Merge branch 'main' into windows/bib-forward-slash

Author: cderv

.github/pull_request_template.md

@@ -22,6 +22,6 @@ print("Hello Quarto!")
 
 I have (if applicable):
 
-- [ ] filed a [contributor agreement](../CONTRIBUTING.md).
+- [ ] filed a [contributor agreement](https://github.com/quarto-dev/quarto-cli/blob/main/CONTRIBUTING.md).
 - [ ] referenced the GitHub issue this PR closes
 - [ ] updated the appropriate changelog

news/changelog-1.3.md

@@ -36,6 +36,7 @@
 - Add support for automatically converting SVG images to PDF ([#2575](https://github.com/quarto-dev/quarto-cli/issues/2575))
 - Previously, if the `pdf-engine` was set to `latexmk`, we would bypass many features of Quarto and use Pandoc to produce the PDF output. Starting in in Quarto 1.3, all Quarto features will be enabled for the `latexmk` engine and `latexmk` will be used to run the PDF generation loop.
 - Fix author processing in default PDFs for complex author names (#3483)
+- Remove excessive vertical space between theorem type blocks ([#3776](https://github.com/quarto-dev/quarto-cli/issues/3776)).
 
 ## Beamer Format
 

src/command/render/render.ts

@@ -20,7 +20,7 @@ import {
 import { inputFilesDir } from "../../core/render.ts";
 import { pathWithForwardSlashes } from "../../core/path.ts";
 
-import { Format, FormatPandoc } from "../../config/types.ts";
+import { FormatPandoc } from "../../config/types.ts";
 import {
   executionEngine,
   executionEngineKeepMd,
@@ -121,6 +121,11 @@ export async function renderPandoc(
     executeResult.markdown,
   );
 
+  if (notebookResult.supporting) {
+    executeResult.supporting = executeResult.supporting || [];
+    executeResult.supporting.push(notebookResult.supporting);
+  }
+
   // Map notebook includes to pandoc includes
   const pandocIncludes: PandocIncludes = {
     [kIncludeAfterBody]: notebookResult.includes?.afterBody
@@ -139,7 +144,9 @@ export async function renderPandoc(
 
   // pandoc options
   const pandocOptions: PandocOptions = {
-    markdown: notebookResult.markdown,
+    markdown: notebookResult.markdown
+      ? notebookResult.markdown
+      : executeResult.markdown,
     source: context.target.source,
     output: recipe.output,
     keepYaml: recipe.keepYaml,

src/core/jupyter/jupyter-embed.ts

@@ -9,6 +9,7 @@ import { resourcePath } from "../resources.ts";
 import { getNamedLifetime, ObjectWithLifetime } from "../lifetimes.ts";
 
 import {
+  cleanEmptyJupyterAssets,
   jupyterAssets,
   jupyterFromFile,
   jupyterToMarkdown,
@@ -44,7 +45,7 @@ import {
 import { globalTempContext } from "../temp.ts";
 import { isAbsolute } from "path/mod.ts";
 import { partitionMarkdown } from "../pandoc/pandoc-partition.ts";
-import { safeExistsSync } from "../path.ts";
+import { removeIfEmptyDir, safeExistsSync } from "../path.ts";
 import { basename } from "path/mod.ts";
 
 export interface JupyterNotebookAddress {
@@ -149,8 +150,16 @@ export async function replaceNotebookPlaceholders(
   markdown: string,
 ) {
   let match = kPlaceholderRegex.exec(markdown);
+  let assets;
   let includes;
   while (match) {
+    if (!assets) {
+      assets = jupyterAssets(
+        context.target.source,
+        to,
+      );
+    }
+
     // Parse the address and if this is a notebook
     // then proceed with the replacement
     const nbAddressStr = match[1];
@@ -166,12 +175,6 @@ export async function replaceNotebookPlaceholders(
         ? placeholderToOptions(placeholderStr)
         : {};
 
-      // Assets
-      const assets = jupyterAssets(
-        input,
-        to,
-      );
-
       // Compute appropriate includes based upon the note
       // dependendencies
       const notebookIncludes = () => {
@@ -215,9 +218,13 @@ export async function replaceNotebookPlaceholders(
     match = kPlaceholderRegex.exec(markdown);
   }
   kPlaceholderRegex.lastIndex = 0;
+  const supporting = assets
+    ? join(assets.base_dir, assets.supporting_dir)
+    : undefined;
   return {
     includes,
     markdown,
+    supporting,
   };
 }
 

src/core/jupyter/jupyter.ts

@@ -145,11 +145,12 @@ import { figuresDir, inputFilesDir } from "../render.ts";
 import { lines } from "../text.ts";
 import { readYamlFromMarkdown } from "../yaml.ts";
 import { languagesInMarkdown } from "../../execute/engine-shared.ts";
-import { pathWithForwardSlashes } from "../path.ts";
+import { pathWithForwardSlashes, removeIfEmptyDir } from "../path.ts";
 import { convertToHtmlSpans, hasAnsiEscapeCodes } from "../ansi-colors.ts";
 import { ProjectContext } from "../../project/types.ts";
 import { mergeConfigs } from "../config.ts";
 import { encode as encodeBase64 } from "encoding/base64.ts";
+import { isIpynbOutput } from "../../config/format.ts";
 
 export const kQuartoMimeType = "quarto_mimetype";
 export const kQuartoOutputOrder = "quarto_order";
@@ -571,7 +572,17 @@ export function jupyterAutoIdentifier(label: string) {
   }
 }
 
-export function jupyterAssets(input: string, to?: string) {
+export interface JupyterNotebookAssetPaths {
+  base_dir: string;
+  files_dir: string;
+  figures_dir: string;
+  supporting_dir: string;
+}
+
+export function jupyterAssets(
+  input: string,
+  to?: string,
+): JupyterNotebookAssetPaths {
   // calculate and create directories
   input = Deno.realPathSync(input);
   const files_dir = join(dirname(input), inputFilesDir(input));
@@ -601,6 +612,16 @@ export function jupyterAssets(input: string, to?: string) {
   };
 }
 
+export function cleanEmptyJupyterAssets(assets: JupyterNotebookAssetPaths) {
+  const figuresRemoved = removeIfEmptyDir(
+    join(assets.base_dir, assets.figures_dir),
+  );
+  const filesRemoved = removeIfEmptyDir(
+    join(assets.base_dir, assets.files_dir),
+  );
+  return figuresRemoved && filesRemoved;
+}
+
 // Attach fully rendered notebook to render services
 // Render notebook only once per document
 // Return cells with markdown instead of complete markdown
@@ -1096,6 +1117,14 @@ async function mdFromCodeCell(
   // write div enclosure
   const divMd: string[] = [`::: {`];
 
+  // If we're targeting ipynb output, include the id in the
+  // markdown. This will cause the id to be included in the
+  // rendered notebook. Note that elsewhere we forard the
+  // label to the id, so that can appear as the cell id.
+  if (isIpynbOutput(options.executeOptions.format.pandoc) && cell.id) {
+    divMd.push(`#${cell.id} `);
+  }
+
   // metadata to exclude from cell div attributes
   const kCellOptionsFilter = kJupyterCellInternalOptionKeys.concat(
     kJupyterCellStandardMetadataKeys,

src/core/path.ts

@@ -40,7 +40,7 @@ export function safeRemoveIfExists(file: string) {
   }
 }
 
-export function removeIfEmptyDir(dir: string) {
+export function removeIfEmptyDir(dir: string): boolean {
   if (existsSync(dir)) {
     let empty = true;
     for (const _entry of Deno.readDirSync(dir)) {
@@ -49,7 +49,11 @@ export function removeIfEmptyDir(dir: string) {
     }
     if (empty) {
       Deno.removeSync(dir, { recursive: true });
+      return true;
     }
+    return false;
+  } else {
+    return false;
   }
 }
 

src/core/sass.ts

@@ -17,6 +17,7 @@ import { dartCompile } from "./dart-sass.ts";
 import * as ld from "./lodash.ts";
 import { lines } from "./text.ts";
 import { md5Hash } from "./hash.ts";
+import { debug } from "log/mod.ts";
 
 export interface SassVariable {
   name: string;
@@ -314,9 +315,13 @@ export async function compileWithCache(
     let cacheIndex: { [key: string]: { key: string; hash: string } } = {};
     let writeCache = true;
     if (existsSync(outputFilePath)) {
-      cacheIndex = JSON.parse(Deno.readTextFileSync(cacheIdxPath));
-      const existingEntry = cacheIndex[identifierHash];
-      writeCache = !existingEntry || (existingEntry.hash !== inputHash);
+      try {
+        cacheIndex = JSON.parse(Deno.readTextFileSync(cacheIdxPath));
+        const existingEntry = cacheIndex[identifierHash];
+        writeCache = !existingEntry || (existingEntry.hash !== inputHash);
+      } catch {
+        debug(`The scss cache index file ${cacheIdxPath} can't be read.`);
+      }
     }
 
     // We need to refresh the cache

src/format/html/format-html-bootstrap.ts

@@ -246,6 +246,7 @@ function bootstrapHtmlPostprocessor(
   ): Promise<HtmlPostProcessResult> => {
     // Resources used in this post processor
     const resources: string[] = [];
+    const supporting: string[] = [];
 
     // use display-7 style for title
     const title = doc.querySelector("header > .title");
@@ -334,7 +335,16 @@ function bootstrapHtmlPostprocessor(
 
     // Look for included / embedded notebooks and include those
     if (format.render[kNotebookLinks] !== false) {
-      await processNotebookEmbeds(input, doc, format, resources, services);
+      const notebookPreviews = await processNotebookEmbeds(
+        input,
+        doc,
+        format,
+        resources,
+        services,
+      );
+      if (notebookPreviews && notebookPreviews.length > 0) {
+        supporting.push(...notebookPreviews);
+      }
     }
 
     // default treatment for computational tables
@@ -421,7 +431,7 @@ function bootstrapHtmlPostprocessor(
     }
 
     // no resource refs
-    return Promise.resolve({ resources, supporting: [] });
+    return Promise.resolve({ resources, supporting });
   };
 }
 

src/format/html/format-html-notebook.ts

@@ -26,9 +26,9 @@ import {
   HtmlPostProcessResult,
   RenderServices,
 } from "../../command/render/types.ts";
-import { render } from "../../command/render/render-shared.ts";
 
 import { basename, dirname, join, relative } from "path/mod.ts";
+import { renderFiles } from "../../command/render/render-files.ts";
 
 interface NotebookView {
   title: string;
@@ -226,6 +226,11 @@ export async function processNotebookEmbeds(
     if (nbViewConfig) {
       nbViewConfig.unused(linkedNotebooks);
     }
+
+    const inputDir = dirname(input);
+    return nbPaths.map((nbPath) => {
+      return join(inputDir, nbPath.href);
+    });
   }
 }
 
@@ -288,7 +293,7 @@ async function renderHtmlView(
 
     // Render the notebook and update the path
     const nbPreviewFile = `${filename}.html`;
-    await render(nbAbsPath, {
+    await renderFiles([{ path: nbAbsPath }], {
       services,
       flags: {
         metadata: {

src/format/html/format-html.ts

@@ -714,6 +714,22 @@ function processCodeAnnotations(format: Format, doc: Document) {
     | string
     | boolean;
 
+  const replaceLineNumberWithAnnote = (annoteEl: Element, dtEl: Element) => {
+    const annotation = annoteEl.getAttribute(kCodeAnnotationAttr);
+    if (annotation !== null) {
+      const ddEl = dtEl.previousElementSibling;
+      if (ddEl) {
+        ddEl.innerHTML = "";
+        ddEl.innerText = annotation;
+        const codeCell = annoteEl.getAttribute(kCodeCellAttr);
+        if (codeCell) {
+          ddEl.setAttribute(kCodeCellTargetAttr, codeCell);
+          ddEl.setAttribute(kCodeAnnotationTargetAttr, annotation);
+        }
+      }
+    }
+  };
+
   if (annotationStyle === false) {
     // Read the definition list values which contain the annotations
     const annoteNodes = doc.querySelectorAll(`span[${kCodeCellAttr}]`);
@@ -732,26 +748,23 @@ function processCodeAnnotations(format: Format, doc: Document) {
       }
     }
   } else if (annotationStyle === "hover" || annotationStyle === "select") {
-    const definitionLists = processCodeBlockAnnotation(doc, true, "start");
+    const definitionLists = processCodeBlockAnnotation(
+      doc,
+      true,
+      "start",
+      replaceLineNumberWithAnnote,
+    );
 
     Object.values(definitionLists).forEach((dl) => {
       dl.classList.add(kCodeAnnotationHiddenClz);
+      dl.classList.add(kCodeAnnotationGridClz);
     });
   } else {
     const definitionLists = processCodeBlockAnnotation(
       doc,
       false,
       "start",
-      (annoteEl: Element, dtEl: Element) => {
-        const annotation = annoteEl.getAttribute(kCodeAnnotationAttr);
-        if (annotation !== null) {
-          const ddEl = dtEl.previousElementSibling;
-          if (ddEl) {
-            ddEl.innerHTML = "";
-            ddEl.innerText = annotation;
-          }
-        }
-      },
+      replaceLineNumberWithAnnote,
     );
 
     Object.values(definitionLists).forEach((dl) => {