Bugfix/safe clone deep

src/command/render/pandoc-dependencies-html.ts

@@ -35,6 +35,7 @@ import { ensureDirSync } from "../../deno_ral/fs.ts";
 import { ProjectContext } from "../../project/types.ts";
 import { projectOutputDir } from "../../project/project-shared.ts";
 import { insecureHash } from "../../core/hash.ts";
+import { safeCloneDeep } from "../../core/safe-clone-deep.ts";
 
 export async function writeDependencies(
   dependenciesFile: string,
@@ -146,7 +147,7 @@ export function resolveDependencies(
   project?: ProjectContext,
 ) {
   // deep copy to not mutate caller's object
-  extras = ld.cloneDeep(extras);
+  extras = safeCloneDeep(extras);
 
   const lines: string[] = [];
   const afterBodyLines: string[] = [];

src/command/render/pandoc-html.ts

@@ -5,7 +5,7 @@
  */
 
 import { join } from "../../deno_ral/path.ts";
-import { cloneDeep, uniqBy } from "../../core/lodash.ts";
+import { uniqBy } from "../../core/lodash.ts";
 
 import {
   Format,
@@ -39,6 +39,7 @@ import { md5HashBytes } from "../../core/hash.ts";
 import { InternalError } from "../../core/lib/error.ts";
 import { assert } from "testing/asserts";
 import { safeModeFromFile } from "../../deno_ral/fs.ts";
+import { safeCloneDeep } from "../../core/safe-clone-deep.ts";
 
 // The output target for a sass bundle
 // (controls the overall style tag that is emitted)
@@ -54,7 +55,7 @@ export async function resolveSassBundles(
   format: Format,
   project: ProjectContext,
 ) {
-  extras = cloneDeep(extras);
+  extras = safeCloneDeep(extras);
 
   const mergedBundles: Record<string, SassBundleWithBrand[]> = {};
 
@@ -102,7 +103,7 @@ export async function resolveSassBundles(
       const userBrand = bundle.user?.findIndex((layer) => layer === "brand");
       let cloned = false;
       if (userBrand && userBrand !== -1) {
-        bundle = cloneDeep(bundle);
+        bundle = safeCloneDeep(bundle);
         cloned = true;
         bundle.user!.splice(userBrand, 1, ...(maybeBrandBundle?.user || []));
         foundBrand.light = true;
@@ -112,7 +113,7 @@ export async function resolveSassBundles(
       );
       if (darkBrand && darkBrand !== -1) {
         if (!cloned) {
-          bundle = cloneDeep(bundle);
+          bundle = safeCloneDeep(bundle);
         }
         bundle.dark!.user!.splice(
           darkBrand,
@@ -158,7 +159,7 @@ export async function resolveSassBundles(
 
       // Provide a dark bundle for this
       const darkBundles = bundles.map((bundle) => {
-        bundle = cloneDeep(bundle);
+        bundle = safeCloneDeep(bundle);
         bundle.user = bundle.dark?.user || bundle.user;
         bundle.quarto = bundle.dark?.quarto || bundle.quarto;
         bundle.framework = bundle.dark?.framework || bundle.framework;
@@ -362,7 +363,7 @@ async function resolveQuartoSyntaxHighlighting(
     return extras;
   }
 
-  extras = cloneDeep(extras);
+  extras = safeCloneDeep(extras);
 
   // If we're using default highlighting, use theme darkness to select highlight style
   const mediaAttr = attribForThemeStyle(style);

src/command/render/pandoc.ts

@@ -203,6 +203,8 @@ import { isWindows } from "../../deno_ral/platform.ts";
 import { appendToCombinedLuaProfile } from "../../core/performance/perfetto-utils.ts";
 import { makeTimedFunctionAsync } from "../../core/performance/function-times.ts";
 import { walkJson } from "../../core/json.ts";
+import { safeCloneDeep } from "../../core/safe-clone-deep.ts";
+import { assert } from "testing/asserts";
 import { call } from "../../deno_ral/process.ts";
 
 // in case we are running multiple pandoc processes
@@ -323,7 +325,9 @@ export async function runPandoc(
       JSON.stringify(paramsJson),
     );
 
-    const traceFilters = pandocMetadata?.["_quarto"]?.["trace-filters"] ||
+    const traceFilters =
+      // deno-lint-ignore no-explicit-any
+      (pandocMetadata as any)?.["_quarto"]?.["trace-filters"] ||
       Deno.env.get("QUARTO_TRACE_FILTERS");
 
     if (traceFilters) {
@@ -438,7 +442,7 @@ export async function runPandoc(
 
   // generate defaults and capture defaults to be printed
   let allDefaults = (await generateDefaults(options)) || {};
-  let printAllDefaults = ld.cloneDeep(allDefaults) as FormatPandoc;
+  let printAllDefaults = safeCloneDeep(allDefaults);
 
   // capture any filterParams in the FormatExtras
   const formatFilterParams = {} as Record<string, unknown>;
@@ -1120,7 +1124,7 @@ export async function runPandoc(
 
   // selectively overwrite some resolved metadata (e.g. ensure that metadata
   // computed from inline r expressions gets included @ the bottom).
-  const pandocMetadata = ld.cloneDeep(options.format.metadata || {});
+  const pandocMetadata = safeCloneDeep(options.format.metadata || {});
   for (const key of Object.keys(engineMetadata)) {
     const isChapterTitle = key === kTitle && projectIsBook(options.project);
 
@@ -1154,6 +1158,7 @@ export async function runPandoc(
   dateFields.forEach((dateField) => {
     const date = pandocMetadata[dateField];
     const format = pandocMetadata[kDateFormat];
+    assert(format === undefined || typeof format === "string");
     pandocMetadata[dateField] = resolveAndFormatDate(
       options.source,
       date,
@@ -1173,15 +1178,19 @@ export async function runPandoc(
   // Expand citation dates into CSL dates
   const citationMetadata = pandocMetadata[kCitation];
   if (citationMetadata) {
+    assert(typeof citationMetadata === "object");
+    // ideally we should be asserting non-arrayness here but that's not very fast.
+    // assert(!Array.isArray(citationMetadata));
+    const citationMetadataObj = citationMetadata as Record<string, unknown>;
     const docCSLDate = dateRaw
       ? cslDate(resolveDate(options.source, dateRaw))
       : undefined;
     const fields = ["issued", "available-date"];
     fields.forEach((field) => {
-      if (citationMetadata[field]) {
-        citationMetadata[field] = cslDate(citationMetadata[field]);
+      if (citationMetadataObj[field]) {
+        citationMetadataObj[field] = cslDate(citationMetadataObj[field]);
       } else if (docCSLDate) {
-        citationMetadata[field] = docCSLDate;
+        citationMetadataObj[field] = docCSLDate;
       }
     });
   }
@@ -1221,8 +1230,9 @@ export async function runPandoc(
     !isBeamerOutput(options.format.pandoc)
   ) {
     const docClass = pandocMetadata[kDocumentClass];
+    assert(!docClass || typeof docClass === "string");
     const isPrintDocumentClass = docClass &&
-      ["book", "scrbook"].includes(docClass);
+      ["book", "scrbook"].includes(docClass as string);
 
     if (!isPrintDocumentClass) {
       if (pandocMetadata[kColorLinks] === undefined) {
@@ -1274,7 +1284,7 @@ export async function runPandoc(
     prefix: "quarto-metadata",
     suffix: ".yml",
   });
-  const pandocPassedMetadata = ld.cloneDeep(pandocMetadata);
+  const pandocPassedMetadata = safeCloneDeep(pandocMetadata);
   delete pandocPassedMetadata.format;
   delete pandocPassedMetadata.project;
   delete pandocPassedMetadata.website;
@@ -1673,7 +1683,7 @@ function runPandocMessage(
 
   const keys = Object.keys(metadata);
   if (keys.length > 0) {
-    const printMetadata = ld.cloneDeep(metadata) as Metadata;
+    const printMetadata = safeCloneDeep(metadata);
     delete printMetadata.format;
 
     // print message

src/command/render/render-contexts.ts

@@ -88,6 +88,7 @@ import {
 } from "../../core/pandoc/pandoc-formats.ts";
 import { ExtensionContext } from "../../extension/types.ts";
 import { NotebookContext } from "../../render/notebook/notebook-types.ts";
+import { safeCloneDeep } from "../../core/safe-clone-deep.ts";
 
 export async function resolveFormatsFromMetadata(
   metadata: Metadata,
@@ -215,7 +216,7 @@ export async function renderContexts(
     // we make it optional because some of the callers have
     // actually just cloned it themselves and don't need to preserve
     // the original
-    options = ld.cloneDeep(options) as RenderOptions;
+    options = safeCloneDeep(options);
   }
 
   const { engine, target } = await fileExecutionEngineAndTarget(
@@ -342,8 +343,8 @@ function mergeQuartoConfigs(
   ...configs: Array<Metadata>
 ): Metadata {
   // copy all configs so we don't mutate them
-  config = ld.cloneDeep(config);
-  configs = ld.cloneDeep(configs);
+  config = safeCloneDeep(config);
+  configs = safeCloneDeep(configs);
 
   // bibliography needs to always be an array so it can be merged
   const fixupMergeableScalars = (metadata: Metadata) => {
@@ -450,7 +451,7 @@ async function resolveFormats(
 
     // Remove any 'to' information that will force the
     // rendering to a particular format
-    options = ld.cloneDeep(options);
+    options = safeCloneDeep(options);
     delete options.flags?.to;
   }
 
@@ -753,10 +754,10 @@ export async function projectMetadataForInputFile(
       projectType(project.config?.project?.[kProjectType]),
       project.dir,
       dirname(input),
-      ld.cloneDeep(project.config),
+      safeCloneDeep(project.config),
     ) as Metadata;
   } else {
     // Just return the config or empty metadata
-    return ld.cloneDeep(project.config) || {};
+    return safeCloneDeep(project.config) || {};
   }
 }

src/config/types.ts

@@ -457,7 +457,7 @@ export interface Format {
 
 export interface LightDarkBrand {
   [kLight]?: Brand;
-  [kDark]?: Brand
+  [kDark]?: Brand;
 }
 
 export interface FormatRender {

src/render/notebook/notebook-contributor-html.ts

@@ -84,7 +84,7 @@ function resolveHtmlNotebook(
   executedFile: ExecutedFile,
   notebookMetadata?: NotebookMetadata,
 ) {
-  const resolved = safeCloneDeep(executedFile) as ExecutedFile;
+  const resolved = safeCloneDeep(executedFile);
 
   // Set the output file
   resolved.recipe.format.pandoc[kOutputFile] = `${outputFile(nbAbsPath)}`;

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

@@ -8371,6 +8371,10 @@ var require_yaml_intelligence_resources = __commonJS({
             }
           ]
         },
+        {
+          id: "date-format",
+          schema: "string"
+        },
         {
           id: "math-methods",
           enum: {
@@ -12670,6 +12674,13 @@ var require_yaml_intelligence_resources = __commonJS({
           },
           description: "Document date"
         },
+        {
+          name: "date-format",
+          schema: {
+            ref: "date-format"
+          },
+          description: "Date format for the document"
+        },
         {
           name: "date-modified",
           tags: {
@@ -24332,12 +24343,12 @@ var require_yaml_intelligence_resources = __commonJS({
         mermaid: "%%"
       },
       "handlers/mermaid/schema.yml": {
-        _internalId: 195562,
+        _internalId: 195861,
         type: "object",
         description: "be an object",
         properties: {
           "mermaid-format": {
-            _internalId: 195554,
+            _internalId: 195853,
             type: "enum",
             enum: [
               "png",
@@ -24353,7 +24364,7 @@ var require_yaml_intelligence_resources = __commonJS({
             exhaustiveCompletions: true
           },
           theme: {
-            _internalId: 195561,
+            _internalId: 195860,
             type: "anyOf",
             anyOf: [
               {

src/resources/editor/tools/yaml/yaml-intelligence-resources.json

@@ -1343,6 +1343,10 @@
         }
       ]
     },
+    {
+      "id": "date-format",
+      "schema": "string"
+    },
     {
       "id": "math-methods",
       "enum": {
@@ -5642,6 +5646,13 @@
       },
       "description": "Document date"
     },
+    {
+      "name": "date-format",
+      "schema": {
+        "ref": "date-format"
+      },
+      "description": "Date format for the document"
+    },
     {
       "name": "date-modified",
       "tags": {
@@ -17304,12 +17315,12 @@
     "mermaid": "%%"
   },
   "handlers/mermaid/schema.yml": {
-    "_internalId": 195562,
+    "_internalId": 195861,
     "type": "object",
     "description": "be an object",
     "properties": {
       "mermaid-format": {
-        "_internalId": 195554,
+        "_internalId": 195853,
         "type": "enum",
         "enum": [
           "png",
@@ -17325,7 +17336,7 @@
         "exhaustiveCompletions": true
       },
       "theme": {
-        "_internalId": 195561,
+        "_internalId": 195860,
         "type": "anyOf",
         "anyOf": [
           {