Merge branch 'quarto-dev:main' into main

CITATION.cff

@@ -16,8 +16,11 @@ authors:
 - family-names: "Dervieux"
   given-names: "Christophe"
   orcid: "https://orcid.org/0000-0003-4474-2498"
+- family-names: "Woodhull"
+  given-names: "Gordon"
+  orcid: "https://orcid.org/0009-0005-1809-8936"
 title: "Quarto"
-version: 1.4
+version: 1.6
 doi: 10.5281/zenodo.5960048
-date-released: 2024-02-15
+date-released: 2024-11-27
 url: "https://github.com/quarto-dev/quarto-cli"

dev-docs/checklist-make-a-new-quarto-release.md

@@ -45,6 +45,7 @@
   - [ ] publish the release blog post that should exist in https://github.com/quarto-dev/quarto-web/tree/main/docs/blog/posts
         by removing the `draft: true` line in the metadata and changing the date to match the release date. Do this on a branch off of `main` to trigger our PR automation to make the corresponding change to `prerelease`.
 
+- [ ] Update https://github.com/quarto-dev/quarto-cli/blob/main/CITATION.cff
 - [ ] Packaging and package managers, etc
   - TBD winget, etc?
   - [ ] chocolatey

news/changelog-1.7.md

@@ -25,9 +25,18 @@ All changes included in 1.7:
 
 - ([#11608](https://github.com/quarto-dev/quarto-cli/pull/11608)): Do not issue error message when calling `quarto check info`.
 
-## `typst` Format
+## `html` format
+
+- ([#11860])(https://github.com/quarto-dev/quarto-cli/issues/11860)): ES6 modules that import other local JS modules in documents with `embed-resources: true` are now correctly embedded.
+
+## `pdf` format
+
+- ([#11835](https://github.com/quarto-dev/quarto-cli/issues/11835)): Take markdown structure into account when detecting minimum heading level.
+
+## `typst` format
 
 - ([#11578](https://github.com/quarto-dev/quarto-cli/issues/11578)): Typst column layout widths use fractional `fr` units instead of percent `%` units for unitless and default widths in order to fill the enclosing block and not spill outside it.
+- ([#11835](https://github.com/quarto-dev/quarto-cli/issues/11835)): Take markdown structure into account when detecting minimum heading level.
 
 ## Lua Filters and extensions
 

package/src/common/prepare-dist.ts

@@ -238,6 +238,7 @@ function inlineFilters(config: Configuration) {
     { name: "crossref" },
     { name: "customwriter" },
     { name: "qmd-reader", dir: "." },
+    { name: "leveloneanalysis", dir: "quarto-internals"}
   ];
 
   filtersToInline.forEach((filter) => {

src/core/config.ts

@@ -5,18 +5,22 @@
  */
 
 import * as ld from "./lodash.ts";
+import { makeTimedFunction } from "./performance/function-times.ts";
 
-export function mergeConfigs<T>(config: T, ...configs: Array<unknown>): T {
-  // copy all configs so we don't mutate them
-  config = ld.cloneDeep(config);
-  configs = ld.cloneDeep(configs);
+export const mergeConfigs = makeTimedFunction(
+  "mergeConfigs",
+  function mergeConfigs<T>(config: T, ...configs: Array<unknown>): T {
+    // copy all configs so we don't mutate them
+    config = ld.cloneDeep(config);
+    configs = ld.cloneDeep(configs);
 
-  return ld.mergeWith(
-    config,
-    ...configs,
-    mergeArrayCustomizer,
-  );
-}
+    return ld.mergeWith(
+      config,
+      ...configs,
+      mergeArrayCustomizer,
+    );
+  },
+);
 
 export function mergeArrayCustomizer(objValue: unknown, srcValue: unknown) {
   if (ld.isArray(objValue) || ld.isArray(srcValue)) {

src/core/data-url.ts

@@ -1,4 +1,4 @@
-import { encode as base64Encode } from "encoding/base64";
+import { encodeBase64 as base64Encode } from "encoding/base64";
 
 export function asDataUrl(
   content: string | ArrayBuffer,

src/core/deno-dom.ts

@@ -9,20 +9,24 @@ import { debug } from "../deno_ral/log.ts";
 import { HTMLDocument, initParser } from "deno_dom/deno-dom-wasm-noinit.ts";
 import { register } from "deno_dom/src/parser.ts";
 import { DOMParser } from "deno_dom/src/dom/dom-parser.ts";
+import { makeTimedFunctionAsync } from "./performance/function-times.ts";
 
 export async function getDomParser() {
   await initDenoDom();
   return new DOMParser();
 }
 
-export async function parseHtml(src: string): Promise<HTMLDocument> {
-  await initDenoDom();
-  const result = (new DOMParser()).parseFromString(src, "text/html");
-  if (!result) {
-    throw new Error("Couldn't parse string into HTML");
-  }
-  return result;
-}
+export const parseHtml = makeTimedFunctionAsync(
+  "parseHtml",
+  async function parseHtml(src: string): Promise<HTMLDocument> {
+    await initDenoDom();
+    const result = (new DOMParser()).parseFromString(src, "text/html");
+    if (!result) {
+      throw new Error("Couldn't parse string into HTML");
+    }
+    return result;
+  },
+);
 
 export async function writeDomToHtmlFile(
   doc: HTMLDocument,

src/core/esbuild.ts

@@ -106,6 +106,8 @@ export async function esbuildCommand(
   if (result.success) {
     return result.stdout;
   } else {
+    console.error(result.stderr);
+
     throw new Error("esbuild command failed");
   }
 }

src/core/lib/break-quarto-md.ts

@@ -7,7 +7,7 @@
  * Copyright (C) 2021-2022 Posit Software, PBC
  */
 
-import { lineOffsets, lines } from "./text.ts";
+import { lineOffsets } from "./text.ts";
 import { Range, rangedLines, RangedSubstring } from "./ranged-text.ts";
 import {
   asMappedString,

src/core/lib/is-circular.ts

@@ -0,0 +1,27 @@
+/*
+ * is-circular.ts
+ *
+ * Copyright (C) 2025 Posit Software, PBC
+ */
+
+// deno-lint-ignore no-explicit-any
+export const isCircular = (obj: any): unknown => {
+  const objectSet = new WeakSet();
+  // deno-lint-ignore no-explicit-any
+  const detect = (obj: any): boolean => {
+    if (obj && typeof obj === "object") {
+      if (objectSet.has(obj)) {
+        return true;
+      }
+      objectSet.add(obj);
+      for (const key in obj) {
+        if (Object.hasOwn(obj, key) && detect(obj[key])) {
+          return true;
+        }
+      }
+      objectSet.delete(obj);
+    }
+    return false;
+  };
+  return detect(obj);
+};

src/core/lib/markdown-analysis/level-one-headings.ts

@@ -0,0 +1,24 @@
+/*
+ * level-one-headings.ts
+ *
+ * Copyright (C) 2025 Posit Software, PBC
+ */
+
+import { join } from "../../../deno_ral/path.ts";
+import { execProcess } from "../../process.ts";
+import { pandocBinaryPath, resourcePath } from "../../resources.ts";
+
+export async function hasLevelOneHeadings(markdown: string): Promise<boolean> {
+  // this is O(n * m) where n is the number of blocks and m is the number of matches
+  // we could do better but won't until we profile and show it's a problem
+
+  const path = pandocBinaryPath();
+  const filterPath = resourcePath(
+    join("filters", "quarto-internals", "leveloneanalysis.lua"),
+  );
+  const result = await execProcess({
+    cmd: [path, "-f", "markdown", "-t", "markdown", "-L", filterPath],
+    stdout: "piped",
+  }, markdown);
+  return result.stdout?.trim() === "true";
+}

src/core/lib/yaml-intelligence/annotated-yaml.ts

@@ -21,6 +21,7 @@ import { QuartoJSONSchema } from "./js-yaml-schema.ts";
 import { createSourceContext } from "../yaml-validation/errors.ts";
 import { tidyverseInfo } from "../errors.ts";
 import { InternalError } from "../error.ts";
+import { isCircular } from "../is-circular.ts";
 
 // deno-lint-ignore no-explicit-any
 type TreeSitterParse = any;
@@ -268,23 +269,10 @@ export function buildJsYamlAnnotation(mappedYaml: MappedString) {
     );
   }
 
-  // console.log(results[0]);
-  try {
-    JSON.stringify(results[0]); // this is here so that we throw on circular structures
-  } catch (e) {
-    if (e.message.match("invalid string length")) {
-      // https://github.com/quarto-dev/quarto-cli/issues/10504
-      // It seems to be relatively easy to hit string length limits in
-      // JSON.stringify. Since this call is only here to check for circular
-      // structures, we chose to ignore this error, even though it's not
-      // ideal
-    } else if (e.message.match(/circular structure/)) {
-      throw new InternalError(
-        `Circular structure detected in parsed yaml: ${e.message}`,
-      );
-    } else {
-
-    }
+  if (isCircular(results[0])) {
+    throw new InternalError(
+      `Circular structure detected in yaml`,
+    );
   }
   return postProcessAnnotation(results[0]);
 }

src/core/lodash.ts

@@ -1,11 +1,10 @@
 /*
-* lodash.ts
-*
-* piecemeal exports of lodash to make the tree-shaker happier
-*
-* Copyright (C) 2022 Posit Software, PBC
-*
-*/
+ * lodash.ts
+ *
+ * piecemeal exports of lodash to make the tree-shaker happier
+ *
+ * Copyright (C) 2022 Posit Software, PBC
+ */
 
 import ld_cloneDeep from "lodash/cloneDeep.js";
 import ld_debounce from "lodash/debounce.js";
@@ -23,8 +22,9 @@ import ld_isObject from "lodash/isObject.js";
 import ld_isEqual from "lodash/isEqual.js";
 import ld_orderBy from "lodash/orderBy.js";
 import ld_escape from "lodash/escape.js";
+import { makeTimedFunction } from "./performance/function-times.ts";
 
-export const cloneDeep = ld_cloneDeep;
+export const cloneDeep = makeTimedFunction("ld_cloneDeep", ld_cloneDeep);
 export const debounce = ld_debounce;
 export const difference = ld_difference;
 export const each = ld_each;

src/core/main.ts

@@ -12,8 +12,10 @@ import { parse } from "flags";
 import { exitWithCleanup } from "./cleanup.ts";
 import {
   captureFileReads,
-  reportPeformanceMetrics,
+  type MetricsKeys,
+  reportPerformanceMetrics,
 } from "./performance/metrics.ts";
+import { makeTimedFunctionAsync } from "./performance/function-times.ts";
 import { isWindows } from "../deno_ral/platform.ts";
 
 type Runner = (args: Args) => Promise<unknown>;
@@ -29,11 +31,15 @@ export async function mainRunner(runner: Runner) {
       Deno.addSignalListener("SIGTERM", abend);
     }
 
-    if (Deno.env.get("QUARTO_REPORT_PERFORMANCE_METRICS") !== undefined) {
+    const metricEnv = Deno.env.get("QUARTO_REPORT_PERFORMANCE_METRICS");
+    if (metricEnv === "true" || metricEnv?.split(",").includes("fileReads")) {
       captureFileReads();
     }
 
-    await runner(args);
+    const main = makeTimedFunctionAsync("main", async () => {
+      return await runner(args);
+    });
+    await main();
 
     // if profiling, wait for 10 seconds before quitting
     if (Deno.env.get("QUARTO_TS_PROFILE") !== undefined) {
@@ -42,8 +48,12 @@ export async function mainRunner(runner: Runner) {
       await new Promise((resolve) => setTimeout(resolve, 10000));
     }
 
-    if (Deno.env.get("QUARTO_REPORT_PERFORMANCE_METRICS") !== undefined) {
-      reportPeformanceMetrics();
+    if (metricEnv !== undefined) {
+      if (metricEnv !== "true") {
+        reportPerformanceMetrics(metricEnv.split(",") as MetricsKeys[]);
+      } else {
+        reportPerformanceMetrics();
+      }
     }
 
     exitWithCleanup(0);

src/core/mapped-text.ts

@@ -15,6 +15,7 @@ import { debug } from "../deno_ral/log.ts";
 
 import * as mt from "./lib/mapped-text.ts";
 import { withTiming } from "./timing.ts";
+import { makeTimedFunction } from "./performance/function-times.ts";
 
 export type EitherString = mt.EitherString;
 export type MappedString = mt.MappedString;
@@ -33,7 +34,7 @@ export {
 // uses a diff algorithm to map on a line-by-line basis target lines
 // for `target` to `source`, allowing us to somewhat recover
 // MappedString information from third-party tools like knitr.
-export function mappedDiff(
+function mappedDiffInner(
   source: MappedString,
   target: string,
 ) {
@@ -82,6 +83,7 @@ export function mappedDiff(
     return mappedString(source, resultChunks, source.fileName);
   });
 }
+export const mappedDiff = makeTimedFunction("mappedDiff", mappedDiffInner);
 
 export function mappedStringFromFile(filename: string): MappedString {
   const value = Deno.readTextFileSync(filename);

src/core/pandoc/self-contained.ts

@@ -4,9 +4,34 @@
  * Copyright (C) 2020-2023 Posit Software, PBC
  */
 
-import { basename, dirname } from "../../deno_ral/path.ts";
+import { basename, dirname, join } from "../../deno_ral/path.ts";
 import { formatResourcePath, pandocBinaryPath } from "../../core/resources.ts";
 import { execProcess } from "../../core/process.ts";
+import { parseHtml } from "../deno-dom.ts";
+import { Element, HTMLDocument } from "deno_dom/deno-dom-wasm-noinit.ts";
+import { esbuildCompile } from "../esbuild.ts";
+import { asDataUrl } from "../data-url.ts";
+
+const bundleModules = async (dom: HTMLDocument, workingDir: string) => {
+  const modules = dom.querySelectorAll("script[type='module']");
+  for (const module of modules) {
+    const src = (module as Element).getAttribute("src");
+    if (src) {
+      const srcName = join(workingDir, src);
+      const srcDir = dirname(srcName);
+      const jsSource = await esbuildCompile(
+        Deno.readTextFileSync(srcName),
+        srcDir,
+        [],
+        "esm",
+      );
+      (module as Element).setAttribute(
+        "src",
+        asDataUrl(jsSource!, "application/javascript"),
+      );
+    }
+  }
+};
 
 export const pandocIngestSelfContainedContent = async (
   file: string,
@@ -23,9 +48,12 @@ export const pandocIngestSelfContainedContent = async (
 
   // The raw html contents
   const contents = Deno.readTextFileSync(file);
+  const dom = await parseHtml(contents);
+  await bundleModules(dom, workingDir);
+
   const input: string[] = [];
   input.push("````````{=html}");
-  input.push(contents);
+  input.push(dom.documentElement!.outerHTML);
   input.push("````````");
 
   // Run pandoc to suck in dependencies