Fix notebook preview files missing from _site when rendering outside the project

news/changelog-1.11.md

@@ -66,6 +66,7 @@ All changes included in 1.11:
 ### Websites
 
 - ([#14974](https://github.com/quarto-dev/quarto-cli/issues/14974)): Fix math in `.llms.md` files from `llms-txt` coming out garbled with the default `mathjax` method, and with `katex` and `webtex`. Math is now written as `$...$` and `$$...$$` with the `mathjax`, `katex`, `webtex` and `mathml` methods.
+- ([#15004](https://github.com/quarto-dev/quarto-cli/issues/15004)): Fix notebook preview pages and notebook sources missing from the output directory when a website with embedded notebooks is rendered from a directory other than the project directory.
 
 ## Lua API
 

src/format/html/format-html-notebook-preview.ts

@@ -223,33 +223,29 @@ export const notebookPreviewer = (
           );
         }
 
-        // Forward along resources and supporting files from previews
+        // Forward along resources and supporting files from previews.
+        // Supporting files must be absolute so they resolve regardless of
+        // the cwd; the stored (project-relative) entries are not mutated.
+        const absoluteSupporting = (entries: string[]) =>
+          entries.map((s) =>
+            project && !isAbsolute(s) ? join(project.dir, s) : s
+          );
         const supporting: string[] = [];
         const resources: string[] = [];
         if (renderedNotebook[kRenderedIPynb]) {
           const renderedIpynb = renderedNotebook[kRenderedIPynb];
           if (renderedIpynb) {
-            if (project) {
-              supporting.push(
-                relative(project.dir, renderedIpynb.hrefPath),
-              );
-            } else {
-              supporting.push(renderedIpynb.hrefPath);
-            }
-            supporting.push(...renderedIpynb.supporting);
+            supporting.push(renderedIpynb.hrefPath);
+            supporting.push(...absoluteSupporting(renderedIpynb.supporting));
             resources.push(...renderedIpynb.resourceFiles.files);
           }
         }
 
         if (renderedNotebook[kHtmlPreview]) {
           const htmlPreview = renderedNotebook[kHtmlPreview];
           if (htmlPreview) {
-            if (project) {
-              supporting.push(relative(project.dir, htmlPreview.hrefPath));
-            } else {
-              supporting.push(htmlPreview.hrefPath);
-            }
-            supporting.push(...htmlPreview.supporting);
+            supporting.push(htmlPreview.hrefPath);
+            supporting.push(...absoluteSupporting(htmlPreview.supporting));
             resources.push(...htmlPreview.resourceFiles.files);
           }
         }

src/format/html/format-html-notebook.ts

@@ -296,7 +296,9 @@ export async function emplaceNotebookPreviews(
 
       if (nbPath.resources) {
         resources.push(...nbPath.resources.map((file) => {
-          return project ? relative(project?.dir, file) : file;
+          return project && isAbsolute(file)
+            ? relative(project.dir, file)
+            : file;
         }));
       }
 

tests/docs/site-qmd-embed/.gitignore

@@ -0,0 +1,3 @@
+/.quarto/
+
+**/*.quarto_ipynb

tests/docs/site-qmd-embed/_quarto.yml

@@ -0,0 +1,2 @@
+project:
+  type: website

tests/docs/site-qmd-embed/computations.qmd

@@ -0,0 +1,9 @@
+---
+title: Computations
+jupyter: python3
+---
+
+```{python}
+#| label: answer
+print(42)
+```

tests/docs/site-qmd-embed/index.qmd

@@ -0,0 +1,5 @@
+---
+title: Home
+---
+
+{{< embed computations.qmd#answer >}}

tests/docs/site/.gitignore

@@ -1 +1,3 @@
 /.quarto/
+
+**/*.quarto_ipynb

tests/smoke/site/render-site.test.ts

@@ -4,9 +4,57 @@
 * Copyright (C) 2020-2022 Posit Software, PBC
 *
 */
+import { existsSync } from "../../../src/deno_ral/fs.ts";
+import { join } from "../../../src/deno_ral/path.ts";
 import { docs } from "../../utils.ts";
+import { fileExists } from "../../verify.ts";
 import { testSite } from "./site.ts";
 
-testSite(docs("site/index.qmd"), docs("site/index.qmd"), [
-  ".quarto-embed-nb-cell", // Embed is present
-], []);
+// The test runs from tests/, outside the project directory, so this also
+// covers notebook preview files reaching _site when cwd != project dir.
+const siteNotebooks = join(docs("site"), "_site", "notebooks");
+
+testSite(
+  docs("site/index.qmd"),
+  docs("site/index.qmd"),
+  [
+    ".quarto-embed-nb-cell", // Embed is present
+  ],
+  [],
+  undefined,
+  fileExists(join(siteNotebooks, "computations-preview.html")),
+  fileExists(join(siteNotebooks, "computations.out.ipynb")),
+  fileExists(
+    join(
+      siteNotebooks,
+      "computations_files",
+      "figure-html",
+      "fig-visualization-output-1.png",
+    ),
+  ),
+);
+
+// A qmd source embed gets a preview page and a downloadable copy of the source.
+const siteQmdEmbed = join(docs("site-qmd-embed"), "_site");
+// A cached embed rendering from a previous render changes what is emitted
+// (see #10756), so each run starts without the scratch directory; testSite
+// removes it on teardown.
+const removeQmdEmbedScratch = () => {
+  const scratch = join(docs("site-qmd-embed"), ".quarto");
+  if (existsSync(scratch)) {
+    Deno.removeSync(scratch, { recursive: true });
+  }
+  return Promise.resolve();
+};
+
+testSite(
+  docs("site-qmd-embed/index.qmd"),
+  docs("site-qmd-embed/index.qmd"),
+  [
+    ".quarto-embed-nb-cell", // Embed is present
+  ],
+  [],
+  { setup: removeQmdEmbedScratch },
+  fileExists(join(siteQmdEmbed, "computations.embed-preview.html")),
+  fileExists(join(siteQmdEmbed, "computations.qmd")),
+);

tests/smoke/site/site.ts

@@ -3,10 +3,10 @@
  *
  * Copyright (C) 2020-2022 Posit Software, PBC
  */
-import { existsSync } from "../../../src/deno_ral/fs.ts";
-import { dirname } from "../../../src/deno_ral/path.ts";
+import { removeIfExists } from "../../../src/core/path.ts";
+import { dirname, join } from "../../../src/deno_ral/path.ts";
 import { testQuartoCmd, Verify, TestContext, mergeTestContexts } from "../../test.ts";
-import { projectOutputForInput } from "../../utils.ts";
+import { findProjectDir, projectOutputForInput } from "../../utils.ts";
 import { ensureHtmlElements, noErrorsOrWarnings } from "../../verify.ts";
 
 export const testSite = (
@@ -26,11 +26,14 @@ export const testSite = (
   );
 
   const baseContext: TestContext = {
-    teardown: async () => {
-      const siteDir = dirname(output.outputPath);
-      if (existsSync(siteDir)) {
-        await Deno.remove(siteDir, { recursive: true });
+    teardown: () => {
+      removeIfExists(dirname(output.outputPath));
+      // Remove the project scratch so its state can't leak into later renders
+      const projectDir = findProjectDir(input);
+      if (projectDir) {
+        removeIfExists(join(projectDir, ".quarto"));
       }
+      return Promise.resolve();
     },
   };