Merge branch 'main' into jk/quartonotebookrunner

.github/workflows/actions/quarto-dev/action.yml

@@ -34,9 +34,19 @@ runs:
     - name: Basic dev mode sanity check
       shell: pwsh
       run: |
-        If ( "$(quarto --version)" -ne "99.9.9") { Exit 1 }
-        If ( $(quarto --paths | Select-String -Pattern "package[/\\]+dist[/\\]+share") -ne $null ) { Exit 1 }
-        If ( "$(git status --porcelain)" -ne "" ) { Exit 1 }
+        If ( "$(quarto --version)" -ne "99.9.9") { 
+          echo "Unexpected version detected: $(quarto --version)"
+          Exit 1 
+        }
+        If ( $(quarto --paths | Select-String -Pattern "package[/\\]+dist[/\\]+share") -ne $null ) { 
+          echo "Unexpected package/dist/share path detected: $(quarto --paths)"
+          Exit 1 
+        }
+        If ( "$(git status --porcelain)" -ne "" ) {
+          echo "Uncommitted changes detected:"
+          git status --porcelain
+          Exit 1 
+        }
 
     - name: Quarto Check
       if:  runner.debug == '1'

.github/workflows/create-release.yml

@@ -60,8 +60,9 @@ jobs:
           echo -e "\n\nFull ${version} changelog up to this version:\n" >> "release_note.md"
           echo -e "  * View: https://github.com/${GITHUB_REPOSITORY}/blob/v${version_full}/news/changelog-${version}.md\n" >> "release_note.md"
           echo -e "  * Download: https://github.com/${GITHUB_REPOSITORY}/releases/download/v${version_full}/changelog.md\n" >> "release_note.md"
-          echo -e "" >> "release_note.md"
-          echo -e "Due to an issue with upstream dependency, the RHEL build may not included in this release. Follow #8944 for more information." >> "release_note.md"
+          # TODO: uncomment this again if new issue with RHEL build
+          # echo -e "" >> "release_note.md"
+          # echo -e "Due to an issue with upstream dependency, the RHEL build may not included in this release." >> "release_note.md"
 
       - name: Upload Artifact
         uses: actions/upload-artifact@v3
@@ -197,9 +198,9 @@ jobs:
           source ./configuration
 
           echo Placing custom Deno ${DENO:1}. See available versions at https://anaconda.org/conda-forge/deno/files
-          curl -L https://anaconda.org/conda-forge/deno/${DENO:1}/download/linux-64/deno-${DENO:1}-h335b0a9_1.conda --output deno.conda
+          curl -L https://anaconda.org/conda-forge/deno/${DENO:1}/download/linux-64/deno-${DENO:1}-hfc7925d_0.conda --output deno.conda
           unzip deno.conda
-          tar --use-compress-program=unzstd -xvf pkg-deno-${DENO:1}-h335b0a9_1.tar.zst
+          tar --use-compress-program=unzstd -xvf pkg-deno-${DENO:1}-hfc7925d_0.tar.zst
           cp bin/deno package/pkg-working/bin/tools/x86_64/deno
 
       - name: Make Tarball

configuration

@@ -24,10 +24,7 @@ export TYPST=0.10.0
 # (use commit hash from bslib repo)
 
 # 0.5.1 + consolidated components
-export BOOTSTRAP=ad946cafdbf1c91cfd714cb39948bb203ae66e66 
-# NOTE: HTML TOOLS has a manually committed fill.css file which will be officially
-# released in htmltools 0.5.7
-
+export BOOTSTRAP=ad946cafdbf1c91cfd714cb39948bb203ae66e66
 export HTMLTOOLS=0.5.7
 export BOOTSTRAP_FONT=1.11.1
 export BOOTSWATCH=5.3.1

dev-docs/feature-format-matrix/create_table.py

@@ -1,6 +1,6 @@
 import yaml
 import json
-import glob
+import pathlib
 
 class Trie:
 
@@ -103,8 +103,8 @@ def table_cell(entry, _feature, _format_name, format_config):
 
 def compute_trie():
     trie = Trie()
-    for entry in glob.glob("qmd-files/**/document.qmd", recursive=True):
-        feature = entry.split("/")[1:-1]
+    for entry in pathlib.Path(".").glob("qmd-files/**/document.qmd"):
+        feature = entry.parts[1:-1]
         front_matter = extract_metadata_from_file(entry)
         try:
             format = front_matter["format"]

news/changelog-1.5.md

@@ -6,6 +6,7 @@ All changes included in 1.5:
 - ([#8118](https://github.com/quarto-dev/quarto-cli/issues/8118)): Add support for `body-classes` to add classes to the document body.
 - ([#8311](https://github.com/quarto-dev/quarto-cli/issues/8311)): Correct z-order for margins with no contents
 - ([#8862](https://github.com/quarto-dev/quarto-cli/issues/8862)): Properly deal with an `aside` within a definition list.
+- ([#8990](https://github.com/quarto-dev/quarto-cli/issues/8990)): Copy button now works for embedded code source in modal window when optin-in `code-tools` feature.
 
 ## PDF Format
 
@@ -65,6 +66,7 @@ All changes included in 1.5:
 - ([#8627](https://github.com/quarto-dev/quarto-cli/issues/8627)): Localize the text that appears as placeholder in listing filters.
 - ([#8715](https://github.com/quarto-dev/quarto-cli/issues/8715)): Listings should respect `image: false`
 - ([#8860](https://github.com/quarto-dev/quarto-cli/discussions/8860)): Don't show duplicate author names.
+- ([#9030](https://github.com/quarto-dev/quarto-cli/discussions/9030)): Warn (rather than error) when listing globs produce an empty listing (as this is permissable).
 
 ## Manuscripts
 
@@ -78,7 +80,8 @@ All changes included in 1.5:
 
 ## Shortcodes
 
-- ([#8316](https://github.com/quarto-dev/quarto-cli/issues/8316)): Add fallback value for the `env` shortcode
+- ([#8316](https://github.com/quarto-dev/quarto-cli/issues/8316)): Add fallback value for the `env` shortcode.
+- ([#9011](https://github.com/quarto-dev/quarto-cli/issues/9011)): `embed` shortcode now renders the embedded document without error when it is using knitr engine and have some outputs with HTML dependencies.
 
 ## Lightbox Images
 
@@ -101,7 +104,7 @@ All changes included in 1.5:
 
 - ([#8939](https://github.com/quarto-dev/quarto-cli/pull/8939)): `quarto inspect` now takes an additional optional parameter to specify the output file, and provides the graph of include dependencies for the inspection target.
 
-## Other Fixes
+## Other Fixes and Improvements
 
 - ([#8119](https://github.com/quarto-dev/quarto-cli/issues/8119)): More intelligently detect when ejs templates are modified during development, improving quality of life during preview.
 - ([#8177](https://github.com/quarto-dev/quarto-cli/issues/8177)): Use an explicit path to `sysctl` when detecting MacOS architecture. (author: @kevinushey)
@@ -117,6 +120,10 @@ All changes included in 1.5:
 - ([#8873](https://github.com/quarto-dev/quarto-cli/issues/8873)): Don't overwrite supporting files when creating a project.
 - ([#8937](https://github.com/quarto-dev/quarto-cli/issues/8937)): Fix unix launcher script to properly handle spaces in the path to the quarto executable.
 - ([#8898](https://github.com/quarto-dev/quarto-cli/issues/8898)): `.deb` and `.tar.gz` bundle contents are now associated to root user and group instead of default user and group for CI build runners.
-- Add support for `{{< lipsum >}}` shortcode, which is useful for emitting placeholder text. Specify a specific number of paragraphs (`{{< lipsum 3 >}}`).
+- ([#9041](https://github.com/quarto-dev/quarto-cli/issues/9041)): When creating an automatic citation key, replace spaces with underscores in inferred keys.
+- ([#9059](https://github.com/quarto-dev/quarto-cli/issues/9059)): `quarto run` now properly works on Windows with Lua scripts.
+- Add support for `{{< lipsum >}}` shortcode, which is useful for emitting placeholder text. Provide a specific number of paragraphs (`{{< lipsum 3 >}}`).
+- Resolve data URIs in Pandoc's mediabag when rendering documents.
 - Increase v8's max heap size by default, to avoid out-of-memory errors when rendering large documents (also cf. https://github.com/denoland/deno/issues/18935).
 - Upgrade Deno to 1.41.0
+- `quarto install tinytex` will now try to set the default CTAN repository to the nearest mirror resolved from https://mirror.ctan.org.

package/src/common/update-html-dependencies.ts

@@ -13,11 +13,12 @@ import * as ld from "../../../src/core/lodash.ts";
 import { runCmd } from "../util/cmd.ts";
 import { applyGitPatches, Repo, withRepo } from "../util/git.ts";
 
-import { download, unzip } from "../util/utils.ts";
+import { download } from "../util/utils.ts";
 import { Configuration } from "./config.ts";
 import { visitLines } from "../../../src/core/file.ts";
 import { copyMinimal } from "../../../src/core/copy.ts";
 import { kSourceMappingRegexes } from "../../../src/config/constants.ts";
+import { unzip } from "../../../src/core/zip.ts";
 
 export async function updateHtmlDependencies(config: Configuration) {
   info("Updating Bootstrap with version info:");

src/command/render/codetools.ts

@@ -1,9 +1,8 @@
 /*
-* codetools.ts
-*
-* Copyright (C) 2020-2022 Posit Software, PBC
-*
-*/
+ * codetools.ts
+ *
+ * Copyright (C) 2020-2022 Posit Software, PBC
+ */
 
 import { Document, Element } from "../../core/deno-dom.ts";
 import {
@@ -32,7 +31,7 @@ const kHideAllCodeLinkId = "quarto-hide-all-code";
 const kShowAllCodeLinkId = "quarto-show-all-code";
 const kViewSourceLinkId = "quarto-view-source";
 const kEmbeddedSourceClass = "quarto-embedded-source-code";
-const kEmbeddedSourceModalId = kEmbeddedSourceClass + "-modal";
+export const kEmbeddedSourceModalId = kEmbeddedSourceClass + "-modal";
 const kEmbeddedSourceModalLabelId = kEmbeddedSourceClass + "-modal-label";
 const kKeepSourceSentinel = "quarto-executable-code-5450563D";
 
@@ -56,7 +55,7 @@ export function resolveKeepSource(
   const codeTools = format.render?.[kCodeTools];
   if (
     codeTools === true ||
-    (typeof (codeTools) === "object" &&
+    (typeof codeTools === "object" &&
       (codeTools?.source === undefined || codeTools?.source === true))
   ) {
     format.render[kKeepSource] = true;
@@ -328,17 +327,17 @@ function resolveCodeTools(format: Format, doc: Document): CodeTools {
   const kCodeCaption = format.language[kCodeToolsMenuCaption]!;
   const codeTools = format?.render[kCodeTools];
   const codeToolsResolved = {
-    source: typeof (codeTools) === "boolean"
+    source: typeof codeTools === "boolean"
       ? codeTools
       : codeTools?.source !== undefined
       ? codeTools?.source
       : true,
-    toggle: typeof (codeTools) === "boolean"
+    toggle: typeof codeTools === "boolean"
       ? codeTools
       : codeTools?.toggle !== undefined
       ? !!codeTools?.toggle
       : true,
-    caption: typeof (codeTools) === "boolean"
+    caption: typeof codeTools === "boolean"
       ? kCodeCaption
       : codeTools?.caption || kCodeCaption,
   };

src/core/csl.ts

@@ -154,7 +154,9 @@ export function suggestId(author: CSLName[], date?: CSLDate) {
   }
 
   // Create a deduplicated string against the existing entries
-  let suggestedId = `${citeIdLeading.toLowerCase()}${datePart}`;
+  let suggestedId = `${
+    citeIdLeading.replaceAll(/\s+/g, "_").toLowerCase()
+  }${datePart}`;
   if (suggestedId.length === 0) {
     suggestedId = "untitled";
   }

src/core/puppeteer.ts

@@ -264,7 +264,7 @@ export async function getBrowserExecutablePath() {
   if (executablePath === undefined) {
     error("Chrome not found");
     info(
-      "\nNo Chrome or Chromium installation was detected.\n\nPlease run 'quarto tools install chromium' to install Chromium.\n",
+      "\nNo Chrome or Chromium installation was detected.\n\nPlease run 'quarto install chromium' to install Chromium.\n",
     );
     throw new Error();
   }

src/core/run/lua.ts

@@ -1,9 +1,8 @@
 /*
-* lua.ts
-*
-* Copyright (C) 2020-2022 Posit Software, PBC
-*
-*/
+ * lua.ts
+ *
+ * Copyright (C) 2020-2022 Posit Software, PBC
+ */
 
 import { info } from "../../deno_ral/log.ts";
 
@@ -25,7 +24,7 @@ export const luaRunHandler: RunHandler = {
     options?: RunHandlerOptions,
   ) => {
     // lua run handlers don't support stdin
-    if (typeof (stdin) === "string") {
+    if (typeof stdin === "string") {
       throw new Error("Lua run handlers cannot be passed stdin");
     }
 
@@ -37,10 +36,6 @@ export const luaRunHandler: RunHandler = {
       "--to",
       "plain",
     ];
-    if (isWindows()) {
-      cmd.push("--lua-filter");
-      cmd.push(resourcePath("filters/init/init.lua"));
-    }
     cmd.push(
       "--lua-filter",
       script,

src/core/zip.ts

@@ -9,8 +9,8 @@ import { isWindows } from "./platform.ts";
 import { execProcess } from "./process.ts";
 import { safeWindowsExec } from "./windows.ts";
 
-export function unzip(file: string) {
-  const dir = dirname(file);
+export function unzip(file: string, dir?: string) {
+  if (!dir) dir = dirname(file);
 
   if (file.endsWith("zip")) {
     // It's a zip file

src/format/html/format-html.ts

@@ -47,7 +47,10 @@ import {
   SassBundle,
 } from "../../config/types.ts";
 
-import { formatHasCodeTools } from "../../command/render/codetools.ts";
+import {
+  formatHasCodeTools,
+  kEmbeddedSourceModalId,
+} from "../../command/render/codetools.ts";
 
 import { createHtmlFormat } from "./../formats-shared.ts";
 
@@ -651,6 +654,9 @@ function htmlFormatPostprocessor(
 
     // process all of the code blocks
     const codeBlocks = doc.querySelectorAll("pre.sourceCode");
+    const EmbedSourceModal = doc.querySelector(
+      `#${kEmbeddedSourceModalId}`,
+    );
     for (let i = 0; i < codeBlocks.length; i++) {
       const code = codeBlocks[i] as Element;
 
@@ -670,10 +676,13 @@ function htmlFormatPostprocessor(
         code.parentElement?.classList.add("hidden");
       }
 
-      // insert code copy button
+      // insert code copy button (with specfic attribute when inside a modal)
       if (codeCopy) {
         code.classList.add("code-with-copy");
         const copyButton = createCodeCopyButton(doc, format);
+        if (EmbedSourceModal && EmbedSourceModal.contains(code)) {
+          copyButton.setAttribute("data-in-quarto-modal", "");
+        }
         code.appendChild(copyButton);
       }
 

src/project/types/website/listing/website-listing-read.ts

@@ -778,7 +778,7 @@ async function readContents(
     });
     if (readFiles.length === 0) {
       const projRelativePath = relative(project.dir, source);
-      throw new Error(
+      warning(
         `The listing in '${projRelativePath}' using the following contents:\n- ${
           contentGlobs.join("\n- ")
         }\ndoesn't match any files or folders.`,

src/resources/editor/tools/vs-code.mjs

@@ -11412,6 +11412,13 @@ var require_yaml_intelligence_resources = __commonJS({
                 string: {
                   description: "The primary title of the item."
                 }
+              },
+              id: {
+                anyOf: [
+                  "string",
+                  "number"
+                ],
+                description: 'Citation identifier for the item (e.g. "item1"). Will be autogenerated if not provided.'
               }
             }
           }
@@ -20385,7 +20392,7 @@ var require_yaml_intelligence_resources = __commonJS({
         },
         "Guest (e.g. on a TV show or podcast).",
         "Host of the item (e.g. of a TV show or podcast).",
-        "A value which uniquely identifies this item.",
+        "Citation identifier for the item (e.g. \u201Citem1\u201D). Will be\nautogenerated if not provided.",
         "Illustrator (e.g. of a children\u2019s book or graphic novel).",
         "Interviewer (e.g. of an interview).",
         "International Standard Book Number (e.g. \u201C978-3-8474-1017-1\u201D).",
@@ -20540,7 +20547,7 @@ var require_yaml_intelligence_resources = __commonJS({
         },
         "Guest (e.g. on a TV show or podcast).",
         "Host of the item (e.g. of a TV show or podcast).",
-        "A value which uniquely identifies this item.",
+        "Citation identifier for the item (e.g. \u201Citem1\u201D). Will be\nautogenerated if not provided.",
         "Illustrator (e.g. of a children\u2019s book or graphic novel).",
         "Interviewer (e.g. of an interview).",
         "International Standard Book Number (e.g. \u201C978-3-8474-1017-1\u201D).",
@@ -22927,12 +22934,12 @@ var require_yaml_intelligence_resources = __commonJS({
         mermaid: "%%"
       },
       "handlers/mermaid/schema.yml": {
-        _internalId: 182250,
+        _internalId: 182259,
         type: "object",
         description: "be an object",
         properties: {
           "mermaid-format": {
-            _internalId: 182242,
+            _internalId: 182251,
             type: "enum",
             enum: [
               "png",
@@ -22948,7 +22955,7 @@ var require_yaml_intelligence_resources = __commonJS({
             exhaustiveCompletions: true
           },
           theme: {
-            _internalId: 182249,
+            _internalId: 182258,
             type: "anyOf",
             anyOf: [
               {