manuscript - do not cloneDeep Kv. create safeCloneDeep

src/core/cache/cache.ts

@@ -19,14 +19,15 @@ import {
   type ImmediateBufferCacheEntry,
   type ImmediateStringCacheEntry,
 } from "./cache-types.ts";
+import { Cloneable } from "../safe-clone-deep.ts";
 export { type ProjectCache } from "./cache-types.ts";
 
 const currentCacheVersion = "1";
 const requiredQuartoVersions: Record<string, string> = {
   "1": ">1.7.0",
 };
 
-class ProjectCacheImpl {
+class ProjectCacheImpl implements Cloneable<ProjectCacheImpl> {
   projectScratchDir: string;
   index: Deno.Kv | null;
 
@@ -35,6 +36,10 @@ class ProjectCacheImpl {
     this.index = null;
   }
 
+  clone() {
+    return this;
+  }
+
   close() {
     if (this.index) {
       this.index.close();

src/core/safe-clone-deep.ts

@@ -0,0 +1,36 @@
+/*
+ * safe-clone-deep.ts
+ *
+ * CloneDeep that uses object's own cloning methods when available
+ *
+ * Copyright (C) 2025 Posit Software, PBC
+ */
+
+export interface Cloneable<T> {
+  clone(): T;
+}
+
+export function safeCloneDeep<T>(obj: T): T {
+  if (obj === null || typeof obj !== "object") {
+    return obj;
+  }
+
+  // Handle arrays
+  if (Array.isArray(obj)) {
+    return obj.map((item) => safeCloneDeep(item)) as T;
+  }
+
+  if (obj && ("clone" in obj) && typeof obj.clone === "function") {
+    return obj.clone();
+  }
+
+  // Handle regular objects
+  const result = {} as T;
+  for (const key in obj) {
+    if (Object.prototype.hasOwnProperty.call(obj, key)) {
+      result[key] = safeCloneDeep(obj[key]);
+    }
+  }
+
+  return result;
+}

src/core/sass.ts

@@ -384,6 +384,9 @@ export async function compileWithCache(
       const result = await memoizedGetVarsBlock(project, input);
       return input + "\n" + result;
     } catch (e) {
+      if (e.name !== "SCSSParsingError") {
+        throw e;
+      }
       console.warn("Error adding css vars block", e);
       console.warn(
         "The resulting CSS file will not have SCSS color variables exported as CSS.",

src/core/sass/add-css-vars.ts

@@ -15,8 +15,22 @@ import { propagateDeclarationTypes } from "./analyzer/declaration-types.ts";
 import { getVariableDependencies } from "./analyzer/get-dependencies.ts";
 
 const { getSassAst } = makeParserModule(parse);
+
+export class SCSSParsingError extends Error {
+  constructor(message: string) {
+    super(`SCSS Parsing Error: ${message}`);
+    this.name = "SCSSParsingError";
+  }
+}
+
 export const cssVarsBlock = (scssSource: string) => {
-  const ast = propagateDeclarationTypes(cleanSassAst(getSassAst(scssSource)));
+  let astOriginal;
+  try {
+    astOriginal = getSassAst(scssSource);
+  } catch (e) {
+    throw new SCSSParsingError(e.message);
+  }
+  const ast = propagateDeclarationTypes(cleanSassAst(astOriginal));
   const deps = getVariableDependencies(ast);
 
   const output: string[] = [":root {"];

src/core/sass/cache.ts

@@ -14,11 +14,16 @@ import { TempContext } from "../temp.ts";
 import { safeRemoveIfExists } from "../path.ts";
 import * as log from "../../deno_ral/log.ts";
 import { onCleanup } from "../cleanup.ts";
+import { Cloneable } from "../safe-clone-deep.ts";
 
-class SassCache {
+class SassCache implements Cloneable<SassCache> {
   kv: Deno.Kv;
   path: string;
 
+  clone() {
+    return this;
+  }
+
   constructor(kv: Deno.Kv, path: string) {
     this.kv = kv;
     this.path = path;

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

@@ -51,6 +51,7 @@ import { isQmdFile } from "../../execute/qmd.ts";
 import { dirAndStem } from "../../core/path.ts";
 import { projectOutputDir } from "../../project/project-shared.ts";
 import { existsSync } from "../../deno_ral/fs.ts";
+import { safeCloneDeep } from "../../core/safe-clone-deep.ts";
 
 export const htmlNotebookContributor: NotebookContributor = {
   resolve: resolveHtmlNotebook,
@@ -85,7 +86,7 @@ function resolveHtmlNotebook(
   executedFile: ExecutedFile,
   notebookMetadata?: NotebookMetadata,
 ) {
-  const resolved = ld.cloneDeep(executedFile) as ExecutedFile;
+  const resolved = safeCloneDeep(executedFile) as ExecutedFile;
 
   // Set the output file
   resolved.recipe.format.pandoc[kOutputFile] = `${outputFile(nbAbsPath)}`;

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

@@ -34,6 +34,7 @@ import { ipynbTitleTemplatePath } from "../../format/ipynb/format-ipynb.ts";
 import { projectOutputDir } from "../../project/project-shared.ts";
 import { existsSync } from "../../deno_ral/fs.ts";
 import { dirname, join, relative } from "../../deno_ral/path.ts";
+import { safeCloneDeep } from "../../core/safe-clone-deep.ts";
 
 export const outputNotebookContributor: NotebookContributor = {
   resolve: resolveOutputNotebook,
@@ -67,7 +68,7 @@ function resolveOutputNotebook(
   executedFile: ExecutedFile,
   _notebookMetadata?: NotebookMetadata,
 ) {
-  const resolved = ld.cloneDeep(executedFile);
+  const resolved = safeCloneDeep(executedFile);
   resolved.recipe.format.pandoc[kOutputFile] = outputFile(nbAbsPath);
   resolved.recipe.output = resolved.recipe.format.pandoc[kOutputFile];
 

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

@@ -37,6 +37,7 @@ import * as ld from "../../core/lodash.ts";
 
 import { error } from "../../deno_ral/log.ts";
 import { Format } from "../../config/types.ts";
+import { safeCloneDeep } from "../../core/safe-clone-deep.ts";
 
 export const jatsContributor: NotebookContributor = {
   resolve: resolveJats,
@@ -56,7 +57,7 @@ function resolveJats(
   executedFile: ExecutedFile,
   _notebookMetadata?: NotebookMetadata,
 ) {
-  const resolved = ld.cloneDeep(executedFile);
+  const resolved = safeCloneDeep(executedFile);
   const to =
     resolved.recipe.format.render[kVariant]?.includes("+element_citations")
       ? "jats+element_citations"

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

@@ -38,6 +38,7 @@ import { ipynbTitleTemplatePath } from "../../format/ipynb/format-ipynb.ts";
 import { projectScratchPath } from "../../project/project-scratch.ts";
 import { ensureDirSync, existsSync } from "../../deno_ral/fs.ts";
 import { dirname, join, relative } from "../../deno_ral/path.ts";
+import { safeCloneDeep } from "../../core/safe-clone-deep.ts";
 
 export const qmdNotebookContributor: NotebookContributor = {
   resolve: resolveOutputNotebook,
@@ -86,7 +87,7 @@ function resolveOutputNotebook(
   executedFile: ExecutedFile,
   _notebookMetadata?: NotebookMetadata,
 ) {
-  const resolved = ld.cloneDeep(executedFile);
+  const resolved = safeCloneDeep(executedFile);
   resolved.recipe.format.pandoc[kOutputFile] = ipynbOutputFile(nbAbsPath);
   resolved.recipe.output = resolved.recipe.format.pandoc[kOutputFile];