bugfix: resolve engines before ignoreDirs

news/changelog-1.9.md

@@ -11,13 +11,20 @@ All changes included in 1.9:
 - ([#13633](https://github.com/quarto-dev/quarto-cli/issues/13633)): Fix detection and auto-installation of babel language packages from newer error format that doesn't explicitly mention `.ldf` filename.
 - ([#13694](https://github.com/quarto-dev/quarto-cli/issues/13694)): Fix `notebook-view.url` being ignored - external notebook links now properly use specified URLs instead of local preview files.
 - ([#13732](https://github.com/quarto-dev/quarto-cli/issues/13732)): Fix automatic font package installation for fonts with spaces in their names (e.g., "Noto Emoji", "DejaVu Sans"). Font file search patterns now match both with and without spaces.
+- ([#13798](https://github.com/quarto-dev/quarto-cli/pull/13798)): Directories specified in `ExecutionEngineDiscovery.ignoreDirs` were not getting ignored.
 
 ## Dependencies
 
 - Update `esbuild` to 0.25.10
 - Update `deno` to 2.4.5
 - ([#13601](https://github.com/quarto-dev/quarto-cli/pull/13601)): Update `mermaid` to 11.12.0 (author: @multimeric)
 
+## Extensions
+
+- Metadata and brand extensions now work without a `_quarto.yml` project. (Engine extensions do too.) A temporary default project is created in memory.
+
+- New **Engine Extensions**, to allow other execution engines than knitr, jupyter, julia. Julia is now a bundled extension. See [the prerelease notes](https://prerelease.quarto.org/docs/prerelease/1.9/) and [engine extension documentation](https://prerelease.quarto.org/docs/extensions/engine.html).
+
 ## Formats
 
 ### `gfm`

src/project/project-context.ts

@@ -63,6 +63,7 @@ import {
   fileExecutionEngine,
   fileExecutionEngineAndTarget,
   projectIgnoreGlobs,
+  resolveEngines,
 } from "../execute/engine.ts";
 import { ExecutionEngineInstance, kMarkdownEngine } from "../execute/types.ts";
 
@@ -884,6 +885,9 @@ async function projectInputFilesInternal(
   project: ProjectContext,
   metadata?: ProjectConfig,
 ): Promise<{ files: string[]; engines: string[] }> {
+  // Resolve engines so engineIgnoreDirs() uses all engines (including external)
+  await resolveEngines(project);
+
   const { dir } = project;
 
   const outputDir = metadata?.project[kProjectOutputDir];

tests/docs/books/book-404-detection/.gitignore

@@ -0,0 +1,2 @@
+/.quarto/
+**/*.quarto_ipynb

tests/docs/books/book-404-detection/404.ipynb

@@ -0,0 +1,27 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "404-page-content",
+   "metadata": {},
+   "source": [
+    "---\n",
+    "title: \"Page Not Found\"\n",
+    "---\n",
+    "\n",
+    "# 404 - Page Not Found\n",
+    "\n",
+    "Sorry, the page you're looking for doesn't exist."
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

tests/docs/books/book-404-detection/_quarto.yml

@@ -0,0 +1,13 @@
+project:
+  type: book
+
+book:
+  title: "Test Book with 404"
+  author: "Test Author"
+  chapters:
+    - index.qmd
+    - chapter1.qmd
+
+format:
+  html:
+    theme: default

tests/docs/books/book-404-detection/chapter1.qmd

@@ -0,0 +1,3 @@
+# Chapter 1
+
+Content here.

tests/docs/books/book-404-detection/index.qmd

@@ -0,0 +1,3 @@
+# Welcome
+
+This is the index page.

tests/docs/books/book-404-rmd/.gitignore

@@ -0,0 +1,2 @@
+/.quarto/
+**/*.quarto_ipynb

tests/docs/books/book-404-rmd/404.rmd

@@ -0,0 +1,7 @@
+---
+title: "Page Not Found"
+---
+
+# 404 - Page Not Found
+
+Sorry, the page you're looking for doesn't exist.

tests/docs/books/book-404-rmd/_quarto.yml

@@ -0,0 +1,13 @@
+project:
+  type: book
+
+book:
+  title: "Test Book with 404 RMD"
+  author: "Test Author"
+  chapters:
+    - index.qmd
+    - chapter1.qmd
+
+format:
+  html:
+    theme: default

tests/docs/books/book-404-rmd/chapter1.qmd

@@ -0,0 +1,3 @@
+# Chapter 1
+
+Content here.

tests/docs/books/book-404-rmd/index.qmd

@@ -0,0 +1,3 @@
+# Welcome
+
+This is the index page.

tests/docs/project/ignore-dirs/.gitignore

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

tests/docs/project/ignore-dirs/_quarto.yml

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

tests/docs/project/ignore-dirs/index.qmd

@@ -0,0 +1,5 @@
+---
+title: "Test Project"
+---
+
+This file should be rendered.

tests/docs/project/ignore-dirs/renv/test.qmd

@@ -0,0 +1,5 @@
+---
+title: "Renv Test"
+---
+
+This file should NOT be rendered (renv is a Knitr ignore directory).

tests/docs/project/ignore-dirs/venv/test.qmd

@@ -0,0 +1,5 @@
+---
+title: "Venv Test"
+---
+
+This file should NOT be rendered (venv is a Jupyter ignore directory).

tests/docs/websites/website-ignore-dirs/.gitignore

@@ -0,0 +1,4 @@
+/.quarto/
+**/*.quarto_ipynb
+*_files/
+_site/

tests/docs/websites/website-ignore-dirs/_quarto.yml

@@ -0,0 +1,13 @@
+project:
+  type: website
+
+website:
+  title: "Test Website"
+  navbar:
+    left:
+      - text: Home
+        file: index.qmd
+
+format:
+  html:
+    theme: default

tests/docs/websites/website-ignore-dirs/index.qmd

@@ -0,0 +1,5 @@
+---
+title: "Test Website"
+---
+
+This file should be rendered.

tests/docs/websites/website-ignore-dirs/renv/test.qmd

@@ -0,0 +1,5 @@
+---
+title: "Renv Test"
+---
+
+This file should NOT be rendered (renv is a Knitr ignore directory).

tests/docs/websites/website-ignore-dirs/venv/test.qmd

@@ -0,0 +1,5 @@
+---
+title: "Venv Test"
+---
+
+This file should NOT be rendered (venv is a Jupyter ignore directory).

tests/docs/websites/website-sidebar-section-index/.gitignore

@@ -0,0 +1,4 @@
+/.quarto/
+**/*.quarto_ipynb
+*_files/
+_site/

tests/docs/websites/website-sidebar-section-index/_quarto.yml

@@ -0,0 +1,14 @@
+project:
+  type: website
+
+website:
+  title: "Sidebar Auto Test"
+  sidebar:
+    contents:
+      - index.qmd
+      - section: "Subdir Section"
+        contents: subdir/*
+
+format:
+  html:
+    theme: default

tests/docs/websites/website-sidebar-section-index/index.qmd

@@ -0,0 +1,5 @@
+---
+title: "Home"
+---
+
+This is the home page.

tests/docs/websites/website-sidebar-section-index/subdir/index.ipynb

@@ -0,0 +1,33 @@
+{
+  "cells": [
+    {
+      "cell_type": "raw",
+      "metadata": {},
+      "source": [
+        "---\n",
+        "title: \"Subdir Index\"\n",
+        "---"
+      ]
+    },
+    {
+      "cell_type": "markdown",
+      "metadata": {},
+      "source": [
+        "This is the index page for the subdir."
+      ]
+    }
+  ],
+  "metadata": {
+    "kernelspec": {
+      "display_name": "Python 3",
+      "language": "python",
+      "name": "python3"
+    },
+    "language_info": {
+      "name": "python",
+      "version": "3.9.0"
+    }
+  },
+  "nbformat": 4,
+  "nbformat_minor": 4
+}

tests/docs/websites/website-sidebar-section-index/subdir/other.qmd

@@ -0,0 +1,5 @@
+---
+title: "Other Page"
+---
+
+This is another page in the subdir.

tests/smoke/book/book-404-detection.test.ts

@@ -0,0 +1,51 @@
+import { testQuartoCmd } from "../../test.ts";
+import { fileExists, noErrorsOrWarnings } from "../../verify.ts";
+import { existsSync } from "../../../src/deno_ral/fs.ts";
+import { join } from "../../../src/deno_ral/path.ts";
+import { docs } from "../../utils.ts";
+
+// Test that book 404 page with .ipynb extension is detected
+const inputIpynb = docs("books/book-404-detection");
+const outputDirIpynb = join(inputIpynb, "_book");
+
+testQuartoCmd(
+  "render",
+  [inputIpynb],
+  [
+    noErrorsOrWarnings,
+    fileExists(join(outputDirIpynb, "index.html")),
+    fileExists(join(outputDirIpynb, "chapter1.html")),
+    fileExists(join(outputDirIpynb, "404.html")),
+    fileExists(join(outputDirIpynb, "search.json")),
+  ],
+  {
+    teardown: async () => {
+      if (existsSync(outputDirIpynb)) {
+        await Deno.remove(outputDirIpynb, { recursive: true });
+      }
+    },
+  },
+);
+
+// Test that book 404 page with .rmd extension is detected
+const inputRmd = docs("books/book-404-rmd");
+const outputDirRmd = join(inputRmd, "_book");
+
+testQuartoCmd(
+  "render",
+  [inputRmd],
+  [
+    noErrorsOrWarnings,
+    fileExists(join(outputDirRmd, "index.html")),
+    fileExists(join(outputDirRmd, "chapter1.html")),
+    fileExists(join(outputDirRmd, "404.html")),
+    fileExists(join(outputDirRmd, "search.json")),
+  ],
+  {
+    teardown: async () => {
+      if (existsSync(outputDirRmd)) {
+        await Deno.remove(outputDirRmd, { recursive: true });
+      }
+    },
+  },
+);

tests/smoke/project/project-ignore-dirs.test.ts

@@ -0,0 +1,46 @@
+/*
+ * project-ignore-dirs.test.ts
+ *
+ * Verifies that engine-specific ignore directories (venv, renv, env, packrat, etc.)
+ * are properly excluded from project file discovery and rendering.
+ *
+ * Copyright (C) 2020-2025 Posit Software, PBC
+ */
+
+import { docs } from "../../utils.ts";
+import { join } from "../../../src/deno_ral/path.ts";
+import { existsSync } from "../../../src/deno_ral/fs.ts";
+import { testQuartoCmd } from "../../test.ts";
+import { fileExists, noErrors, pathDoNotExists } from "../../verify.ts";
+
+const renderDir = docs("project/ignore-dirs");
+const outDir = join(Deno.cwd(), renderDir);
+
+// Test that engine ignore directories are properly excluded
+testQuartoCmd(
+  "render",
+  [renderDir],
+  [
+    noErrors,
+    fileExists(join(outDir, "index.html")),              // Control: regular file should be rendered
+    pathDoNotExists(join(outDir, "venv", "test.html")),  // venv (Jupyter) should be ignored
+    pathDoNotExists(join(outDir, "renv", "test.html")),  // renv (Knitr) should be ignored
+    pathDoNotExists(join(outDir, "env", "test.html")),   // env (Jupyter) should be ignored
+  ],
+  {
+    teardown: async () => {
+      // Clean up rendered HTML files
+      const htmlFiles = [
+        join(outDir, "index.html"),
+        join(outDir, "venv", "test.html"),
+        join(outDir, "renv", "test.html"),
+        join(outDir, "env", "test.html"),
+      ];
+      for (const file of htmlFiles) {
+        if (existsSync(file)) {
+          await Deno.remove(file);
+        }
+      }
+    },
+  },
+);

tests/smoke/website/website-ignore-dirs.test.ts

@@ -0,0 +1,37 @@
+/*
+ * website-ignore-dirs.test.ts
+ *
+ * Verifies that engine-specific ignore directories (venv, renv, env, packrat, etc.)
+ * are properly excluded from website file discovery and rendering.
+ *
+ * Copyright (C) 2020-2025 Posit Software, PBC
+ */
+
+import { docs } from "../../utils.ts";
+import { join } from "../../../src/deno_ral/path.ts";
+import { existsSync } from "../../../src/deno_ral/fs.ts";
+import { testQuartoCmd } from "../../test.ts";
+import { fileExists, noErrors, pathDoNotExists } from "../../verify.ts";
+
+const renderDir = docs("websites/website-ignore-dirs");
+const outDir = join(Deno.cwd(), renderDir, "_site");
+
+// Test that engine ignore directories are properly excluded
+testQuartoCmd(
+  "render",
+  [renderDir],
+  [
+    noErrors,
+    fileExists(join(outDir, "index.html")),              // Control: regular file should be rendered
+    pathDoNotExists(join(outDir, "venv", "test.html")),  // venv (Jupyter) should be ignored
+    pathDoNotExists(join(outDir, "renv", "test.html")),  // renv (Knitr) should be ignored
+    pathDoNotExists(join(outDir, "env", "test.html")),   // env (Jupyter) should be ignored
+  ],
+  {
+    teardown: async () => {
+      if (existsSync(outDir)) {
+        await Deno.remove(outDir, { recursive: true });
+      }
+    },
+  },
+);