available(error = FALSE)) {
@@ -233,13 +286,3 @@ if (!rmarkdown::pandoc_available(error = FALSE)) {
 
 # run main
 .main()
-
-
-
-
-
-
-
-
-
-
diff --git a/tests/docs/knitr-spin.R b/tests/docs/knitr-spin.R
index 6f5f92761e..98b4285a59 100644
--- a/tests/docs/knitr-spin.R
+++ b/tests/docs/knitr-spin.R
@@ -4,7 +4,7 @@
 #' ---
 #'
 #' This is a report generated by `knitr::spin()`.
-#' 
+#'
 #' ## Code block {#block}
 #'
 #' Let's try some **knitr** options:
@@ -15,8 +15,11 @@
 plot(cars)
 
 #' ## Inline value {#inline}
-#' 
+#'
 #' Now write an inline value. We know the value of $\pi$ is
+# /*
+# fmt: skip
+# */
 {{ pi }}
 #' .
 #'
diff --git a/tests/docs/manuscript/qmd-full/notebook.qmd b/tests/docs/manuscript/qmd-full/notebook.qmd
index ac21e748c0..6677aa1b3c 100644
--- a/tests/docs/manuscript/qmd-full/notebook.qmd
+++ b/tests/docs/manuscript/qmd-full/notebook.qmd
@@ -18,7 +18,8 @@ df_ign <- df_ign |>
       `Depth(km)` >= 28 ~ "Deep (>28km)",
       `Depth(km)` >= 18 ~ "Interchange (18km>x>28km)",
       TRUE ~ "Shallow (< 18km)"
-    ))
+    )
+  )
 df_ign
 ```
 
@@ -27,14 +28,15 @@ df_ign
 #| label: epochs
 cut_times <- ymd_hms(c("2021-09-11", "2021-09-19 14:13:00", "2021-10-01", "2021-12-01", "2021-12-31", "2022-01-01"), truncated = 3)
 epochs <- tibble(
-  start = cut_times[-length(cut_times)], 
-  end = cut_times[-1], 
+  start = cut_times[-length(cut_times)],
+  end = cut_times[-1],
   label = c("pre", "early", "phase1", "phase2", "phase3"),
-  text = c('Pre\nEruptive\nSwarm', 
-           'Early Eruptive\nPhase',
-           'Main Eruptive Phase\n(sustained gas and lava ejection)', 
-           'Final Eruptive Phase\n(reducing gas and lava ejection)',
-            NA
+  text = c(
+    "Pre\nEruptive\nSwarm",
+    "Early Eruptive\nPhase",
+    "Main Eruptive Phase\n(sustained gas and lava ejection)",
+    "Final Eruptive Phase\n(reducing gas and lava ejection)",
+    NA
   )
 )
 ```
@@ -43,19 +45,22 @@ epochs <- tibble(
 ```{r}
 #| label: "erupt-data"
 mag_breaks <- c(0, 1, 2, 3, 4, 6)
-mag_labels <- c("0 < M <= 1","1 < M <= 2","2 < M <= 3","3 < M <= 4","M > 4")
+mag_labels <- c("0 < M <= 1", "1 < M <= 2", "2 < M <= 3", "3 < M <= 4", "M > 4")
 df_erupt <- df_ign |>
   filter(Date < as.Date("2022-01-01") & Date > as.Date("2021-09-11")) |>
-  mutate(Magnitude_categories = cut(Magnitude, 
-    breaks = mag_breaks, labels = mag_labels, right = FALSE))
+  mutate(Magnitude_categories = cut(Magnitude,
+    breaks = mag_breaks, labels = mag_labels, right = FALSE
+  ))
 ```
 
 
 ```{r}
 #| label: colors
-colors <- c("#1f77b4","#aec7e8","#ff7f0e","#ffbb78","#2ca02c","#98df8a",
-  "#d62728","#ff9896","#9467bd","#c5b0d5","#8c564b","#c49c94","#e377c2",
-  "#f7b6d2","#7f7f7f","#c7c7c7","#bcbd22","#dbdb8d","#17becf","#9edae5")
+colors <- c(
+  "#1f77b4", "#aec7e8", "#ff7f0e", "#ffbb78", "#2ca02c", "#98df8a",
+  "#d62728", "#ff9896", "#9467bd", "#c5b0d5", "#8c564b", "#c49c94", "#e377c2",
+  "#f7b6d2", "#7f7f7f", "#c7c7c7", "#bcbd22", "#dbdb8d", "#17becf", "#9edae5"
+)
 ```
 
 ```{r}
@@ -64,41 +69,55 @@ colors <- c("#1f77b4","#aec7e8","#ff7f0e","#ffbb78","#2ca02c","#98df8a",
 #| fig-width: 24
 #| fig-height: 12
 eruption <- ymd_hms("2021-09-19 14:13:00")
-date_axis_breaks <- as.Date("2021-10-15") + months(rep(0:2, each = 2)) - 
-      days(rep(c(14, 0), times = 3))
+date_axis_breaks <- as.Date("2021-10-15") + months(rep(0:2, each = 2)) -
+  days(rep(c(14, 0), times = 3))
 date_axis_breaks <- c(eruption, date_axis_breaks[-1])
 
 # Custom Magnitude Scale transform
 trans_mag <- scales::trans_new(
   name = "Magnitude transformation",
-  transform = \(x) 3*2^(1.3*x),
-  inverse = \(x) (1/1.3) * log2(x/3)
+  transform = \(x) 3 * 2^(1.3 * x),
+  inverse = \(x) (1 / 1.3) * log2(x / 3)
 )
 
-  
+
 df_erupt |>
-  arrange(Magnitude) |> 
-  ggplot(aes(DateTime, `Depth(km)`)) + 
-  geom_point(aes(fill = Magnitude_categories, size = Magnitude,
-    alpha = Magnitude_categories), shape = 21, color = "black") +
+  arrange(Magnitude) |>
+  ggplot(aes(DateTime, `Depth(km)`)) +
+  geom_point(aes(
+    fill = Magnitude_categories, size = Magnitude,
+    alpha = Magnitude_categories
+  ), shape = 21, color = "black") +
   geom_vline(xintercept = eruption, color = colors[7]) +
-  annotate("text", x = eruption, y = 20, label = "ERUPTION", 
-    color = colors[7], angle = 90, hjust = 1, vjust = -0.2, size = 6) +
-  annotate("rect", xmin = epochs$start, xmax = epochs$end,
-    ymin = -Inf, ymax = Inf, fill = colors[c(1, 3, 5, 7, 7)], alpha = 0.1) + 
-  annotate("text", x =  epochs$start + 0.5*(epochs$end - epochs$start), y = -4, 
-    label = epochs$text, color = colors[c(1, 3, 5, 7, NA)], size = 7) +
-  scale_y_continuous("Depth (km)", trans = scales::reverse_trans(), 
-    breaks = seq(0, 40, 10), limits = c( 45, -5), sec.axis = dup_axis()) +
-  scale_x_datetime("Eruption Timeline", expand = c(0, 0), 
-    date_labels = "%Y-%m-%d", breaks = date_axis_breaks) +
+  annotate("text",
+    x = eruption, y = 20, label = "ERUPTION",
+    color = colors[7], angle = 90, hjust = 1, vjust = -0.2, size = 6
+  ) +
+  annotate("rect",
+    xmin = epochs$start, xmax = epochs$end,
+    ymin = -Inf, ymax = Inf, fill = colors[c(1, 3, 5, 7, 7)], alpha = 0.1
+  ) +
+  annotate("text",
+    x = epochs$start + 0.5 * (epochs$end - epochs$start), y = -4,
+    label = epochs$text, color = colors[c(1, 3, 5, 7, NA)], size = 7
+  ) +
+  scale_y_continuous("Depth (km)",
+    trans = scales::reverse_trans(),
+    breaks = seq(0, 40, 10), limits = c(45, -5), sec.axis = dup_axis()
+  ) +
+  scale_x_datetime("Eruption Timeline",
+    expand = c(0, 0),
+    date_labels = "%Y-%m-%d", breaks = date_axis_breaks
+  ) +
   scale_fill_manual("Event Magnitude (M)", values = colors[c(13, 17, 5, 3, 7)]) +
   scale_alpha_manual("Event Magnitude (M)", values = c(0.3, 0.4, 0.5, 0.6, 0.8)) +
-  scale_size("Event Magnitude (M)", breaks = 1:5, labels = mag_labels, 
-    trans = trans_mag) +
-  theme_bw(base_size = 20, base_family = "Helvetica") + 
+  scale_size("Event Magnitude (M)",
+    breaks = 1:5, labels = mag_labels,
+    trans = trans_mag
+  ) +
+  theme_bw(base_size = 20, base_family = "Helvetica") +
   theme(
-    legend.position = c(0.01, 0.01), 
+    legend.position = c(0.01, 0.01),
     legend.justification = c("left", "bottom"),
     panel.grid.major.x = element_blank(),
     panel.grid.minor.x = element_blank(),
@@ -117,17 +136,18 @@ df_erupt |>
 #| fig-width: 8
 blue <- "#336699"
 
-p <- df_ign |> 
+p <- df_ign |>
   ggplot(aes(Magnitude, `Depth(km)`)) +
   geom_point(alpha = 0.6, color = blue) +
-  geom_density2d(color = blue, n = 100, h = c(1, 8), bins = 20) + 
+  geom_density2d(color = blue, n = 100, h = c(1, 8), bins = 20) +
   scale_y_continuous(trans = "reverse") +
-  coord_fixed(ratio = 1/8) +
-  labs(title = "Cumulative Events 01-01-2017 to 01-01-2022") + 
+  coord_fixed(ratio = 1 / 8) +
+  labs(title = "Cumulative Events 01-01-2017 to 01-01-2022") +
   theme_bw() +
   theme(
-    plot.title = element_text(hjust = 0.5, margin = margin(t = 20, b = 20))) 
-  
+    plot.title = element_text(hjust = 0.5, margin = margin(t = 20, b = 20))
+  )
+
 
 ggMarginal(p, type = "histogram", bins = 20, fill = blue, color = "white") 
 ```
diff --git a/tests/docs/manuscript/qmd-single/index.qmd b/tests/docs/manuscript/qmd-single/index.qmd
index 81f1102100..e5acd7a517 100644
--- a/tests/docs/manuscript/qmd-single/index.qmd
+++ b/tests/docs/manuscript/qmd-single/index.qmd
@@ -131,7 +131,8 @@ df_ign <- df_ign |>
       `Depth(km)` >= 28 ~ "Deep (>28km)",
       `Depth(km)` >= 18 ~ "Interchange (18km>x>28km)",
       TRUE ~ "Shallow (< 18km)"
-    ))
+    )
+  )
 df_ign
 ```
 
@@ -140,14 +141,15 @@ df_ign
 #| label: epochs
 cut_times <- ymd_hms(c("2021-09-11", "2021-09-19 14:13:00", "2021-10-01", "2021-12-01", "2021-12-31", "2022-01-01"), truncated = 3)
 epochs <- tibble(
-  start = cut_times[-length(cut_times)], 
-  end = cut_times[-1], 
+  start = cut_times[-length(cut_times)],
+  end = cut_times[-1],
   label = c("pre", "early", "phase1", "phase2", "phase3"),
-  text = c('Pre\nEruptive\nSwarm', 
-           'Early Eruptive\nPhase',
-           'Main Eruptive Phase\n(sustained gas and lava ejection)', 
-           'Final Eruptive Phase\n(reducing gas and lava ejection)',
-            NA
+  text = c(
+    "Pre\nEruptive\nSwarm",
+    "Early Eruptive\nPhase",
+    "Main Eruptive Phase\n(sustained gas and lava ejection)",
+    "Final Eruptive Phase\n(reducing gas and lava ejection)",
+    NA
   )
 )
 ```
@@ -156,19 +158,22 @@ epochs <- tibble(
 ```{r}
 #| label: "erupt-data"
 mag_breaks <- c(0, 1, 2, 3, 4, 6)
-mag_labels <- c("0 < M <= 1","1 < M <= 2","2 < M <= 3","3 < M <= 4","M > 4")
+mag_labels <- c("0 < M <= 1", "1 < M <= 2", "2 < M <= 3", "3 < M <= 4", "M > 4")
 df_erupt <- df_ign |>
   filter(Date < as.Date("2022-01-01") & Date > as.Date("2021-09-11")) |>
-  mutate(Magnitude_categories = cut(Magnitude, 
-    breaks = mag_breaks, labels = mag_labels, right = FALSE))
+  mutate(Magnitude_categories = cut(Magnitude,
+    breaks = mag_breaks, labels = mag_labels, right = FALSE
+  ))
 ```
 
 
 ```{r}
 #| label: colors
-colors <- c("#1f77b4","#aec7e8","#ff7f0e","#ffbb78","#2ca02c","#98df8a",
-  "#d62728","#ff9896","#9467bd","#c5b0d5","#8c564b","#c49c94","#e377c2",
-  "#f7b6d2","#7f7f7f","#c7c7c7","#bcbd22","#dbdb8d","#17becf","#9edae5")
+colors <- c(
+  "#1f77b4", "#aec7e8", "#ff7f0e", "#ffbb78", "#2ca02c", "#98df8a",
+  "#d62728", "#ff9896", "#9467bd", "#c5b0d5", "#8c564b", "#c49c94", "#e377c2",
+  "#f7b6d2", "#7f7f7f", "#c7c7c7", "#bcbd22", "#dbdb8d", "#17becf", "#9edae5"
+)
 ```
 
 
@@ -178,41 +183,55 @@ colors <- c("#1f77b4","#aec7e8","#ff7f0e","#ffbb78","#2ca02c","#98df8a",
 #| fig-width: 24
 #| fig-height: 12
 eruption <- ymd_hms("2021-09-19 14:13:00")
-date_axis_breaks <- as.Date("2021-10-15") + months(rep(0:2, each = 2)) - 
-      days(rep(c(14, 0), times = 3))
+date_axis_breaks <- as.Date("2021-10-15") + months(rep(0:2, each = 2)) -
+  days(rep(c(14, 0), times = 3))
 date_axis_breaks <- c(eruption, date_axis_breaks[-1])
 
 # Custom Magnitude Scale transform
 trans_mag <- scales::trans_new(
   name = "Magnitude transformation",
-  transform = \(x) 3*2^(1.3*x),
-  inverse = \(x) (1/1.3) * log2(x/3)
+  transform = \(x) 3 * 2^(1.3 * x),
+  inverse = \(x) (1 / 1.3) * log2(x / 3)
 )
 
-  
+
 df_erupt |>
-  arrange(Magnitude) |> 
-  ggplot(aes(DateTime, `Depth(km)`)) + 
-  geom_point(aes(fill = Magnitude_categories, size = Magnitude,
-    alpha = Magnitude_categories), shape = 21, color = "black") +
+  arrange(Magnitude) |>
+  ggplot(aes(DateTime, `Depth(km)`)) +
+  geom_point(aes(
+    fill = Magnitude_categories, size = Magnitude,
+    alpha = Magnitude_categories
+  ), shape = 21, color = "black") +
   geom_vline(xintercept = eruption, color = colors[7]) +
-  annotate("text", x = eruption, y = 20, label = "ERUPTION", 
-    color = colors[7], angle = 90, hjust = 1, vjust = -0.2, size = 6) +
-  annotate("rect", xmin = epochs$start, xmax = epochs$end,
-    ymin = -Inf, ymax = Inf, fill = colors[c(1, 3, 5, 7, 7)], alpha = 0.1) + 
-  annotate("text", x =  epochs$start + 0.5*(epochs$end - epochs$start), y = -4, 
-    label = epochs$text, color = colors[c(1, 3, 5, 7, NA)], size = 7) +
-  scale_y_continuous("Depth (km)", trans = scales::reverse_trans(), 
-    breaks = seq(0, 40, 10), limits = c( 45, -5), sec.axis = dup_axis()) +
-  scale_x_datetime("Eruption Timeline", expand = c(0, 0), 
-    date_labels = "%Y-%m-%d", breaks = date_axis_breaks) +
+  annotate("text",
+    x = eruption, y = 20, label = "ERUPTION",
+    color = colors[7], angle = 90, hjust = 1, vjust = -0.2, size = 6
+  ) +
+  annotate("rect",
+    xmin = epochs$start, xmax = epochs$end,
+    ymin = -Inf, ymax = Inf, fill = colors[c(1, 3, 5, 7, 7)], alpha = 0.1
+  ) +
+  annotate("text",
+    x = epochs$start + 0.5 * (epochs$end - epochs$start), y = -4,
+    label = epochs$text, color = colors[c(1, 3, 5, 7, NA)], size = 7
+  ) +
+  scale_y_continuous("Depth (km)",
+    trans = scales::reverse_trans(),
+    breaks = seq(0, 40, 10), limits = c(45, -5), sec.axis = dup_axis()
+  ) +
+  scale_x_datetime("Eruption Timeline",
+    expand = c(0, 0),
+    date_labels = "%Y-%m-%d", breaks = date_axis_breaks
+  ) +
   scale_fill_manual("Event Magnitude (M)", values = colors[c(13, 17, 5, 3, 7)]) +
   scale_alpha_manual("Event Magnitude (M)", values = c(0.3, 0.4, 0.5, 0.6, 0.8)) +
-  scale_size("Event Magnitude (M)", breaks = 1:5, labels = mag_labels, 
-    trans = trans_mag) +
-  theme_bw(base_size = 20, base_family = "Helvetica") + 
+  scale_size("Event Magnitude (M)",
+    breaks = 1:5, labels = mag_labels,
+    trans = trans_mag
+  ) +
+  theme_bw(base_size = 20, base_family = "Helvetica") +
   theme(
-    legend.position = c(0.01, 0.01), 
+    legend.position = c(0.01, 0.01),
     legend.justification = c("left", "bottom"),
     panel.grid.major.x = element_blank(),
     panel.grid.minor.x = element_blank(),
@@ -233,19 +252,20 @@ df_erupt |>
 #| fig-width: 8
 blue <- "#336699"
 
-p <- df_ign |> 
+p <- df_ign |>
   ggplot(aes(Magnitude, `Depth(km)`)) +
   geom_point(alpha = 0.6, color = blue) +
-  geom_density2d(color = blue, n = 100, h = c(1, 8), bins = 20) + 
+  geom_density2d(color = blue, n = 100, h = c(1, 8), bins = 20) +
   scale_y_continuous(trans = "reverse") +
-  coord_fixed(ratio = 1/8) +
-  labs(title = "Cumulative Events 01-01-2017 to 01-01-2022") + 
+  coord_fixed(ratio = 1 / 8) +
+  labs(title = "Cumulative Events 01-01-2017 to 01-01-2022") +
   theme_bw() +
   theme(
-    plot.title = element_text(hjust = 0.5, margin = margin(t = 20, b = 20))) 
-  
+    plot.title = element_text(hjust = 0.5, margin = margin(t = 20, b = 20))
+  )
+
 
-ggMarginal(p, type = "histogram", bins = 20, fill = blue, color = "white") 
+ggMarginal(p, type = "histogram", bins = 20, fill = blue, color = "white")
 ```
 
 # Results
diff --git a/tests/docs/ojs/test-dependency-traversal-2.qmd b/tests/docs/ojs/test-dependency-traversal-2.qmd
index 6f0286f16b..e1ac9e0709 100644
--- a/tests/docs/ojs/test-dependency-traversal-2.qmd
+++ b/tests/docs/ojs/test-dependency-traversal-2.qmd
@@ -4,7 +4,7 @@ format: html
 ---
 
 ```{r}
-print(c(1,2,3))
+print(c(1, 2, 3))
 ```
 
 ```{ojs}
diff --git a/tests/docs/page-layout/tufte-html.qmd b/tests/docs/page-layout/tufte-html.qmd
index fcb90245c4..0ab5214d66 100644
--- a/tests/docs/page-layout/tufte-html.qmd
+++ b/tests/docs/page-layout/tufte-html.qmd
@@ -140,7 +140,8 @@ You can use the `kable()` function from the **knitr** package to format tables t
 ```{r}
 #| tbl-cap-location: margin
 knitr::kable(
-  mtcars[1:6, 1:6], caption = 'A subset of mtcars.'
+  mtcars[1:6, 1:6],
+  caption = "A subset of mtcars."
 )
 ```
 
@@ -188,7 +189,7 @@ Then two plots from the same code chunk placed in different figure environments:
 
 ```{r}
 #| echo: false
-knitr::kable(head(iris[,c(1,2,3,4)], 15))
+knitr::kable(head(iris[, c(1, 2, 3, 4)], 15))
 ```
 
 ```{r}
@@ -205,7 +206,7 @@ plot(iris)
 
 ```{r}
 #| echo: false
-knitr::kable(head(iris[,c(1,2,3,4)], 12))
+knitr::kable(head(iris[, c(1, 2, 3, 4)], 12))
 ```
 
 We blended some tables in the above code chunk only as _placeholders_ to make sure there is enough vertical space among the margin figures, otherwise they will be stacked tightly together. For a practical document, you should not insert too many margin figures consecutively and make the margin crowded.
diff --git a/tests/docs/page-layout/tufte-pdf.qmd b/tests/docs/page-layout/tufte-pdf.qmd
index 4403cc36a7..23712bb176 100644
--- a/tests/docs/page-layout/tufte-pdf.qmd
+++ b/tests/docs/page-layout/tufte-pdf.qmd
@@ -140,7 +140,8 @@ You can use the `kable()` function from the **knitr** package to format tables t
 ```{r}
 #| tbl-cap-location: margin
 knitr::kable(
-  mtcars[1:6, 1:6], caption = 'A subset of mtcars.'
+  mtcars[1:6, 1:6],
+  caption = "A subset of mtcars."
 )
 ```
 
@@ -188,7 +189,7 @@ Then two plots from the same code chunk placed in different figure environments:
 
 ```{r}
 #| echo: false
-knitr::kable(head(iris[,c(1,2,3,4)], 15))
+knitr::kable(head(iris[, c(1, 2, 3, 4)], 15))
 ```
 
 ```{r}
@@ -205,7 +206,7 @@ plot(iris)
 
 ```{r}
 #| echo: false
-knitr::kable(head(iris[,c(1,2,3,4)], 12))
+knitr::kable(head(iris[, c(1, 2, 3, 4)], 12))
 ```
 
 We blended some tables in the above code chunk only as _placeholders_ to make sure there is enough vertical space among the margin figures, otherwise they will be stacked tightly together. For a practical document, you should not insert too many margin figures consecutively and make the margin crowded.
diff --git a/tests/docs/playwright/html/dark-brand/brand-after-theme.qmd b/tests/docs/playwright/html/dark-brand/brand-after-theme.qmd
index 258a5b610e..65f7d610bf 100644
--- a/tests/docs/playwright/html/dark-brand/brand-after-theme.qmd
+++ b/tests/docs/playwright/html/dark-brand/brand-after-theme.qmd
@@ -18,19 +18,19 @@ library(ggplot2)
 
 ggplot_theme <- function(bgcolor, fgcolor) {
   theme_minimal(base_size = 11) %+%
-  theme(
-    panel.border = element_blank(),
-    panel.grid.major.y = element_blank(),
-    panel.grid.minor.y = element_blank(),
-    panel.grid.major.x = element_blank(),
-    panel.grid.minor.x = element_blank(),
-    text = element_text(colour = fgcolor),
-    axis.text = element_text(colour = fgcolor),
-    rect = element_rect(colour = bgcolor, fill = bgcolor),
-    plot.background = element_rect(fill = bgcolor, colour = NA),
-    axis.line = element_line(colour = fgcolor),
-    axis.ticks = element_line(colour = fgcolor)
-  )
+    theme(
+      panel.border = element_blank(),
+      panel.grid.major.y = element_blank(),
+      panel.grid.minor.y = element_blank(),
+      panel.grid.major.x = element_blank(),
+      panel.grid.minor.x = element_blank(),
+      text = element_text(colour = fgcolor),
+      axis.text = element_text(colour = fgcolor),
+      rect = element_rect(colour = bgcolor, fill = bgcolor),
+      plot.background = element_rect(fill = bgcolor, colour = NA),
+      axis.line = element_line(colour = fgcolor),
+      axis.ticks = element_line(colour = fgcolor)
+    )
 }
 
 brand_ggplot <- function(brand_yml) {
@@ -48,7 +48,11 @@ colour_scale <- scale_colour_manual(values = c("darkorange", "purple", "cyan4"))
 ```{r}
 #| renderings: [light, dark]
 ggplot(mtcars, aes(mpg, wt)) +
-  geom_point(aes(colour = factor(cyl))) + blue_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  blue_theme +
+  colour_scale
 ggplot(mtcars, aes(mpg, wt)) +
-  geom_point(aes(colour = factor(cyl))) + red_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  red_theme +
+  colour_scale
 ```
diff --git a/tests/docs/playwright/html/dark-brand/brand-before-theme.qmd b/tests/docs/playwright/html/dark-brand/brand-before-theme.qmd
index 9efb99a753..6909504219 100644
--- a/tests/docs/playwright/html/dark-brand/brand-before-theme.qmd
+++ b/tests/docs/playwright/html/dark-brand/brand-before-theme.qmd
@@ -18,19 +18,19 @@ library(ggplot2)
 
 ggplot_theme <- function(bgcolor, fgcolor) {
   theme_minimal(base_size = 11) %+%
-  theme(
-    panel.border = element_blank(),
-    panel.grid.major.y = element_blank(),
-    panel.grid.minor.y = element_blank(),
-    panel.grid.major.x = element_blank(),
-    panel.grid.minor.x = element_blank(),
-    text = element_text(colour = fgcolor),
-    axis.text = element_text(colour = fgcolor),
-    rect = element_rect(colour = bgcolor, fill = bgcolor),
-    plot.background = element_rect(fill = bgcolor, colour = NA),
-    axis.line = element_line(colour = fgcolor),
-    axis.ticks = element_line(colour = fgcolor)
-  )
+    theme(
+      panel.border = element_blank(),
+      panel.grid.major.y = element_blank(),
+      panel.grid.minor.y = element_blank(),
+      panel.grid.major.x = element_blank(),
+      panel.grid.minor.x = element_blank(),
+      text = element_text(colour = fgcolor),
+      axis.text = element_text(colour = fgcolor),
+      rect = element_rect(colour = bgcolor, fill = bgcolor),
+      plot.background = element_rect(fill = bgcolor, colour = NA),
+      axis.line = element_line(colour = fgcolor),
+      axis.ticks = element_line(colour = fgcolor)
+    )
 }
 
 brand_ggplot <- function(brand_yml) {
@@ -48,7 +48,11 @@ colour_scale <- scale_colour_manual(values = c("darkorange", "purple", "cyan4"))
 ```{r}
 #| renderings: [light, dark]
 ggplot(mtcars, aes(mpg, wt)) +
-  geom_point(aes(colour = factor(cyl))) + blue_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  blue_theme +
+  colour_scale
 ggplot(mtcars, aes(mpg, wt)) +
-  geom_point(aes(colour = factor(cyl))) + red_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  red_theme +
+  colour_scale
 ```
diff --git a/tests/docs/playwright/html/dark-brand/project-light-dark/brand-false.qmd b/tests/docs/playwright/html/dark-brand/project-light-dark/brand-false.qmd
index ee2207d47c..2b46d0cf3e 100644
--- a/tests/docs/playwright/html/dark-brand/project-light-dark/brand-false.qmd
+++ b/tests/docs/playwright/html/dark-brand/project-light-dark/brand-false.qmd
@@ -13,19 +13,19 @@ library(ggplot2)
 
 ggplot_theme <- function(bgcolor, fgcolor) {
   theme_minimal(base_size = 11) %+%
-  theme(
-    panel.border = element_blank(),
-    panel.grid.major.y = element_blank(),
-    panel.grid.minor.y = element_blank(),
-    panel.grid.major.x = element_blank(),
-    panel.grid.minor.x = element_blank(),
-    text = element_text(colour = fgcolor),
-    axis.text = element_text(colour = fgcolor),
-    rect = element_rect(colour = bgcolor, fill = bgcolor),
-    plot.background = element_rect(fill = bgcolor, colour = NA),
-    axis.line = element_line(colour = fgcolor),
-    axis.ticks = element_line(colour = fgcolor)
-  )
+    theme(
+      panel.border = element_blank(),
+      panel.grid.major.y = element_blank(),
+      panel.grid.minor.y = element_blank(),
+      panel.grid.major.x = element_blank(),
+      panel.grid.minor.x = element_blank(),
+      text = element_text(colour = fgcolor),
+      axis.text = element_text(colour = fgcolor),
+      rect = element_rect(colour = bgcolor, fill = bgcolor),
+      plot.background = element_rect(fill = bgcolor, colour = NA),
+      axis.line = element_line(colour = fgcolor),
+      axis.ticks = element_line(colour = fgcolor)
+    )
 }
 
 brand_ggplot <- function(brand_yml) {
@@ -43,7 +43,11 @@ colour_scale <- scale_colour_manual(values = c("darkorange", "purple", "cyan4"))
 ```{r}
 #| renderings: [light, dark]
 ggplot(mtcars, aes(mpg, wt)) +
-  geom_point(aes(colour = factor(cyl))) + blue_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  blue_theme +
+  colour_scale
 ggplot(mtcars, aes(mpg, wt)) +
-  geom_point(aes(colour = factor(cyl))) + red_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  red_theme +
+  colour_scale
 ```
diff --git a/tests/docs/playwright/html/dark-brand/project-light-dark/brand-under-theme.qmd b/tests/docs/playwright/html/dark-brand/project-light-dark/brand-under-theme.qmd
index a71696e631..caf298f1e2 100644
--- a/tests/docs/playwright/html/dark-brand/project-light-dark/brand-under-theme.qmd
+++ b/tests/docs/playwright/html/dark-brand/project-light-dark/brand-under-theme.qmd
@@ -15,19 +15,19 @@ library(ggplot2)
 
 ggplot_theme <- function(bgcolor, fgcolor) {
   theme_minimal(base_size = 11) %+%
-  theme(
-    panel.border = element_blank(),
-    panel.grid.major.y = element_blank(),
-    panel.grid.minor.y = element_blank(),
-    panel.grid.major.x = element_blank(),
-    panel.grid.minor.x = element_blank(),
-    text = element_text(colour = fgcolor),
-    axis.text = element_text(colour = fgcolor),
-    rect = element_rect(colour = bgcolor, fill = bgcolor),
-    plot.background = element_rect(fill = bgcolor, colour = NA),
-    axis.line = element_line(colour = fgcolor),
-    axis.ticks = element_line(colour = fgcolor)
-  )
+    theme(
+      panel.border = element_blank(),
+      panel.grid.major.y = element_blank(),
+      panel.grid.minor.y = element_blank(),
+      panel.grid.major.x = element_blank(),
+      panel.grid.minor.x = element_blank(),
+      text = element_text(colour = fgcolor),
+      axis.text = element_text(colour = fgcolor),
+      rect = element_rect(colour = bgcolor, fill = bgcolor),
+      plot.background = element_rect(fill = bgcolor, colour = NA),
+      axis.line = element_line(colour = fgcolor),
+      axis.ticks = element_line(colour = fgcolor)
+    )
 }
 
 brand_ggplot <- function(brand_yml) {
@@ -45,7 +45,11 @@ colour_scale <- scale_colour_manual(values = c("darkorange", "purple", "cyan4"))
 ```{r}
 #| renderings: [light, dark]
 ggplot(mtcars, aes(mpg, wt)) +
-  geom_point(aes(colour = factor(cyl))) + blue_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  blue_theme +
+  colour_scale
 ggplot(mtcars, aes(mpg, wt)) +
-  geom_point(aes(colour = factor(cyl))) + red_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  red_theme +
+  colour_scale
 ```
diff --git a/tests/docs/playwright/html/dark-brand/project-light-dark/simple.qmd b/tests/docs/playwright/html/dark-brand/project-light-dark/simple.qmd
index b626d1f663..ff402f3ee3 100644
--- a/tests/docs/playwright/html/dark-brand/project-light-dark/simple.qmd
+++ b/tests/docs/playwright/html/dark-brand/project-light-dark/simple.qmd
@@ -12,19 +12,19 @@ library(ggplot2)
 
 ggplot_theme <- function(bgcolor, fgcolor) {
   theme_minimal(base_size = 11) %+%
-  theme(
-    panel.border = element_blank(),
-    panel.grid.major.y = element_blank(),
-    panel.grid.minor.y = element_blank(),
-    panel.grid.major.x = element_blank(),
-    panel.grid.minor.x = element_blank(),
-    text = element_text(colour = fgcolor),
-    axis.text = element_text(colour = fgcolor),
-    rect = element_rect(colour = bgcolor, fill = bgcolor),
-    plot.background = element_rect(fill = bgcolor, colour = NA),
-    axis.line = element_line(colour = fgcolor),
-    axis.ticks = element_line(colour = fgcolor)
-  )
+    theme(
+      panel.border = element_blank(),
+      panel.grid.major.y = element_blank(),
+      panel.grid.minor.y = element_blank(),
+      panel.grid.major.x = element_blank(),
+      panel.grid.minor.x = element_blank(),
+      text = element_text(colour = fgcolor),
+      axis.text = element_text(colour = fgcolor),
+      rect = element_rect(colour = bgcolor, fill = bgcolor),
+      plot.background = element_rect(fill = bgcolor, colour = NA),
+      axis.line = element_line(colour = fgcolor),
+      axis.ticks = element_line(colour = fgcolor)
+    )
 }
 
 brand_ggplot <- function(brand_yml) {
@@ -42,7 +42,11 @@ colour_scale <- scale_colour_manual(values = c("darkorange", "purple", "cyan4"))
 ```{r}
 #| renderings: [light, dark]
 ggplot(mtcars, aes(mpg, wt)) +
-  geom_point(aes(colour = factor(cyl))) + blue_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  blue_theme +
+  colour_scale
 ggplot(mtcars, aes(mpg, wt)) +
-  geom_point(aes(colour = factor(cyl))) + red_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  red_theme +
+  colour_scale
 ```
diff --git a/tests/docs/reveal/stretch.qmd b/tests/docs/reveal/stretch.qmd
index 504b1629dc..d139604dbd 100644
--- a/tests/docs/reveal/stretch.qmd
+++ b/tests/docs/reveal/stretch.qmd
@@ -18,7 +18,7 @@ Without stretch feature
 ![revealjs logo](https://revealjs.com/images/logo/reveal-black-text.svg)
 
 ```{r, echo = TRUE}
-1 + 1 
+1 + 1
 ```
 
 ## Insert an image with no caption {#no-caption}
diff --git a/tests/docs/smoke-all/2022/11/22/annote/test.qmd b/tests/docs/smoke-all/2022/11/22/annote/test.qmd
index aa7964600f..271d5ab44e 100644
--- a/tests/docs/smoke-all/2022/11/22/annote/test.qmd
+++ b/tests/docs/smoke-all/2022/11/22/annote/test.qmd
@@ -12,23 +12,27 @@ format: html
 #| warning: false
 #| fig-cap: Bro this chart is fire and is definitely not sus.
 library(ggplot2)
-theme_set(theme_bw())  
+theme_set(theme_bw())
 
 data("mtcars")
-mtcars$`car name` <- rownames(mtcars)  # <2>
-mtcars$mpg_z <- round((mtcars$mpg - mean(mtcars$mpg))/sd(mtcars$mpg), 2)  # <3>
-mtcars$mpg_type <- ifelse(mtcars$mpg_z < 0, "below", "above")  # <4>
-mtcars <- mtcars[order(mtcars$mpg_z), ]  # <5>
-mtcars$`car name` <- factor(mtcars$`car name`, levels = mtcars$`car name`)  # <6>
+mtcars$`car name` <- rownames(mtcars) # <2>
+mtcars$mpg_z <- round((mtcars$mpg - mean(mtcars$mpg)) / sd(mtcars$mpg), 2) # <3>
+mtcars$mpg_type <- ifelse(mtcars$mpg_z < 0, "below", "above") # <4>
+mtcars <- mtcars[order(mtcars$mpg_z), ] # <5>
+mtcars$`car name` <- factor(mtcars$`car name`, levels = mtcars$`car name`) # <6>
 
-ggplot(mtcars, aes(x=`car name`, y=mpg_z, label=mpg_z)) + # <7> 
-  geom_bar(stat='identity', aes(fill=mpg_type), width=.5)  + # <7> 
-  scale_fill_manual(name="Mileage", # <7> 
-                    labels = c("Above Average", "Below Average"), # <7> 
-                    values = c("above"="#00ba38", "below"="#f8766d")) + # <7> 
-  labs(subtitle="Normalised mileage from 'mtcars'", # <7> 
-       title= "Diverging Bars") + # <7> 
-  coord_flip() # <7> 
+ggplot(mtcars, aes(x = `car name`, y = mpg_z, label = mpg_z)) + # <7>
+  geom_bar(stat = "identity", aes(fill = mpg_type), width = .5) + # <7>
+  scale_fill_manual(
+    name = "Mileage", # <7>
+    labels = c("Above Average", "Below Average"), # <7>
+    values = c("above" = "#00ba38", "below" = "#f8766d") # <7>
+  ) +
+  labs(
+    subtitle = "Normalised mileage from 'mtcars'", # <7>
+    title = "Diverging Bars" # <7>
+  ) +
+  coord_flip() # <7>
 ```
 
 
diff --git a/tests/docs/smoke-all/2022/12/12/code-annotation.qmd b/tests/docs/smoke-all/2022/12/12/code-annotation.qmd
index 3ff128b159..43575b81d7 100644
--- a/tests/docs/smoke-all/2022/12/12/code-annotation.qmd
+++ b/tests/docs/smoke-all/2022/12/12/code-annotation.qmd
@@ -15,24 +15,28 @@ keep-tex: true
 #| warning: false
 #| fig-cap: Bro this chart is fire and is definitely not sus.
 library(ggplot2)
-theme_set(theme_bw())  
+theme_set(theme_bw())
 
 
 data("mtcars")
-mtcars$`car name` <- rownames(mtcars)                  # <1>
-mtcars$mpg_z <- round((mtcars$mpg-mean(mtcars$mpg))/sd(mtcars$mpg),2) # <2>
+mtcars$`car name` <- rownames(mtcars) # <1>
+mtcars$mpg_z <- round((mtcars$mpg - mean(mtcars$mpg)) / sd(mtcars$mpg), 2) # <2>
 mtcars$mpg_type <- ifelse(mtcars$mpg_z < 0, "below", "above") # <3>
 mtcars <- mtcars[order(mtcars$mpg_z), ] # <4>
-mtcars$`name` <- factor(mtcars$`car name`, levels = mtcars$`car name`)              # <5>
+mtcars$`name` <- factor(mtcars$`car name`, levels = mtcars$`car name`) # <5>
 
-ggplot(mtcars, aes(x=`name`, y=mpg_z, label=mpg_z)) + # <6> 
-  geom_bar(stat='identity', aes(fill=mpg_type), width=.5)  + # <7> 
-  scale_fill_manual(name="Mileage", # <7> 
-                    labels = c("Above Average", "Below Average"), # <7> 
-                    values = c("above"="#00ba38", "below"="#f8766d")) + 
-  labs(subtitle="Normalised mileage from 'mtcars'", # <7> 
-       title= "Diverging Bars") + # <7> 
-  coord_flip() # <8> 
+ggplot(mtcars, aes(x = `name`, y = mpg_z, label = mpg_z)) + # <6>
+  geom_bar(stat = "identity", aes(fill = mpg_type), width = .5) + # <7>
+  scale_fill_manual(
+    name = "Mileage", # <7>
+    labels = c("Above Average", "Below Average"), # <7>
+    values = c("above" = "#00ba38", "below" = "#f8766d") # <7>
+  ) +
+  labs(
+    subtitle = "Normalised mileage from 'mtcars'", # <7>
+    title = "Diverging Bars" # <7>
+  ) +
+  coord_flip() # <8>
 ```
 
 1. `mtcars` is a built in data set that we'll use for the purposes of making this plot. For more about built in data sets in R, see <https://vincentarelbundock.github.io/Rdatasets/>
@@ -50,24 +54,28 @@ ggplot(mtcars, aes(x=`name`, y=mpg_z, label=mpg_z)) + # <6>
 #| warning: false
 #| fig-cap: Bro this chart is fire and is definitely not sus.
 library(ggplot2)
-theme_set(theme_bw())  
+theme_set(theme_bw())
 
 
 data("mtcars")
 mtcars$`car name` <- rownames(mtcars) # <1>
-mtcars$mpg_z <- round((mtcars$mpg - mean(mtcars$mpg))/sd(mtcars$mpg), 2) # <2>
+mtcars$mpg_z <- round((mtcars$mpg - mean(mtcars$mpg)) / sd(mtcars$mpg), 2) # <2>
 mtcars$mpg_type <- ifelse(mtcars$mpg_z < 0, "below", "above") # <3>
 mtcars <- mtcars[order(mtcars$mpg_z), ] # <4>
 mtcars$`car name` <- factor(mtcars$`car name`, levels = mtcars$`car name`) # <5>
 
-ggplot(mtcars, aes(x=`car name`, y=mpg_z, label=mpg_z)) + # <6> 
-  geom_bar(stat='identity', aes(fill=mpg_type), width=.5)  + # <7> 
-  scale_fill_manual(name="Mileage", # <7> 
-                    labels = c("Above Average", "Below Average"), # <7> 
-                    values = c("above"="#00ba38", "below"="#f8766d")) + 
-  labs(subtitle="Normalised mileage from 'mtcars'", # <7> 
-       title= "Diverging Bars") + # <7> 
-  coord_flip() # <8> 
+ggplot(mtcars, aes(x = `car name`, y = mpg_z, label = mpg_z)) + # <6>
+  geom_bar(stat = "identity", aes(fill = mpg_type), width = .5) + # <7>
+  scale_fill_manual(
+    name = "Mileage", # <7>
+    labels = c("Above Average", "Below Average"), # <7>
+    values = c("above" = "#00ba38", "below" = "#f8766d") # <7>
+  ) +
+  labs(
+    subtitle = "Normalised mileage from 'mtcars'", # <7>
+    title = "Diverging Bars" # <7>
+  ) + 
+  coord_flip() # <8>
 ```
 
 1. Item 1
diff --git a/tests/docs/smoke-all/2022/12/9/jats/example.qmd b/tests/docs/smoke-all/2022/12/9/jats/example.qmd
index fbde333b4a..9f296add79 100644
--- a/tests/docs/smoke-all/2022/12/9/jats/example.qmd
+++ b/tests/docs/smoke-all/2022/12/9/jats/example.qmd
@@ -163,7 +163,7 @@ In vel luctus ligula, sit amet tincidunt ex. Aliquam erat volutpat. Nullam lacus
 #| label: tbl-stuff
 #| tbl-cap: A table of car related activities.
 #| warning: false
-library('gt')
+library("gt")
 knitr::kable(head(mtcars))
 ```
 
diff --git a/tests/docs/smoke-all/2023/01/03/code-annote-simple.qmd b/tests/docs/smoke-all/2023/01/03/code-annote-simple.qmd
index 032f9fd9a1..7b3fd7bcc4 100644
--- a/tests/docs/smoke-all/2023/01/03/code-annote-simple.qmd
+++ b/tests/docs/smoke-all/2023/01/03/code-annote-simple.qmd
@@ -26,7 +26,8 @@ _quarto:
 #| label: fig-air
 #| fig-cap: "Air Quality"
 library(ggplot2) # <1>
-ggplot(airquality, aes(Temp, Ozone)) + geom_point() + # <2> 
+ggplot(airquality, aes(Temp, Ozone)) + # <2>
+  geom_point() + # <2>
   geom_smooth(method = "loess", se = FALSE) # <2>
 ```
 
diff --git a/tests/docs/smoke-all/2023/01/05/notebook-preview-complex.qmd b/tests/docs/smoke-all/2023/01/05/notebook-preview-complex.qmd
index 6c5cd0b541..b7eaae6856 100644
--- a/tests/docs/smoke-all/2023/01/05/notebook-preview-complex.qmd
+++ b/tests/docs/smoke-all/2023/01/05/notebook-preview-complex.qmd
@@ -38,17 +38,17 @@ _quarto:
 ## Sample Code. Cool!
 
 ```{r}
-num = 47
-factorial = 1
-if(num < 0) { # <2>
+num <- 47
+factorial <- 1
+if (num < 0) { # <2>
   print("Sorry, factorial does not exist for negative numbers")
-} else if(num == 0) {
+} else if (num == 0) {
   print("The factorial of 0 is 1")
 } else {
-  for(i in 1:num) {             # <3>
-    factorial = factorial * i   # <3>
-  }                             # <3>
-  print(paste("The factorial of", num ,"is",format(factorial)))
+  for (i in 1:num) { # <3>
+    factorial <- factorial * i # <3>
+  } # <3>
+  print(paste("The factorial of", num, "is", format(factorial)))
 }
 ```
 
@@ -65,17 +65,17 @@ Also, see the figure below, which shows something cool.
 3. foo
 
 ```{r}
-num = 47
-factorial = 1
-if(num < 0) { # <2>
+num <- 47
+factorial <- 1
+if (num < 0) { # <2>
   print("Sorry, factorial does not exist for negative numbers")
-} else if(num == 0) {
+} else if (num == 0) {
   print("The factorial of 0 is 1")
 } else {
-  for(i in 1:num) {             # <3>
-    factorial = factorial * i   # <3>
-  }                             # <3>
-  print(paste("The factorial of", num ,"is",format(factorial)))
+  for (i in 1:num) { # <3>
+    factorial <- factorial * i # <3>
+  } # <3>
+  print(paste("The factorial of", num, "is", format(factorial)))
 }
 ```
 
diff --git a/tests/docs/smoke-all/2023/01/05/notebook-preview-simple.qmd b/tests/docs/smoke-all/2023/01/05/notebook-preview-simple.qmd
index 911fdd8e3c..341ac8d638 100644
--- a/tests/docs/smoke-all/2023/01/05/notebook-preview-simple.qmd
+++ b/tests/docs/smoke-all/2023/01/05/notebook-preview-simple.qmd
@@ -36,17 +36,17 @@ _quarto:
 ## Sample Code. Cool!
 
 ```{r}
-num = 47
-factorial = 1
-if(num < 0) { # <2>
+num <- 47
+factorial <- 1
+if (num < 0) { # <2>
   print("Sorry, factorial does not exist for negative numbers")
-} else if(num == 0) {
+} else if (num == 0) {
   print("The factorial of 0 is 1")
 } else {
-  for(i in 1:num) {             # <3>
-    factorial = factorial * i   # <3>
-  }                             # <3>
-  print(paste("The factorial of", num ,"is",format(factorial)))
+  for (i in 1:num) { # <3>
+    factorial <- factorial * i # <3>
+  } # <3>
+  print(paste("The factorial of", num, "is", format(factorial)))
 }
 ```
 
@@ -63,17 +63,17 @@ Also, see the figure below, which shows something cool.
 3. foo
 
 ```{r}
-num = 47
-factorial = 1
-if(num < 0) { # <2>
+num <- 47
+factorial <- 1
+if (num < 0) { # <2>
   print("Sorry, factorial does not exist for negative numbers")
-} else if(num == 0) {
+} else if (num == 0) {
   print("The factorial of 0 is 1")
 } else {
-  for(i in 1:num) {             # <3>
-    factorial = factorial * i   # <3>
-  }                             # <3>
-  print(paste("The factorial of", num ,"is",format(factorial)))
+  for (i in 1:num) { # <3>
+    factorial <- factorial * i # <3>
+  } # <3>
+  print(paste("The factorial of", num, "is", format(factorial)))
 }
 ```
 
diff --git a/tests/docs/smoke-all/2023/01/26/4034.qmd b/tests/docs/smoke-all/2023/01/26/4034.qmd
index 6d350ebc99..66fdb1a202 100644
--- a/tests/docs/smoke-all/2023/01/26/4034.qmd
+++ b/tests/docs/smoke-all/2023/01/26/4034.qmd
@@ -14,6 +14,6 @@ _quarto:
 #| warning: false
 #| message: false
 #| output: false
-z=3+4
+z <- 3 + 4
 z
 ```
diff --git a/tests/docs/smoke-all/2023/02/25/issue-4316.qmd b/tests/docs/smoke-all/2023/02/25/issue-4316.qmd
index 89a60f28a6..e44039c911 100644
--- a/tests/docs/smoke-all/2023/02/25/issue-4316.qmd
+++ b/tests/docs/smoke-all/2023/02/25/issue-4316.qmd
@@ -19,15 +19,16 @@ library(gt)
 #| label: tbl-test
 dat <- data.frame(
   a = c("A", "B"),
-  x = c(1, 2), 
-  y = c(12, 9), 
-  z = c(13, 11))
+  x = c(1, 2),
+  y = c(12, 9),
+  z = c(13, 11)
+)
 
 dat %>%
   gt() %>%
   tab_spanner(
-	label = "Subheader",
-	columns = c(x, y)
+    label = "Subheader",
+    columns = c(x, y)
   )
 ```
 
diff --git a/tests/docs/smoke-all/2023/03/14/issue-1093.qmd b/tests/docs/smoke-all/2023/03/14/issue-1093.qmd
index 20a1d6cd60..b5f563bcae 100644
--- a/tests/docs/smoke-all/2023/03/14/issue-1093.qmd
+++ b/tests/docs/smoke-all/2023/03/14/issue-1093.qmd
@@ -8,5 +8,7 @@ format: pdf
 #| tbl-cap: "A table"
 #| echo: fenced
 
-mtcars[1:2,] |> tibble::rownames_to_column() |> gt::gt(rowname_col = "rowname")
+mtcars[1:2, ] |>
+  tibble::rownames_to_column() |>
+  gt::gt(rowname_col = "rowname")
 ```
\ No newline at end of file
diff --git a/tests/docs/smoke-all/2023/03/14/issue-4748.qmd b/tests/docs/smoke-all/2023/03/14/issue-4748.qmd
index 433f0ca427..93d2d7b493 100644
--- a/tests/docs/smoke-all/2023/03/14/issue-4748.qmd
+++ b/tests/docs/smoke-all/2023/03/14/issue-4748.qmd
@@ -11,7 +11,7 @@ title: boo
 library(tidyverse)
 library(kableExtra)
 
-mtcars %>% 
-  kableExtra::kbl(longtable = T) %>% 
+mtcars %>%
+  kableExtra::kbl(longtable = T) %>%
   column_spec(column = 1:2, width = "4cm")
 ```
\ No newline at end of file
diff --git a/tests/docs/smoke-all/2023/07/03/table-colwidths.qmd b/tests/docs/smoke-all/2023/07/03/table-colwidths.qmd
index 71ac08346b..0ed026f324 100644
--- a/tests/docs/smoke-all/2023/07/03/table-colwidths.qmd
+++ b/tests/docs/smoke-all/2023/07/03/table-colwidths.qmd
@@ -17,5 +17,5 @@ _quarto:
 #| label: tbl-res1
 #| tbl-cap: "mtcars using colwidths doesn't work."
 #| tbl-colwidths: [25, 25, 25, 25]
-knitr::kable(mtcars[,1:3])
+knitr::kable(mtcars[, 1:3])
 ```
\ No newline at end of file
diff --git a/tests/docs/smoke-all/2023/07/31/4057.qmd b/tests/docs/smoke-all/2023/07/31/4057.qmd
index 504c1564ee..1c4bca539c 100644
--- a/tests/docs/smoke-all/2023/07/31/4057.qmd
+++ b/tests/docs/smoke-all/2023/07/31/4057.qmd
@@ -13,7 +13,9 @@ Should output as a list of one level not two. First spaces should not be trimmed
 
 ```{r}
 knitr::asis_output(
-  paste0(c("", "  * 1", "  * 2", "  * _3_", "  * _1_ and _2_", "", 
-"<!-- end of list -->", ""), collapse = "\n")
+  paste0(c(
+    "", "  * 1", "  * 2", "  * _3_", "  * _1_ and _2_", "",
+    "<!-- end of list -->", ""
+  ), collapse = "\n")
 )
 ```
\ No newline at end of file
diff --git a/tests/docs/smoke-all/2023/08/30/6658.qmd b/tests/docs/smoke-all/2023/08/30/6658.qmd
index 81139c9183..08cf8b1513 100644
--- a/tests/docs/smoke-all/2023/08/30/6658.qmd
+++ b/tests/docs/smoke-all/2023/08/30/6658.qmd
@@ -14,6 +14,6 @@ See https://github.com/quarto-dev/quarto-cli/issues/6658
 
 ```{r}
 #| fig-cap: !expr caption
-caption = character(0)
+caption <- character(0)
 knitr::include_graphics("https://quarto.org/quarto.png")
 ```
\ No newline at end of file
diff --git a/tests/docs/smoke-all/2023/09/25/6993.qmd b/tests/docs/smoke-all/2023/09/25/6993.qmd
index 987788d577..7a2cd4e023 100644
--- a/tests/docs/smoke-all/2023/09/25/6993.qmd
+++ b/tests/docs/smoke-all/2023/09/25/6993.qmd
@@ -23,7 +23,7 @@ _quarto:
 ```{r}
 #| label: fig-1
 #| fig-cap: "Charts"
-#| fig-subcap: 
+#| fig-subcap:
 #|   - "Cars"
 #|   - "Pressure"
 #| layout: "[1, 1]"
@@ -47,7 +47,7 @@ See @fig-2, @fig-2-1, @fig-2-2.
 
 ```{r}
 #| label: fig-3
-#| fig-subcap: 
+#| fig-subcap:
 #|   - "Cars"
 #|   - "Pressure"
 #| layout: "[1, 1]"
@@ -72,7 +72,7 @@ See @fig-4, @fig-4-1, @fig-4-1.
 ```{r}
 #| label: fig-5
 #| fig-cap: "Charts"
-#| fig-subcap: 
+#| fig-subcap:
 #|   - "Cars"
 #|   - "Pressure"
 #|   - "Mtcars"
diff --git a/tests/docs/smoke-all/2023/10/03/7118.qmd b/tests/docs/smoke-all/2023/10/03/7118.qmd
index 29d387d8ea..ffb634acaf 100644
--- a/tests/docs/smoke-all/2023/10/03/7118.qmd
+++ b/tests/docs/smoke-all/2023/10/03/7118.qmd
@@ -5,7 +5,7 @@ title: Layout test
 ```{r}
 #| label: fig-charts
 #| fig-cap: "Charts"
-#| fig-subcap: 
+#| fig-subcap:
 #|   - "Cars"
 #|   - "Pressure"
 #| layout: "[1, 1]"
diff --git a/tests/docs/smoke-all/2023/10/18/7267.qmd b/tests/docs/smoke-all/2023/10/18/7267.qmd
index 31f5013ec2..9252d9e233 100644
--- a/tests/docs/smoke-all/2023/10/18/7267.qmd
+++ b/tests/docs/smoke-all/2023/10/18/7267.qmd
@@ -8,7 +8,7 @@ format: pdf
 \listoftables
 
 ```{r}
-df = data.frame(a=1:3,b=letters[1:3])
+df <- data.frame(a = 1:3, b = letters[1:3])
 ```
 
 
diff --git a/tests/docs/smoke-all/2023/10/19/7197b.qmd b/tests/docs/smoke-all/2023/10/19/7197b.qmd
index 6b77e61247..d43c42a970 100644
--- a/tests/docs/smoke-all/2023/10/19/7197b.qmd
+++ b/tests/docs/smoke-all/2023/10/19/7197b.qmd
@@ -20,7 +20,7 @@ _quarto:
 ```{r}
 #| label: tbl-example
 #| tbl-cap: "Example"
-#| tbl-subcap: 
+#| tbl-subcap:
 #|   - "Cars"
 #|   - "Pressure"
 #| echo: fenced
diff --git a/tests/docs/smoke-all/2023/11/08/7516.qmd b/tests/docs/smoke-all/2023/11/08/7516.qmd
index dd8467dcfe..31bae921ab 100644
--- a/tests/docs/smoke-all/2023/11/08/7516.qmd
+++ b/tests/docs/smoke-all/2023/11/08/7516.qmd
@@ -14,7 +14,7 @@ _quarto:
 #| fig-align: right
 library(ggplot2)
 ggplot(mtcars, aes(x = cyl, y = mpg)) +
-    geom_point()
+  geom_point()
 ```
 
 
@@ -22,7 +22,7 @@ ggplot(mtcars, aes(x = cyl, y = mpg)) +
 #| fig-align: center
 library(ggplot2)
 ggplot(mtcars, aes(x = cyl, y = mpg)) +
-    geom_point()
+  geom_point()
 ```
 
 
@@ -32,5 +32,5 @@ ggplot(mtcars, aes(x = cyl, y = mpg)) +
 #| fig-cap: Hello this works.
 library(ggplot2)
 ggplot(mtcars, aes(x = cyl, y = mpg)) +
-    geom_point()
+  geom_point()
 ```
\ No newline at end of file
diff --git a/tests/docs/smoke-all/2023/11/15/7516-b.qmd b/tests/docs/smoke-all/2023/11/15/7516-b.qmd
index e9dbbc5af0..cc7c47fb28 100644
--- a/tests/docs/smoke-all/2023/11/15/7516-b.qmd
+++ b/tests/docs/smoke-all/2023/11/15/7516-b.qmd
@@ -16,7 +16,7 @@ _quarto:
 #| fig-align: right
 library(ggplot2)
 ggplot(mtcars, aes(x = cyl, y = mpg)) +
-    geom_point()
+  geom_point()
 ```
 
 
@@ -24,7 +24,7 @@ ggplot(mtcars, aes(x = cyl, y = mpg)) +
 #| fig-align: center
 library(ggplot2)
 ggplot(mtcars, aes(x = cyl, y = mpg)) +
-    geom_point()
+  geom_point()
 ```
 
 
@@ -34,5 +34,5 @@ ggplot(mtcars, aes(x = cyl, y = mpg)) +
 #| fig-cap: Hello this works.
 library(ggplot2)
 ggplot(mtcars, aes(x = cyl, y = mpg)) +
-    geom_point()
+  geom_point()
 ```
\ No newline at end of file
diff --git a/tests/docs/smoke-all/2023/11/16/7604.qmd b/tests/docs/smoke-all/2023/11/16/7604.qmd
index 9577b89cc2..7ca94292c5 100644
--- a/tests/docs/smoke-all/2023/11/16/7604.qmd
+++ b/tests/docs/smoke-all/2023/11/16/7604.qmd
@@ -9,7 +9,7 @@ library(kableExtra)
 
 ```{r}
 #| label: tbl-sad-broken
-#| tbl-cap: "This table is cross-referenceable but no longer breaks across pages because it's inside `\\centering{}`" 
+#| tbl-cap: "This table is cross-referenceable but no longer breaks across pages because it's inside `\\centering{}`"
 rbind(mtcars, mtcars) |>
   kbl(longtable = TRUE, booktabs = TRUE) |>
   kable_styling()
diff --git a/tests/docs/smoke-all/2023/11/21/7655.qmd b/tests/docs/smoke-all/2023/11/21/7655.qmd
index c5fc6c7eaf..11a510d4e8 100644
--- a/tests/docs/smoke-all/2023/11/21/7655.qmd
+++ b/tests/docs/smoke-all/2023/11/21/7655.qmd
@@ -14,7 +14,8 @@ vec_prob <- c(
 )
 vec_df <- 1:10
 
-tmp <- mapply(FUN = qt,
+tmp <- mapply(
+  FUN = qt,
   p = vec_prob,
   MoreArgs = list(df = vec_df), SIMPLIFY = TRUE
 )
diff --git a/tests/docs/smoke-all/2023/12/01/file.r b/tests/docs/smoke-all/2023/12/01/file.r
index e83811edb6..6ca77cfe66 100644
--- a/tests/docs/smoke-all/2023/12/01/file.r
+++ b/tests/docs/smoke-all/2023/12/01/file.r
@@ -1 +1 @@
-cat("Hello.")
\ No newline at end of file
+cat("Hello.")
diff --git a/tests/docs/smoke-all/2023/12/11/7861.qmd b/tests/docs/smoke-all/2023/12/11/7861.qmd
index af7fec00e4..e5f68576d7 100644
--- a/tests/docs/smoke-all/2023/12/11/7861.qmd
+++ b/tests/docs/smoke-all/2023/12/11/7861.qmd
@@ -11,7 +11,7 @@ See @tbl-cars-gt
 #| echo: false
 mtcars |>
   head() |>
-  gt::gt() |> 
+  gt::gt() |>
   gt::tab_footnote(
     footnote = "Here's a note",
     locations = gt::cells_body(columns = cyl, rows = 2)
diff --git a/tests/docs/smoke-all/2023/12/19/6157.qmd b/tests/docs/smoke-all/2023/12/19/6157.qmd
index 219daf7989..3d88386e1e 100644
--- a/tests/docs/smoke-all/2023/12/19/6157.qmd
+++ b/tests/docs/smoke-all/2023/12/19/6157.qmd
@@ -14,7 +14,7 @@ _quarto:
 #| echo: true
 #| layout-ncol: 2
 #| fig-cap: "Caption."
-#| fig-subcap: 
+#| fig-subcap:
 #|   - "Subcaption 1."
 #|   - "Subcaption 2."
 #| fig-align: center
diff --git a/tests/docs/smoke-all/2024/02/12/issue-8712/notebooks/explore-earthquakes.qmd b/tests/docs/smoke-all/2024/02/12/issue-8712/notebooks/explore-earthquakes.qmd
index ecec84b8ee..cdfb502a87 100644
--- a/tests/docs/smoke-all/2024/02/12/issue-8712/notebooks/explore-earthquakes.qmd
+++ b/tests/docs/smoke-all/2024/02/12/issue-8712/notebooks/explore-earthquakes.qmd
@@ -11,6 +11,7 @@ Create spatial plot:
 #| fig-alt: "A scatterplot of earthquake locations plotting latitude
 #|   against longitude."
 library(ggplot2)
-mtcars |> ggplot(aes(mpg, cyl)) + geom_point()
+mtcars |> ggplot(aes(mpg, cyl)) +
+  geom_point()
 ```
 
diff --git a/tests/docs/smoke-all/2024/05/08/6945.qmd b/tests/docs/smoke-all/2024/05/08/6945.qmd
index 85bd4ede95..47d66c40a1 100644
--- a/tests/docs/smoke-all/2024/05/08/6945.qmd
+++ b/tests/docs/smoke-all/2024/05/08/6945.qmd
@@ -16,6 +16,6 @@ tibble::tribble(
   "apple",  2.05,
   "pear",   1.37,
   "orange", 3.09
-) |> 
+) |>
   gt::gt()
 ```
diff --git a/tests/docs/smoke-all/2024/05/16/9680.qmd b/tests/docs/smoke-all/2024/05/16/9680.qmd
index 2dd56e0fb1..f2f5b4afe9 100644
--- a/tests/docs/smoke-all/2024/05/16/9680.qmd
+++ b/tests/docs/smoke-all/2024/05/16/9680.qmd
@@ -45,9 +45,9 @@ _quarto:
 
 ```{r}
 #| label: test
-head(iris, 1) |>  
-    gt::gt() |> 
-    gt::as_raw_html()
+head(iris, 1) |>
+  gt::gt() |>
+  gt::as_raw_html()
 ```
 
 ## Test table Md {#table-md}
diff --git a/tests/docs/smoke-all/2024/06/03/9850.qmd b/tests/docs/smoke-all/2024/06/03/9850.qmd
index 0fabaaac3c..4aa51ec8ba 100644
--- a/tests/docs/smoke-all/2024/06/03/9850.qmd
+++ b/tests/docs/smoke-all/2024/06/03/9850.qmd
@@ -11,6 +11,6 @@ _quarto:
 
 ```{r}
 #| label: tbl-problem
-gt::gtcars[1:5, 1:5] |> 
-    gt::gt()
+gt::gtcars[1:5, 1:5] |>
+  gt::gt()
 ```
diff --git a/tests/docs/smoke-all/2024/06/04/9862.qmd b/tests/docs/smoke-all/2024/06/04/9862.qmd
index 896b7d857c..98acb0e320 100644
--- a/tests/docs/smoke-all/2024/06/04/9862.qmd
+++ b/tests/docs/smoke-all/2024/06/04/9862.qmd
@@ -9,5 +9,7 @@ execute:
 #| eval: false
 #| label: tbl-t2
 #| tbl-cap: hggfh
-mtcars |> head() |> knitr::kable()
+mtcars |>
+  head() |>
+  knitr::kable()
 ```
diff --git a/tests/docs/smoke-all/2024/06/19/9208.qmd b/tests/docs/smoke-all/2024/06/19/9208.qmd
index 13b10503aa..87f1d36150 100644
--- a/tests/docs/smoke-all/2024/06/19/9208.qmd
+++ b/tests/docs/smoke-all/2024/06/19/9208.qmd
@@ -16,16 +16,17 @@ _quarto:
 ---
 
 ```{r}
-sliderInput("bins", "Number of bins:", 
-            min = 1, max = 50, value = 30)
+sliderInput("bins", "Number of bins:",
+  min = 1, max = 50, value = 30
+)
 plotOutput("distPlot")
 ```
 
 ```{r}
 #| context: server
 output$distPlot <- renderPlot({
-  x <- faithful[, 2]  # Old Faithful Geyser data
+  x <- faithful[, 2] # Old Faithful Geyser data
   bins <- seq(min(x), max(x), length.out = input$bins + 1)
-  hist(x, breaks = bins, col = 'darkgray', border = 'white')
+  hist(x, breaks = bins, col = "darkgray", border = "white")
 })
 ```
diff --git a/tests/docs/smoke-all/2024/06/24/10112.qmd b/tests/docs/smoke-all/2024/06/24/10112.qmd
index b22c3a62d0..3fad8bcc6b 100644
--- a/tests/docs/smoke-all/2024/06/24/10112.qmd
+++ b/tests/docs/smoke-all/2024/06/24/10112.qmd
@@ -5,5 +5,5 @@ format: pdf
 
 ```{r}
 #| column: margin
-knitr::kable(head(mtcars[,1:2], 5))
+knitr::kable(head(mtcars[, 1:2], 5))
 ```
diff --git a/tests/docs/smoke-all/article-layout/grid.qmd b/tests/docs/smoke-all/article-layout/grid.qmd
index 78b7abe6be..b332769c66 100644
--- a/tests/docs/smoke-all/article-layout/grid.qmd
+++ b/tests/docs/smoke-all/article-layout/grid.qmd
@@ -26,6 +26,7 @@ The below two computational chunks are expected to produce a table and a plot si
 "there was a table here...but it was unnecessary for the reprex."
 
 ```
+
 :::
 
 ::: {.g-col-6}
@@ -42,6 +43,7 @@ hist(iris$Sepal.Length)
 
 
 ```
+
 :::
 
 :::::
diff --git a/tests/docs/smoke-all/article-layout/tables/tufte.qmd b/tests/docs/smoke-all/article-layout/tables/tufte.qmd
index 3ae29403c2..d145ae41a6 100644
--- a/tests/docs/smoke-all/article-layout/tables/tufte.qmd
+++ b/tests/docs/smoke-all/article-layout/tables/tufte.qmd
@@ -62,11 +62,13 @@ Images and graphics play an integral role in Tufte's work. To place figures in t
 library(ggplot2)
 mtcars2 <- mtcars
 mtcars2$am <- factor(
-  mtcars$am, labels = c('automatic', 'manual')
+  mtcars$am,
+  labels = c("automatic", "manual")
 )
 ggplot(mtcars2, aes(hp, mpg, color = am)) +
-  geom_point() + geom_smooth() +
-  theme(legend.position = 'bottom')
+  geom_point() +
+  geom_smooth() +
+  theme(legend.position = "bottom")
 ```
 
 Note the use of the `fig-cap` chunk option to provide a figure caption. You can adjust the proportions of figures using the `fig-width` and `fig-height` chunk options. These are specified in inches, and will be automatically scaled down to fit within the handout margin.
@@ -92,8 +94,9 @@ You can arrange for figures to span across the entire page by using the chunk op
 #| fig-height: 3
 #| fig-column: page-right
 #| warning: false
-ggplot(diamonds, aes(carat, price)) + geom_smooth() +
-  facet_grid(~ cut)
+ggplot(diamonds, aes(carat, price)) +
+  geom_smooth() +
+  facet_grid(~cut)
 ```
 
 Other chunk options related to figures can still be used, such as `fig-width`, `fig-cap`, and so on. For full width figures, usually `fig-width` is large and `fig-height` is small. In the above example, the plot size is $11 \times 3$.
@@ -121,7 +124,8 @@ Besides margin and full width figures, you can of course also include figures co
 ```{r}
 #| label: fig-main
 #| fig-cap: "A figure in the main column."
-ggplot(diamonds, aes(cut, price)) + geom_boxplot()
+ggplot(diamonds, aes(cut, price)) +
+  geom_boxplot()
 ```
 
 ## Margin Captions
@@ -132,7 +136,8 @@ When you include a figure constrained to the main column, you can choose to plac
 #| label: fig-main-margin-cap
 #| fig-cap: "A figure with a longer caption. The figure appears in the main column, but the caption is placed in the margin. Captions can even contain elements like a citation such as @xie2018."
 #| cap-location: margin
-ggplot(diamonds, aes(cut, price)) + geom_boxplot()
+ggplot(diamonds, aes(cut, price)) +
+  geom_boxplot()
 ```
 
 # Sidenotes
@@ -156,7 +161,8 @@ You can use the `kable()` function from the **knitr** package to format tables t
 ```{r}
 #| tbl-cap-location: margin
 knitr::kable(
-  mtcars[1:6, 1:6], caption = 'A subset of mtcars.'
+  mtcars[1:6, 1:6],
+  caption = "A subset of mtcars."
 )
 ```
 
@@ -205,14 +211,14 @@ Next we show multiple plots in margin figures. Similarly, two plots in the same
 #| warning: false
 #| echo: false
 p
-p + geom_smooth(method = 'lm')
+p + geom_smooth(method = "lm")
 ```
 
 Then two plots from the same code chunk placed in different figure environments:
 
 ```{r}
 #| echo: false
-knitr::kable(head(iris[,c(1,2,3,4)], 13))
+knitr::kable(head(iris[, c(1, 2, 3, 4)], 13))
 ```
 
 ```{r}
@@ -224,12 +230,12 @@ knitr::kable(head(iris[,c(1,2,3,4)], 13))
 #| warning: false
 #| echo: false
 p
-p + geom_smooth(method = 'lm')
+p + geom_smooth(method = "lm")
 ```
 
 ```{r}
 #| echo: false
-knitr::kable(head(iris[,c(1,2,3,4)], 11))
+knitr::kable(head(iris[, c(1, 2, 3, 4)], 11))
 ```
 
 We blended some tables in the above code chunk only as *placeholders* to make sure there is enough vertical space among the margin figures, otherwise they will be stacked tightly together. For a practical document, you should not insert too many margin figures consecutively and make the margin crowded.
@@ -242,14 +248,16 @@ You do not have to assign captions to figures. We show three figures with no cap
 #| column: margin
 # a boxplot of weight vs transmission; this figure
 # will be placed in the margin
-ggplot(mtcars2, aes(am, wt)) + geom_boxplot() +
+ggplot(mtcars2, aes(am, wt)) +
+  geom_boxplot() +
   coord_flip()
 ```
 
 ```{r}
 #| warning: false
 # a figure in the main column
-p <- ggplot(mtcars, aes(wt, hp)) + geom_point()
+p <- ggplot(mtcars, aes(wt, hp)) +
+  geom_point()
 p
 ```
 
@@ -259,7 +267,7 @@ p
 #| column: page-right
 #| warning: false
 # a fullwidth figure
-p + geom_smooth(method = 'lm') + facet_grid(~ gear)
+p + geom_smooth(method = "lm") + facet_grid(~gear)
 ```
 
 # Some Notes on Page Layout
diff --git a/tests/docs/smoke-all/book/htmlbook/code.qmd b/tests/docs/smoke-all/book/htmlbook/code.qmd
index 88462a1910..93ed663c00 100644
--- a/tests/docs/smoke-all/book/htmlbook/code.qmd
+++ b/tests/docs/smoke-all/book/htmlbook/code.qmd
@@ -35,4 +35,4 @@ This is some html code:
 #| fig-cap: This is a histogram
 #| fig-alt: This is some alt-text
 hist(1:10)
-```
+```
\ No newline at end of file
diff --git a/tests/docs/smoke-all/code-line-numbers/code-line-numbers-document.qmd b/tests/docs/smoke-all/code-line-numbers/code-line-numbers-document.qmd
index c68236e13d..370e65b6b9 100644
--- a/tests/docs/smoke-all/code-line-numbers/code-line-numbers-document.qmd
+++ b/tests/docs/smoke-all/code-line-numbers/code-line-numbers-document.qmd
@@ -51,5 +51,5 @@ plt.show()
 #| results: hold
 1 + 1
 2 + 2
-3 + 3 
+3 + 3
 ```
diff --git a/tests/docs/smoke-all/code-line-numbers/code-line-numbers-highlight.qmd b/tests/docs/smoke-all/code-line-numbers/code-line-numbers-highlight.qmd
index 9434a0e1f3..aeeb1c2c81 100644
--- a/tests/docs/smoke-all/code-line-numbers/code-line-numbers-highlight.qmd
+++ b/tests/docs/smoke-all/code-line-numbers/code-line-numbers-highlight.qmd
@@ -75,5 +75,5 @@ plt.show()
 #| results: hold
 1 + 1
 2 + 2
-3 + 3 
+3 + 3
 ```
diff --git a/tests/docs/smoke-all/confluence/confluence-smoke-test.qmd b/tests/docs/smoke-all/confluence/confluence-smoke-test.qmd
index 580d3823ac..a069619ceb 100644
--- a/tests/docs/smoke-all/confluence/confluence-smoke-test.qmd
+++ b/tests/docs/smoke-all/confluence/confluence-smoke-test.qmd
@@ -476,7 +476,7 @@ plot(pressure)
 
 ```{r}
 #| layout-ncol: 2
-#| fig-cap: 
+#| fig-cap:
 #|   - "Speed and Stopping Distances of Cars"
 #|   - "Vapor Pressure of Mercury as a Function of Temperature"
 
@@ -507,7 +507,7 @@ plot(pressure)
 ```{r}
 #| label: fig-charts
 #| fig-cap: Charts
-#| fig-subcap: 
+#| fig-subcap:
 #|   - "Cars"
 #|   - "Pressure"
 #| layout-ncol: 2
diff --git a/tests/docs/smoke-all/crossrefs/float/latex/latex-longtable-fixup-caption-no-crossref.qmd b/tests/docs/smoke-all/crossrefs/float/latex/latex-longtable-fixup-caption-no-crossref.qmd
index d886d255e1..5f1fcb67ff 100644
--- a/tests/docs/smoke-all/crossrefs/float/latex/latex-longtable-fixup-caption-no-crossref.qmd
+++ b/tests/docs/smoke-all/crossrefs/float/latex/latex-longtable-fixup-caption-no-crossref.qmd
@@ -25,9 +25,10 @@ df <- tibble::tibble(
   y = rnorm(20),
   z = rnorm(20)
 )
-knitr::kable(df, 
-  format = "latex", 
-  longtable = TRUE, 
-  booktabs = TRUE, 
-  caption = "A long table with a caption")
+knitr::kable(df,
+  format = "latex",
+  longtable = TRUE,
+  booktabs = TRUE,
+  caption = "A long table with a caption"
+)
 ```
diff --git a/tests/docs/smoke-all/crossrefs/float/latex/latex-longtable-fixup-no-cap-no-crossref.qmd b/tests/docs/smoke-all/crossrefs/float/latex/latex-longtable-fixup-no-cap-no-crossref.qmd
index 6511d5582e..0f5310cbe0 100644
--- a/tests/docs/smoke-all/crossrefs/float/latex/latex-longtable-fixup-no-cap-no-crossref.qmd
+++ b/tests/docs/smoke-all/crossrefs/float/latex/latex-longtable-fixup-no-cap-no-crossref.qmd
@@ -21,9 +21,10 @@ df <- tibble::tibble(
   y = rnorm(20),
   z = rnorm(20)
 )
-knitr::kable(df, 
-  format = "latex", 
-  longtable = TRUE, 
-  booktabs = TRUE)
+knitr::kable(df,
+  format = "latex",
+  longtable = TRUE,
+  booktabs = TRUE
+)
 ```
 
diff --git a/tests/docs/smoke-all/crossrefs/float/latex/latex-longtable-fixup-test.qmd b/tests/docs/smoke-all/crossrefs/float/latex/latex-longtable-fixup-test.qmd
index e8365a52b1..0ce75c6e86 100644
--- a/tests/docs/smoke-all/crossrefs/float/latex/latex-longtable-fixup-test.qmd
+++ b/tests/docs/smoke-all/crossrefs/float/latex/latex-longtable-fixup-test.qmd
@@ -26,11 +26,12 @@ df <- tibble(
   y = rnorm(20),
   z = rnorm(20)
 )
-kable(df, 
-  format = "latex", 
-  longtable = TRUE, 
-  booktabs = TRUE, 
-  caption = "A long table with a caption")
+kable(df,
+  format = "latex",
+  longtable = TRUE,
+  booktabs = TRUE,
+  caption = "A long table with a caption"
+)
 ```
 
 See @tbl-test.
diff --git a/tests/docs/smoke-all/dark-mode/ggplot-duobrand.qmd b/tests/docs/smoke-all/dark-mode/ggplot-duobrand.qmd
index e9c3ba793f..d7953d54c6 100644
--- a/tests/docs/smoke-all/dark-mode/ggplot-duobrand.qmd
+++ b/tests/docs/smoke-all/dark-mode/ggplot-duobrand.qmd
@@ -25,19 +25,19 @@ library(ggplot2)
 
 ggplot_theme <- function(bgcolor, fgcolor) {
   theme_minimal(base_size = 11) %+%
-  theme(
-    panel.border = element_blank(),
-    panel.grid.major.y = element_blank(),
-    panel.grid.minor.y = element_blank(),
-    panel.grid.major.x = element_blank(),
-    panel.grid.minor.x = element_blank(),
-    text = element_text(colour = fgcolor),
-    axis.text = element_text(colour = fgcolor),
-    rect = element_rect(colour = bgcolor, fill = bgcolor),
-    plot.background = element_rect(fill = bgcolor, colour = NA),
-    axis.line = element_line(colour = fgcolor),
-    axis.ticks = element_line(colour = fgcolor)
-  )
+    theme(
+      panel.border = element_blank(),
+      panel.grid.major.y = element_blank(),
+      panel.grid.minor.y = element_blank(),
+      panel.grid.major.x = element_blank(),
+      panel.grid.minor.x = element_blank(),
+      text = element_text(colour = fgcolor),
+      axis.text = element_text(colour = fgcolor),
+      rect = element_rect(colour = bgcolor, fill = bgcolor),
+      plot.background = element_rect(fill = bgcolor, colour = NA),
+      axis.line = element_line(colour = fgcolor),
+      axis.ticks = element_line(colour = fgcolor)
+    )
 }
 
 brand_ggplot <- function(brand_yml) {
@@ -56,9 +56,13 @@ colour_scale <- scale_colour_manual(values = c("darkorange", "purple", "cyan4"))
 ```{r}
 #| renderings: [light, dark]
 ggplot(mtcars, aes(mpg, wt)) +
-  geom_point(aes(colour = factor(cyl))) + united_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  united_theme +
+  colour_scale
 ggplot(mtcars, aes(mpg, wt)) +
-  geom_point(aes(colour = factor(cyl))) + slate_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  slate_theme +
+  colour_scale
 ```
 
 ### with crossref but no caption
@@ -73,9 +77,13 @@ and `echo: true`
 #|   - dark
 #|   - light
 ggplot(mtcars, aes(mpg, disp)) +
-  geom_point(aes(colour = factor(cyl))) + slate_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  slate_theme +
+  colour_scale
 ggplot(mtcars, aes(mpg, disp)) +
-  geom_point(aes(colour = factor(cyl))) + united_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  united_theme +
+  colour_scale
 ```
 
 :::
@@ -88,7 +96,9 @@ ggplot(mtcars, aes(mpg, disp)) +
 ```{r}
 #| renderings: [dark]
 ggplot(mtcars, aes(mpg, disp)) +
-  geom_point(aes(colour = factor(cyl))) + slate_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  slate_theme +
+  colour_scale
 ```
 
 ggplot - dark only
@@ -102,9 +112,13 @@ ggplot - dark only
 ```{r}
 #| renderings: [light, dark]
 ggplot(mtcars, aes(mpg, hp)) +
-  geom_point(aes(colour = factor(cyl))) + united_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  united_theme +
+  colour_scale
 ggplot(mtcars, aes(mpg, hp)) +
-  geom_point(aes(colour = factor(cyl))) + slate_theme + colour_scale
+  geom_point(aes(colour = factor(cyl))) +
+  slate_theme +
+  colour_scale
 ```
 
 mtcars - mpg vs hp
diff --git a/tests/docs/smoke-all/dashboard/3-valuebox-knitr.qmd b/tests/docs/smoke-all/dashboard/3-valuebox-knitr.qmd
index 5d34811659..cc20a5abd6 100644
--- a/tests/docs/smoke-all/dashboard/3-valuebox-knitr.qmd
+++ b/tests/docs/smoke-all/dashboard/3-valuebox-knitr.qmd
@@ -57,9 +57,9 @@ if (currentVal < 100) {
 }
 
 list(
-  value=currentVal,
-  color=color,
-  icon=icon
+  value = currentVal,
+  color = color,
+  icon = icon
 )
 ```
 
@@ -78,9 +78,9 @@ if (currentVal < 100) {
 }
 
 list(
-  value=currentVal,
-  color=color,
-  icon=icon
+  value = currentVal,
+  color = color,
+  icon = icon
 )
 ```
 
@@ -88,8 +88,8 @@ list(
 #| component: valuebox
 #| title: Cool things
 #| icon: facebook
-foo = 45
-bar = 3
+foo <- 45
+bar <- 3
 foo * bar
 ```
 
diff --git a/tests/docs/smoke-all/dashboard/6-sidebar-global.qmd b/tests/docs/smoke-all/dashboard/6-sidebar-global.qmd
index 8801e60b94..c0375f87b1 100644
--- a/tests/docs/smoke-all/dashboard/6-sidebar-global.qmd
+++ b/tests/docs/smoke-all/dashboard/6-sidebar-global.qmd
@@ -41,11 +41,11 @@ library(bslib)
 library(bsicons)
 library(shiny)
 value_box(
-    title = "3rd value",
-    value = "789",
-    showcase = bs_icon("pie-chart"),
-    theme = "pink",
-  )
+  title = "3rd value",
+  value = "789",
+  showcase = bs_icon("pie-chart"),
+  theme = "pink",
+)
 ```
 
 ## Row
diff --git a/tests/docs/smoke-all/dashboard/9-bslib.qmd b/tests/docs/smoke-all/dashboard/9-bslib.qmd
index 52910f3842..4719cbe0ad 100644
--- a/tests/docs/smoke-all/dashboard/9-bslib.qmd
+++ b/tests/docs/smoke-all/dashboard/9-bslib.qmd
@@ -9,21 +9,21 @@ format: dashboard
 library(bslib)
 library(bsicons)
 value_box(
-    title = "1st value",
-    value = "789",
-    showcase = bs_icon("pie-chart"),
-    theme = "pink"
-  )
+  title = "1st value",
+  value = "789",
+  showcase = bs_icon("pie-chart"),
+  theme = "pink"
+)
 value_box(
-    title = "2nd value",
-    value = "789",
-    showcase = bs_icon("pie-chart"),
-    theme = "blue"
-  )
+  title = "2nd value",
+  value = "789",
+  showcase = bs_icon("pie-chart"),
+  theme = "blue"
+)
 value_box(
-    title = "3rd value",
-    value = "789",
-    showcase = bs_icon("pie-chart"),
-    theme = "green"
-  )  
+  title = "3rd value",
+  value = "789",
+  showcase = bs_icon("pie-chart"),
+  theme = "green"
+)
 ```
\ No newline at end of file
diff --git a/tests/docs/smoke-all/inline-execution/inline-knitr.qmd b/tests/docs/smoke-all/inline-execution/inline-knitr.qmd
index 62804b069c..40995b7c5b 100644
--- a/tests/docs/smoke-all/inline-execution/inline-knitr.qmd
+++ b/tests/docs/smoke-all/inline-execution/inline-knitr.qmd
@@ -4,18 +4,18 @@ engine: knitr
 ---
 
 ```{r}
-x = 1
-y = "foo"
-z = '"foo"'
-a = '"foo'
-b = '*foo*'
-c = "*foo*"
-d = "'foo"
-e = "1"
-f = FALSE
-g = TRUE
-h = NULL
-i = "*foo*"
+x <- 1
+y <- "foo"
+z <- '"foo"'
+a <- '"foo'
+b <- "*foo*"
+c <- "*foo*"
+d <- "'foo"
+e <- "1"
+f <- FALSE
+g <- TRUE
+h <- NULL
+i <- "*foo*"
 class(i) <- c("character", "asis")
 ```
 
diff --git a/tests/docs/smoke-all/knitr/embed-verbatim-engine/code.R b/tests/docs/smoke-all/knitr/embed-verbatim-engine/code.R
index 041a291f37..e4b13dfc24 100644
--- a/tests/docs/smoke-all/knitr/embed-verbatim-engine/code.R
+++ b/tests/docs/smoke-all/knitr/embed-verbatim-engine/code.R
@@ -1 +1 @@
-cat("this is code.R\n")
\ No newline at end of file
+cat("this is code.R\n")
diff --git a/tests/docs/smoke-all/knitr/in-chunk-layout.qmd b/tests/docs/smoke-all/knitr/in-chunk-layout.qmd
index e39b1b54d7..3b914f7e27 100644
--- a/tests/docs/smoke-all/knitr/in-chunk-layout.qmd
+++ b/tests/docs/smoke-all/knitr/in-chunk-layout.qmd
@@ -22,7 +22,7 @@ _quarto:
 
 ```{r}
 #| label: fig-charts1
-#| fig-cap: 
+#| fig-cap:
 #|   - "Speed and Stopping Distances of Cars"
 #|   - "Vapor Pressure of Mercury as a Function of Temperature"
 #| layout: "[1, 1]"
@@ -36,7 +36,7 @@ plot(pressure)
 
 ```{r}
 #| label: fig-charts2
-#| fig-cap: 
+#| fig-cap:
 #|   - "Speed and Stopping Distances of Cars"
 #|   - "Vapor Pressure of Mercury as a Function of Temperature"
 #| layout: "[1, 1]"
@@ -50,7 +50,7 @@ plot(pressure)
 
 ```{r}
 #| label: fig-charts3
-#| fig-cap: 
+#| fig-cap:
 #|   - "Speed and Stopping Distances of Cars"
 #|   - "Vapor Pressure of Mercury as a Function of Temperature"
 #| layout: "[1, 1]"
@@ -64,7 +64,7 @@ plot(pressure)
 
 ```{r}
 #| label: fig-charts4
-#| fig-cap: 
+#| fig-cap:
 #|   - "Speed and Stopping Distances of Cars"
 #|   - "Vapor Pressure of Mercury as a Function of Temperature"
 #| layout: "[1, 1]"
diff --git a/tests/docs/smoke-all/lightbox/example.qmd b/tests/docs/smoke-all/lightbox/example.qmd
index 8bf4c34410..86cc5e48b0 100644
--- a/tests/docs/smoke-all/lightbox/example.qmd
+++ b/tests/docs/smoke-all/lightbox/example.qmd
@@ -46,7 +46,7 @@ description="The Edgartown Lighthouse is a short walk from downtown and has beau
 Options for lightbox can be passed using chunk options.
 
 ```{r}
-#| fig-cap: Simple demo R plot 
+#| fig-cap: Simple demo R plot
 #| lightbox:
 #|   group: r-graph
 #|   description: This is 1 to 10 plot
@@ -63,12 +63,12 @@ plot(cars)
 
 It is possible to create several plots, and group them in a lightbox gallery. Use list in YAML for options when you have several plots, on per plot.
 ```{r}
-#| fig-cap: 
+#| fig-cap:
 #|   - Caption for first plot
 #|   - Caption for second plot
-#| lightbox: 
+#| lightbox:
 #|   group: cars
-#|   description: 
+#|   description:
 #|     - This is the decription for first graph
 #|     - This is the decription for second graph
 plot(mtcars)
@@ -102,7 +102,7 @@ plot(iris)
 #|   provided.
 #| fig-subcap:
 #|   - "Clowning Fools Up In Here: This chart shows me clowning on fools up in this piece. It's embarrassing!"
-#|   - "A Graph of Cool Stuff: This chart shows some cool things, most frequently in the form of a visualization which makes a pretty strong point." 
+#|   - "A Graph of Cool Stuff: This chart shows some cool things, most frequently in the form of a visualization which makes a pretty strong point."
 #| layout-ncol: 2
 plot(ToothGrowth)
 plot(PlantGrowth)
diff --git a/tests/docs/typst/tables/gt/gtcars.qmd b/tests/docs/typst/tables/gt/gtcars.qmd
index e5fb2d984e..d80f157453 100644
--- a/tests/docs/typst/tables/gt/gtcars.qmd
+++ b/tests/docs/typst/tables/gt/gtcars.qmd
@@ -35,21 +35,27 @@ gtcars %>%
     columns = vars(hp),
     colors = scales::col_numeric(
       palette = c(
-        "white", "orange", "red"),
-      domain = c(500, 750))
+        "white", "orange", "red"
+      ),
+      domain = c(500, 750)
+    )
   ) %>%
   data_color(
     columns = vars(mpg_c, mpg_h),
     colors = scales::col_numeric(
       palette = c(
-        "white", "green"),
-      domain = c(10, 25))
+        "white", "green"
+      ),
+      domain = c(10, 25)
+    )
   ) %>%
   data_color(
     columns = vars(msrp),
     colors = scales::col_numeric(
       palette = c(
-        "white", "pink", "red"),
-      domain = NULL)
+        "white", "pink", "red"
+      ),
+      domain = NULL
+    )
   )
 ```
\ No newline at end of file
diff --git a/tests/docs/typst/tables/gt/red-blue-palette.qmd b/tests/docs/typst/tables/gt/red-blue-palette.qmd
index 2bb5cc1e5d..458e0d3757 100644
--- a/tests/docs/typst/tables/gt/red-blue-palette.qmd
+++ b/tests/docs/typst/tables/gt/red-blue-palette.qmd
@@ -26,6 +26,7 @@ temps %>%
     columns = vars(month.abb),
     colors = scales::col_numeric(
       colorspace::diverge_hcl(n = 9, palette = "Blue-Red 3"),
-      domain = range(nottem))
+      domain = range(nottem)
+    )
   )
 ```
\ No newline at end of file