manuscript - do not cloneDeep Kv. create safeCloneDeep

src/command/render/pandoc-html.ts

@@ -19,7 +19,6 @@ import {
 } from "../../config/types.ts";
 import { ProjectContext } from "../../project/types.ts";
 
-import { TempContext } from "../../core/temp.ts";
 import { cssImports, cssResources } from "../../core/css.ts";
 import { cleanSourceMappingUrl, compileSass } from "../../core/sass.ts";
 
@@ -91,10 +90,12 @@ export async function resolveSassBundles(
     const maybeBrandBundle = bundlesWithBrand.find((bundle) =>
       bundle.key === "brand"
     );
-    assert(!maybeBrandBundle ||
-      !maybeBrandBundle.user?.find((v) => v === "brand") &&
-      !maybeBrandBundle.dark?.user?.find((v) => v === "brand"));
-    let foundBrand = {light: false, dark: false};
+    assert(
+      !maybeBrandBundle ||
+        !maybeBrandBundle.user?.find((v) => v === "brand") &&
+          !maybeBrandBundle.dark?.user?.find((v) => v === "brand"),
+    );
+    const foundBrand = { light: false, dark: false };
     const bundles: SassBundle[] = bundlesWithBrand.filter((bundle) =>
       bundle.key !== "brand"
     ).map((bundle) => {
@@ -106,12 +107,18 @@ export async function resolveSassBundles(
         bundle.user!.splice(userBrand, 1, ...(maybeBrandBundle?.user || []));
         foundBrand.light = true;
       }
-      const darkBrand = bundle.dark?.user?.findIndex((layer) => layer === "brand");
+      const darkBrand = bundle.dark?.user?.findIndex((layer) =>
+        layer === "brand"
+      );
       if (darkBrand && darkBrand !== -1) {
         if (!cloned) {
           bundle = cloneDeep(bundle);
         }
-        bundle.dark!.user!.splice(darkBrand, 1, ...(maybeBrandBundle?.dark?.user || []))
+        bundle.dark!.user!.splice(
+          darkBrand,
+          1,
+          ...(maybeBrandBundle?.dark?.user || []),
+        );
         foundBrand.dark = true;
       }
       return bundle as SassBundle;
@@ -122,18 +129,19 @@ export async function resolveSassBundles(
         key: "brand",
         user: !foundBrand.light && maybeBrandBundle?.user as SassLayer[] || [],
         dark: !foundBrand.dark && maybeBrandBundle?.dark?.user && {
-          user: maybeBrandBundle.dark.user as SassLayer[],
-          default: maybeBrandBundle.dark.default
-        } || undefined
+              user: maybeBrandBundle.dark.user as SassLayer[],
+              default: maybeBrandBundle.dark.default,
+            } || undefined,
       });
     }
 
     // See if any bundles are providing dark specific css
     const hasDark = bundles.some((bundle) => bundle.dark !== undefined);
-    defaultStyle =
-      bundles.some((bundle) => bundle.dark !== undefined && bundle.dark.default)
-        ? "dark"
-        : "light";
+    defaultStyle = bundles.some((bundle) =>
+        bundle.dark !== undefined && bundle.dark.default
+      )
+      ? "dark"
+      : "light";
     const targets: SassTarget[] = [{
       name: `${dependency}.min.css`,
       bundles: (bundles as any),

src/command/render/project.ts

@@ -81,7 +81,6 @@ import { fileExecutionEngine } from "../../execute/engine.ts";
 import { projectContextForDirectory } from "../../project/project-context.ts";
 import { ProjectType } from "../../project/types/types.ts";
 import { ProjectConfig as ProjectConfig_Project } from "../../resources/types/schema-types.ts";
-import { Extension } from "../../extension/types.ts";
 
 const noMutationValidations = (
   projType: ProjectType,

src/command/render/render-contexts.ts

@@ -89,21 +89,6 @@ import {
 import { ExtensionContext } from "../../extension/types.ts";
 import { NotebookContext } from "../../render/notebook/notebook-types.ts";
 
-// we can't naively ld.cloneDeep everything
-// because that destroys class instances
-// with private members
-//
-// Currently, that's ProjectContext.
-//
-// TODO: Ideally, we shouldn't be copying the RenderContext at all.
-export function copyRenderContext(
-  context: RenderContext,
-): RenderContext {
-  return {
-    ...ld.cloneDeep(context),
-    project: context.project,
-  };
-}
 export async function resolveFormatsFromMetadata(
   metadata: Metadata,
   input: string,

src/command/render/render-files.ts

@@ -48,7 +48,7 @@ import { outputRecipe } from "./output.ts";
 
 import { renderPandoc } from "./render.ts";
 import { PandocRenderCompletion, RenderServices } from "./types.ts";
-import { copyRenderContext, renderContexts } from "./render-contexts.ts";
+import { renderContexts } from "./render-contexts.ts";
 import { renderProgress } from "./render-info.ts";
 import {
   ExecutedFile,
@@ -114,6 +114,7 @@ import {
 } from "../../project/project-shared.ts";
 import { NotebookContext } from "../../render/notebook/notebook-types.ts";
 import { setExecuteEnvironment } from "../../execute/environment.ts";
+import { safeCloneDeep } from "../../core/safe-clone-deep.ts";
 
 export async function renderExecute(
   context: RenderContext,
@@ -503,7 +504,7 @@ async function renderFileInternal(
 
   for (const format of Object.keys(contexts)) {
     pushTiming("render-context");
-    const context = copyRenderContext(contexts[format]); // since we're going to mutate it...
+    const context = safeCloneDeep(contexts[format]); // since we're going to mutate it...
 
     // disquality some documents from server: shiny
     if (isServerShiny(context.format) && context.project) {

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 +1,54 @@
+/*
+ * 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 Maps
+  if (obj instanceof Map) {
+    const clonedMap = new Map();
+    for (const [key, value] of obj.entries()) {
+      clonedMap.set(key, safeCloneDeep(value));
+    }
+    return clonedMap as T;
+  }
+
+  // Handle Sets
+  if (obj instanceof Set) {
+    const clonedSet = new Set();
+    for (const value of obj.values()) {
+      clonedSet.add(safeCloneDeep(value));
+    }
+    return clonedSet as T;
+  }
+
+  // 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

@@ -8,7 +8,6 @@ import { existsSync } from "../deno_ral/fs.ts";
 import { join } from "../deno_ral/path.ts";
 
 import { quartoCacheDir } from "./appdirs.ts";
-import { TempContext } from "./temp.ts";
 
 import { SassBundleLayers, SassLayer } from "../config/types.ts";
 import { dartCompile } from "./dart-sass.ts";
@@ -384,6 +383,9 @@ 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/execute/engine.ts

@@ -4,7 +4,7 @@
  * Copyright (C) 2020-2022 Posit Software, PBC
  */
 
-import { extname, join, resolve } from "../deno_ral/path.ts";
+import { extname, join } from "../deno_ral/path.ts";
 
 import * as ld from "../core/lodash.ts";
 
@@ -23,7 +23,6 @@ import { kMdExtensions, markdownEngine } from "./markdown.ts";
 import { ExecutionEngine, kQmdExtensions } from "./types.ts";
 import { languagesInMarkdown } from "./engine-shared.ts";
 import { languages as handlerLanguages } from "../core/handlers/base.ts";
-import { MappedString } from "../core/lib/text-types.ts";
 import { RenderContext, RenderFlags } from "../command/render/types.ts";
 import { mergeConfigs } from "../core/config.ts";
 import { ProjectContext } from "../project/types.ts";

src/project/project-context.ts

@@ -102,7 +102,7 @@ import { NotebookContext } from "../render/notebook/notebook-types.ts";
 import { MappedString } from "../core/mapped-text.ts";
 import { makeTimedFunctionAsync } from "../core/performance/function-times.ts";
 import { createProjectCache } from "../core/cache/cache.ts";
-import { createTempContext, globalTempContext } from "../core/temp.ts";
+import { createTempContext } from "../core/temp.ts";
 
 export async function projectContext(
   path: string,