Merge branch 'main' into when-format-more

Author: cscheid

news/changelog-1.7.md

@@ -9,6 +9,7 @@ import { createTempContext } from "../../core/temp.ts";
 import { installExtension } from "../../extension/install.ts";
 
 import { info } from "../../deno_ral/log.ts";
+import { signalCommandFailure } from "../utils.ts";
 
 export const addCommand = new Command()
   .name("add")
@@ -44,16 +45,19 @@ export const addCommand = new Command()
       await initYamlIntelligenceResourcesFromFilesystem();
       const temp = createTempContext();
       try {
-        // Install an extension
-        if (extension) {
-          await installExtension(
-            extension,
-            temp,
-            options.prompt !== false,
-            options.embed,
-          );
-        } else {
+        if (!extension) {
           info("Please provide an extension name, url, or path.");
+          signalCommandFailure();
+        }
+        // Install an extension
+        const result = await installExtension(
+          extension,
+          temp,
+          options.prompt !== false,
+          options.embed,
+        );
+        if (!result) {
+          signalCommandFailure();
         }
       } finally {
         temp.cleanup();

src/command/add/cmd.ts

@@ -132,8 +132,6 @@ export async function jupyterNotebookToMarkdown(
     }
   }
 
-  console.log({ md });
-
   // join into source
   const mdSource = md.join("");
 

src/command/convert/jupyter.ts

@@ -17,7 +17,6 @@ import { outputTools } from "../../tools/tools-console.ts";
 import { notebookContext } from "../../render/notebook/notebook-context.ts";
 
 export const listCommand = new Command()
-  .hidden()
   .name("list")
   .arguments("<type:string>")
   .description(

src/command/list/cmd.ts

@@ -22,6 +22,7 @@ import {
   selectTool,
 } from "../../tools/tools-console.ts";
 import { notebookContext } from "../../render/notebook/notebook-context.ts";
+import { signalCommandFailure } from "../utils.ts";
 
 export const removeCommand = new Command()
   .name("remove")
@@ -69,6 +70,7 @@ export const removeCommand = new Command()
             const allTools = await loadTools();
             if (allTools.filter((tool) => tool.installed).length === 0) {
               info("No tools are installed.");
+              signalCommandFailure();
             } else {
               // Select which tool should be installed
               const toolTarget = await selectTool(allTools, "remove");
@@ -118,6 +120,7 @@ export const removeCommand = new Command()
               await removeExtensions(extensions.slice(), options.prompt);
             } else {
               info("No matching extension found.");
+              signalCommandFailure();
             }
           } else {
             const nbContext = notebookContext();
@@ -138,6 +141,7 @@ export const removeCommand = new Command()
               }
             } else {
               info("No extensions installed.");
+              signalCommandFailure();
             }
           }
         }

src/command/remove/cmd.ts

@@ -142,7 +142,7 @@ export async function resolveSassBundles(
       )
       ? "dark"
       : "light";
-    const targets: SassTarget[] = [{
+    let targets: SassTarget[] = [{
       name: `${dependency}.min.css`,
       bundles: (bundles as any),
       attribs: {
@@ -175,10 +175,22 @@ export async function resolveSassBundles(
           ...attribForThemeStyle("dark"),
         },
       };
-      if (defaultStyle === "dark") {
+      if (defaultStyle === "dark") { // light, dark
         targets.push(darkTarget);
-      } else {
-        targets.unshift(darkTarget);
+      } else { // light, dark, light
+        const lightTargetExtra = {
+          ...targets[0],
+          attribs: {
+            ...targets[0].attribs,
+            class: "quarto-color-scheme-extra",
+          },
+        };
+
+        targets = [
+          targets[0],
+          darkTarget,
+          lightTargetExtra,
+        ];
       }
 
       hasDarkStyles = true;
@@ -498,34 +510,67 @@ function generateThemeCssClasses(
     Record<string, unknown>
   >;
   if (textStyles) {
-    const lines: string[] = [];
+    const otherLines: string[] = [];
+    otherLines.push("/* syntax highlight based on Pandoc's rules */");
+    const tokenCssByAbbr: Record<string, string[]> = {};
+
+    const toCSS = function (
+      abbr: string,
+      styleName: string,
+      cssValues: string[],
+    ) {
+      const lines: string[] = [];
+      lines.push(`/* ${styleName} */`);
+      lines.push(`\ncode span${abbr !== "" ? `.${abbr}` : ""} {`);
+      cssValues.forEach((value) => {
+        lines.push(`  ${value}`);
+      });
+      lines.push("}\n");
+
+      // Store by abbreviation for sorting later
+      tokenCssByAbbr[abbr] = lines;
+    };
 
     Object.keys(textStyles).forEach((styleName) => {
       const abbr = kAbbrevs[styleName];
       if (abbr !== undefined) {
         const textValues = textStyles[styleName];
         const cssValues = generateCssKeyValues(textValues);
 
-        if (abbr !== "") {
-          lines.push(`\ncode span.${abbr} {`);
-          lines.push(...cssValues);
-          lines.push("}\n");
-        } else {
+        toCSS(abbr, styleName, cssValues);
+
+        if (abbr == "") {
           [
             "pre > code.sourceCode > span",
-            "code span",
             "code.sourceCode > span",
             "div.sourceCode,\ndiv.sourceCode pre.sourceCode",
           ]
             .forEach((selector) => {
-              lines.push(`\n${selector} {`);
-              lines.push(...cssValues);
-              lines.push("}\n");
+              otherLines.push(`\n${selector} {`);
+              otherLines.push(...cssValues);
+              otherLines.push("}\n");
             });
         }
       }
     });
-    return lines;
+
+    // Sort tokenCssLines by abbr and flatten them
+    // Ensure empty abbr ("") comes first by using a custom sort function
+    const sortedTokenCssLines: string[] = [];
+    Object.keys(tokenCssByAbbr)
+      .sort((a, b) => {
+        // Empty string ("") should come first
+        if (a === "") return -1;
+        if (b === "") return 1;
+        // Otherwise normal alphabetical sort
+        return a.localeCompare(b);
+      })
+      .forEach((abbr) => {
+        sortedTokenCssLines.push(...tokenCssByAbbr[abbr]);
+      });
+
+    // return otherLines followed by tokenCssLines (now sorted by abbr)
+    return otherLines.concat(sortedTokenCssLines);
   }
   return undefined;
 }

src/command/render/pandoc-html.ts

@@ -270,26 +270,47 @@ function katexScript(url: string) {
       link.rel = "stylesheet";
       link.href = "${url}katex.min.css";
       head.appendChild(link);
-
-      var script = document.createElement("script");
-      script.type = "text/javascript";
-      script.src  = "${url}katex.min.js";
-      script.async = false;
-      script.addEventListener('load', function() {
+      
+      function renderMathElements() {
         var mathElements = document.getElementsByClassName("math");
-          var macros = [];
-          for (var i = 0; i < mathElements.length; i++) {
-            var texText = mathElements[i].firstChild;
-            if (mathElements[i].tagName == "SPAN") {
+        var macros = [];
+        for (var i = 0; i < mathElements.length; i++) {
+          var texText = mathElements[i].firstChild;
+          if (mathElements[i].tagName == "SPAN") {
+            if (window.katex) {
               window.katex.render(texText.data, mathElements[i], {
                 displayMode: mathElements[i].classList.contains('display'),
                 throwOnError: false,
                 macros: macros,
                 fleqn: false
               });
+            } else {
+              console.error("KaTeX has not been loaded correctly, as not found globally.");
             }
           }
-      });
+        }
+      }
+
+      var script = document.createElement("script");
+      script.src = "${url}katex.min.js";
+      script.onload = renderMathElements;
+      
+      // Check for RequireJS and AMD detection as it conflicts with KaTeX loading.
+      if (typeof require === 'function' && typeof define === 'function' && define.amd) {
+        // Disable require.js AMD detection temporarily, as it conflicts with KaTeX loading using CommonJS
+        var disableAmdScript = document.createElement("script");
+        disableAmdScript.textContent = 'window._amd_backup = window.define.amd; window.define.amd = false;';
+        head.appendChild(disableAmdScript);
+        
+        // overwrite onload to restore Require.js AMD detection
+        script.onload = function() {
+          // Restore Require.js AMD detection
+          window.define.amd = window._amd_backup;
+          delete window._amd_backup;
+          renderMathElements();
+        };
+      }
+
       head.appendChild(script);
     });
   </script>

src/command/render/template.ts

@@ -0,0 +1,17 @@
+/*
+ * utils.ts
+ *
+ * Copyright (C) 2025 Posit Software, PBC
+ */
+
+let someCommandFailed = false;
+
+// we do this the roundabout way because there doesn't seem to be any clean way
+// for cliffy commands to return values? Likely a skill issue on my part
+export const signalCommandFailure = () => {
+  someCommandFailed = true;
+};
+
+export const commandFailed = () => {
+  return someCommandFailed;
+};

src/command/utils.ts

@@ -174,6 +174,8 @@ import {
   jupyterCellSrcAsLines,
   jupyterCellSrcAsStr,
 } from "./jupyter-shared.ts";
+import { error } from "../../deno_ral/log.ts";
+import { valid } from "semver/mod.ts";
 
 export const kQuartoMimeType = "quarto_mimetype";
 export const kQuartoOutputOrder = "quarto_order";
@@ -921,8 +923,44 @@ export function jupyterCellWithOptions(
     }
   };
 
+  const validMetadata: Record<
+    string,
+    string | number | boolean | null | Array<unknown>
+  > = {};
+  for (const key of Object.keys(cell.metadata)) {
+    const value = cell.metadata[key];
+    let jsonEncodedKeyIndex = 0;
+    if (value !== undefined) {
+      if (!value && typeof value === "object") {
+        validMetadata[key] = null;
+      } else if (value && typeof value === "object" && !Array.isArray(value)) {
+        // https://github.com/quarto-dev/quarto-cli/issues/9089
+        // we need to json-encode this and signal the encoding in the key
+        // we can't use the key as is since it may contain invalid characters
+        // and modifying the key might introduce collisions
+        // we ensure the key is unique with a counter, and assume
+        // "quarto-private-*" to be a private namespace for quarto.
+        // we'd prefer to use _quarto-* instead, but Pandoc doesn't allow keys to start
+        // with an underscore.
+        validMetadata[
+          `quarto-private-${++jsonEncodedKeyIndex}`
+        ] = JSON.stringify({ key, value });
+      } else if (
+        typeof value === "string" || typeof value === "number" ||
+        typeof value === "boolean" || Array.isArray(value)
+      ) {
+        validMetadata[key] = value;
+      } else {
+        error(
+          `Invalid metadata type for key ${key}: ${typeof value}. Entry will not be serialized.`,
+        );
+      }
+    }
+  }
+
   return {
     ...cell,
+    metadata: validMetadata,
     id: cellId(cell),
     source,
     optionsSource,
@@ -1766,7 +1804,10 @@ function isMarkdown(output: JupyterOutput, options: JupyterToMarkdownOptions) {
   return isDisplayDataType(output, options, displayDataIsMarkdown);
 }
 
-async function mdOutputStream(output: JupyterOutputStream, options: JupyterToMarkdownOptions) {
+async function mdOutputStream(
+  output: JupyterOutputStream,
+  options: JupyterToMarkdownOptions,
+) {
   let text: string[] = [];
   if (typeof output.text === "string") {
     text = [output.text];
@@ -1873,8 +1914,11 @@ async function mdOutputDisplayData(
       // if output is invalid, warn and emit empty
       const data = output.data[mimeType] as unknown;
       if (!Array.isArray(data) || data.some((s) => typeof s !== "string")) {
-        return await mdWarningOutput(`Unable to process text plain output data 
-which does not appear to be plain text: ${JSON.stringify(data)}`, options);
+        return await mdWarningOutput(
+          `Unable to process text plain output data 
+which does not appear to be plain text: ${JSON.stringify(data)}`,
+          options,
+        );
       }
       const lines = data as string[];
       // pandas inexplicably outputs html tables as text/plain with an enclosing single-quote
@@ -1911,7 +1955,7 @@ which does not appear to be plain text: ${JSON.stringify(data)}`, options);
   // no type match found
   return await mdWarningOutput(
     "Unable to display output for mime type(s): " +
-    Object.keys(output.data).join(", "),
+      Object.keys(output.data).join(", "),
     options,
   );
 }

src/core/jupyter/jupyter.ts

@@ -48,11 +48,15 @@ export const pandocIngestSelfContainedContent = async (
 
   // The raw html contents
   const contents = Deno.readTextFileSync(file);
+  const doctypeMatch = contents.match(/^<!DOCTYPE.*?>/);
   const dom = await parseHtml(contents);
   await bundleModules(dom, workingDir);
 
   const input: string[] = [];
   input.push("````````{=html}");
+  if (doctypeMatch) {
+    input.push(doctypeMatch[0]);
+  }
   input.push(dom.documentElement!.outerHTML);
   input.push("````````");