Merge branch 'main' of github.com:quarto-dev/quarto-cli into main

Author: jjallaire

src/command/render/pandoc.ts

@@ -153,9 +153,7 @@ import {
   parsePandocDate,
   parseSpecialDate,
 } from "../../core/date.ts";
-import { copyFileIfNewer } from "../../core/copy.ts";
 import { katexPostProcessor } from "../../format/html/format-html-math.ts";
-import { lines } from "../../core/lib/text.ts";
 import {
   readAndInjectDependencies,
   writeDependencies,
@@ -860,25 +858,31 @@ export async function runPandoc(
     },
   );
 
-  // TODO: Process Dependencies
-
   // resolve resource files from metadata
   const resources: string[] = resourcesFromMetadata(
     options.format.metadata[kResources],
   );
 
   // read any resourceFiles generated by filters
+  let inputTraits = {};
   if (existsSync(filterResultsFile)) {
     const filterResultsJSON = Deno.readTextFileSync(filterResultsFile);
     if (filterResultsJSON.trim().length > 0) {
       const filterResults = JSON.parse(filterResultsJSON);
-      resources.push(...(filterResults.resourceFiles || []));
+
+      // Read any input traits
+      inputTraits = filterResults.inputTraits;
+
+      // Read any resource files
+      const resourceFiles = filterResults.resourceFiles || [];
+      resources.push(...resourceFiles);
     }
   }
 
   if (result.success) {
     return {
       inputMetadata: pandocMetadata,
+      inputTraits,
       resources,
       postprocessors,
       htmlPostprocessors: isHtmlOutput(options.format.pandoc)

src/command/render/render.ts

@@ -22,7 +22,12 @@ import {
   executionEngineKeepMd,
 } from "../../execute/engine.ts";
 
-import { HtmlPostProcessResult, PandocOptions } from "./types.ts";
+import {
+  HtmlPostProcessor,
+  HtmlPostProcessResult,
+  PandocInputTraits,
+  PandocOptions,
+} from "./types.ts";
 import { runPandoc } from "./pandoc.ts";
 import { renderCleanup } from "./cleanup.ts";
 import { projectOffset } from "../../project/project-shared.ts";
@@ -140,6 +145,7 @@ export async function renderPandoc(
 
   const htmlPostProcessResult = await runHtmlPostprocessors(
     pandocResult.inputMetadata,
+    pandocResult.inputTraits,
     pandocOptions,
     htmlPostProcessors,
     htmlFinalizers,
@@ -326,10 +332,9 @@ function mergePandocIncludes(
 
 async function runHtmlPostprocessors(
   inputMetadata: Metadata,
+  inputTraits: PandocInputTraits,
   options: PandocOptions,
-  htmlPostprocessors: Array<
-    (doc: Document, inputMetadata: Metadata) => Promise<HtmlPostProcessResult>
-  >,
+  htmlPostprocessors: Array<HtmlPostProcessor>,
   htmlFinalizers: Array<(doc: Document) => Promise<void>>,
 ): Promise<HtmlPostProcessResult> {
   const postProcessResult: HtmlPostProcessResult = {
@@ -345,7 +350,7 @@ async function runHtmlPostprocessors(
     const doc = await parseHtml(htmlInput);
     for (let i = 0; i < htmlPostprocessors.length; i++) {
       const postprocessor = htmlPostprocessors[i];
-      const result = await postprocessor(doc, inputMetadata);
+      const result = await postprocessor(doc, inputMetadata, inputTraits);
 
       postProcessResult.resources.push(...result.resources);
       postProcessResult.supporting.push(...result.supporting);

src/command/render/types.ts

@@ -17,6 +17,7 @@ import { Metadata } from "../../config/types.ts";
 import { ProjectContext } from "../../project/types.ts";
 import { TempContext } from "../../core/temp-types.ts";
 import { ExtensionContext } from "../../extension/extension-shared.ts";
+import { kPositionedRefs } from "../../config/constants.ts";
 
 // options for render
 export interface RenderOptions {
@@ -49,15 +50,21 @@ export interface RenderContext {
 
 export interface RunPandocResult {
   inputMetadata: Metadata;
+  inputTraits: PandocInputTraits;
   resources: string[];
   postprocessors?: Array<(output: string) => Promise<void>>;
   htmlPostprocessors: Array<HtmlPostProcessor>;
   htmlFinalizers?: Array<(doc: Document) => Promise<void>>;
 }
 
+export interface PandocInputTraits {
+  [kPositionedRefs]?: boolean;
+}
+
 export type HtmlPostProcessor = (
   doc: Document,
   inputMedata: Metadata,
+  inputTraits: PandocInputTraits,
 ) => Promise<HtmlPostProcessResult>;
 
 export interface HtmlPostProcessResult {

src/config/constants.ts

@@ -443,6 +443,9 @@ export const kTblCapLoc = "tbl-cap-location";
 export const kCapTop = "top";
 export const kCapBottom = "bottom";
 
+// Pandoc Input Traits
+export const kPositionedRefs = "positioned-refs";
+
 // https://pandoc.org/MANUAL.html#default-files
 // note: we are keeping some things out of 'defaults' b/ca
 // they are known to be valid in metadata. this includes:

src/core/lib/yaml-validation/schema-navigation.ts

@@ -111,6 +111,7 @@ export function navigateSchemaBySchemaPathSingle(
 
   // deno-lint-ignore no-explicit-any
   const inner = (subschema: any, index: number): any => {
+    subschema = resolveSchema(subschema);
     if (subschema === undefined) {
       throw new Error(
         `Internal Error in navigateSchemaBySchemaPathSingle: invalid path navigation`,

src/format/html/format-html-appendix.ts

@@ -5,10 +5,12 @@
 *
 */
 
+import { PandocInputTraits } from "../../command/render/types.ts";
 import {
   kAppendixAttributionBibTex,
   kAppendixAttributionCiteAs,
   kLang,
+  kPositionedRefs,
   kSectionTitleCitation,
   kSectionTitleReuse,
 } from "../../config/constants.ts";
@@ -51,6 +53,7 @@ const kAppendixId = "quarto-appendix";
 
 export async function processDocumentAppendix(
   input: string,
+  inputTraits: PandocInputTraits,
   format: Format,
   flags: PandocFlags,
   doc: Document,
@@ -102,7 +105,7 @@ export async function processDocumentAppendix(
     };
 
     // Move the refs into the appendix
-    if (!hasMarginCites(format)) {
+    if (!hasMarginCites(format) && !inputTraits[kPositionedRefs]) {
       const refsEl = doc.getElementById("refs");
       if (refsEl) {
         const findRefTitle = (refsEl: Element) => {

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

@@ -28,6 +28,7 @@ import {
   kHtmlFinalizers,
   kHtmlPostprocessors,
   kSassBundles,
+  Metadata,
   SassLayer,
 } from "../../config/types.ts";
 import { PandocFlags } from "../../config/types.ts";
@@ -49,6 +50,7 @@ import {
 import {
   HtmlPostProcessor,
   HtmlPostProcessResult,
+  PandocInputTraits,
 } from "../../command/render/types.ts";
 import { processDocumentAppendix } from "./format-html-appendix.ts";
 import {
@@ -211,6 +213,8 @@ function bootstrapHtmlPostprocessor(
 ): HtmlPostProcessor {
   return async (
     doc: Document,
+    _inputMedata: Metadata,
+    inputTraits: PandocInputTraits,
   ): Promise<HtmlPostProcessResult> => {
     // use display-7 style for title
     const title = doc.querySelector("header > .title");
@@ -356,7 +360,7 @@ function bootstrapHtmlPostprocessor(
       format.metadata[kAppendixStyle] !== false &&
       format.metadata[kAppendixStyle] !== "none"
     ) {
-      await processDocumentAppendix(input, format, flags, doc, offset);
+      await processDocumentAppendix(input, inputTraits, format, flags, doc, offset);
     }
 
     // no resource refs

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

@@ -9668,11 +9668,7 @@ var require_yaml_intelligence_resources = __commonJS({
                 maybeArrayOf: {
                   anyOf: [
                     "string",
-                    {
-                      object: {
-                        additionalProperties: true
-                      }
-                    }
+                    "object"
                   ]
                 },
                 description: "The files or path globs of Quarto documents or YAML files that should be included in the listing."
@@ -16902,6 +16898,7 @@ var require_yaml_intelligence_resources = __commonJS({
         "Re-render input files when they change (defaults to true)",
         "Navigate the browser automatically when outputs are updated (defaults\nto true)",
         "Time (in seconds) after which to exit if there are no active\nclients",
+        "Sites published from project",
         "Unique identifier for site",
         "Published URL for site",
         "Website title",
@@ -18385,7 +18382,6 @@ var require_yaml_intelligence_resources = __commonJS({
         "Additional file resources to be copied to output directory",
         "Additional file resources to be copied to output directory",
         "Options for <code>quarto preview</code>",
-        "Sites published from project",
         "MISSING_DESCRIPTION",
         "MISSING_DESCRIPTION",
         "Book title",
@@ -18585,7 +18581,6 @@ var require_yaml_intelligence_resources = __commonJS({
         "Additional file resources to be copied to output directory",
         "Additional file resources to be copied to output directory",
         "Options for <code>quarto preview</code>",
-        "Sites published from project",
         "MISSING_DESCRIPTION",
         "MISSING_DESCRIPTION",
         "Book title",
@@ -18771,8 +18766,7 @@ var require_yaml_intelligence_resources = __commonJS({
         "Download buttons for other formats to include on navbar or sidebar\n(one or more of <code>pdf</code>, <code>epub</code>, and `docx)",
         "Download buttons for other formats to include on navbar or sidebar\n(one or more of <code>pdf</code>, <code>epub</code>, and `docx)",
         "Custom tools for navbar or sidebar",
-        "internal-schema-hack",
-        "Sites published from project"
+        "internal-schema-hack"
       ],
       "schema/external-schemas.yml": [
         {
@@ -24250,6 +24244,7 @@ function navigateSchemaBySchemaPathSingle(schema2, path) {
     }
   };
   const inner = (subschema, index) => {
+    subschema = resolveSchema(subschema);
     if (subschema === void 0) {
       throw new Error(`Internal Error in navigateSchemaBySchemaPathSingle: invalid path navigation`);
     }
@@ -25013,6 +25008,7 @@ function createLocalizedError(obj) {
       end: { line: 0, column: 0 }
     };
   }
+  console.log({ schemaPath });
   return {
     source: mappedString(source, [{
       start: violatingObject.start,

src/resources/editor/tools/yaml/web-worker.js

@@ -2647,11 +2647,7 @@
             "maybeArrayOf": {
               "anyOf": [
                 "string",
-                {
-                  "object": {
-                    "additionalProperties": true
-                  }
-                }
+                "object"
               ]
             },
             "description": "The files or path globs of Quarto documents or YAML files that should be included in the listing."
@@ -9881,6 +9877,7 @@
     "Re-render input files when they change (defaults to true)",
     "Navigate the browser automatically when outputs are updated (defaults\nto true)",
     "Time (in seconds) after which to exit if there are no active\nclients",
+    "Sites published from project",
     "Unique identifier for site",
     "Published URL for site",
     "Website title",
@@ -11364,7 +11361,6 @@
     "Additional file resources to be copied to output directory",
     "Additional file resources to be copied to output directory",
     "Options for <code>quarto preview</code>",
-    "Sites published from project",
     "MISSING_DESCRIPTION",
     "MISSING_DESCRIPTION",
     "Book title",
@@ -11564,7 +11560,6 @@
     "Additional file resources to be copied to output directory",
     "Additional file resources to be copied to output directory",
     "Options for <code>quarto preview</code>",
-    "Sites published from project",
     "MISSING_DESCRIPTION",
     "MISSING_DESCRIPTION",
     "Book title",
@@ -11750,8 +11745,7 @@
     "Download buttons for other formats to include on navbar or sidebar\n(one or more of <code>pdf</code>, <code>epub</code>, and `docx)",
     "Download buttons for other formats to include on navbar or sidebar\n(one or more of <code>pdf</code>, <code>epub</code>, and `docx)",
     "Custom tools for navbar or sidebar",
-    "internal-schema-hack",
-    "Sites published from project"
+    "internal-schema-hack"
   ],
   "schema/external-schemas.yml": [
     {