Merge commit '034890e334b0b653562e2da07dc89fe7bba95f4c'

MichaelHatherly · MichaelHatherly · commit 15613d0cda1a · 2026-03-25T14:58:43.000Z
diff --git a/src/resources/extension-subtrees/julia-engine/.github/workflows/EnforceChangelog.yml b/src/resources/extension-subtrees/julia-engine/.github/workflows/EnforceChangelog.yml
@@ -0,0 +1,14 @@
+name: "Enforce changelog"
+on:
+  pull_request:
+    types: [opened, synchronize, reopened, ready_for_review, labeled, unlabeled]
+
+jobs:
+  changelog:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      - uses: dangoslen/changelog-enforcer@204e7d3ef26579f4cd0fd759c57032656fdf23c7 # v3.6.1
+        with:
+          changeLogPath: 'CHANGELOG.md'
+          skipLabels: 'skip-changelog'
diff --git a/src/resources/extension-subtrees/julia-engine/AGENTS.md b/src/resources/extension-subtrees/julia-engine/AGENTS.md
@@ -59,3 +59,7 @@ CI runs on all three platforms (Linux, macOS, Windows) against a pinned quarto-c
 3. Runs the full test suite
 
 When bumping `QUARTO_CLI_REV`, use the full commit hash annotated with the version tag for clarity (e.g. `abc123 # v1.9.35`).
+
+## Changelog
+
+Every PR with user-facing or otherwise meaningful changes must include an update to `CHANGELOG.md` (enforced by CI). Add entries under the `## Unreleased` section. Use the `skip-changelog` label to bypass the check for PRs that don't need an entry (e.g. internal cleanups, CI, or docs changes).
diff --git a/src/resources/extension-subtrees/julia-engine/CHANGELOG.md b/src/resources/extension-subtrees/julia-engine/CHANGELOG.md
@@ -0,0 +1,28 @@
+# Quarto Julia Engine changelog
+
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## Unreleased
+
+## [0.2.0](https://github.com/PumasAI/quarto-julia-engine/releases/tag/v0.2.0) - 2026-03-24
+
+- Added `keep-ipynb` support. When `keep-ipynb: true` is set in document YAML, the executed notebook is written to `<stem>.ipynb` alongside the source file [#8](https://github.com/PumasAI/quarto-julia-engine/pull/8).
+- Updated to QuartoNotebookRunner 0.18.1 [#11](https://github.com/PumasAI/quarto-julia-engine/pull/11):
+  - **`fig-format: retina` support**: Normalized to `png` with doubled `fig-dpi`, matching Quarto's Jupyter and knitr backends. Fixes blurry plots with default HTML settings.
+  - **Improved cache invalidation**: Cache key now hashes full `Manifest.toml` content (SHA-224) so dependency version changes correctly invalidate the cache.
+- Updated to QuartoNotebookRunner 0.18.0 [#7](https://github.com/PumasAI/quarto-julia-engine/pull/7):
+  - **Shared worker processes**: Multiple notebooks can share a single worker process when their configs match. Enable with `share_worker_process: true`.
+  - **`execute-dir` support**: Quarto's `execute-dir` option (e.g. `execute-dir: project`) is now passed through correctly.
+  - **Cached worker environments**: Worker envs persist across sessions, skipping environment setup on subsequent runs when Julia and QNR versions haven't changed.
+  - **Relaxed manifest version checking**: Only major.minor is checked by default, matching Julia's Pkg behavior. Opt into strict major.minor.patch via `julia: strict_manifest_versions: true`.
+  - **Diagnostic file logging**: Set `QUARTONOTEBOOKRUNNER_LOG` to a directory path to enable timestamped log files.
+  - **Echo handling for Python/R cells**: Fixed duplicate YAML keys and added proper support for `echo: false` and `echo: fenced`.
+
+## [0.1.0](https://github.com/PumasAI/quarto-julia-engine/releases/tag/v0.1.0) - 2026-03-19
+
+- Initial release as a standalone Quarto extension, extracted from [quarto-cli](https://github.com/quarto-dev/quarto-cli).
+- Bundled Julia resource files (`Project.toml`, `ensure_environment.jl`, `quartonotebookrunner.jl`, `start_quartonotebookrunner_detached.jl`) into the extension, making it fully self-contained [#6](https://github.com/PumasAI/quarto-julia-engine/pull/6).
+- Added CI workflow with tests on Linux, macOS, and Windows [#6](https://github.com/PumasAI/quarto-julia-engine/pull/6).
diff --git a/src/resources/extension-subtrees/julia-engine/_extensions/julia-engine/Project.toml b/src/resources/extension-subtrees/julia-engine/_extensions/julia-engine/Project.toml
@@ -2,4 +2,4 @@
 QuartoNotebookRunner = "4c0109c6-14e9-4c88-93f0-2b974d3468f4"
 
 [compat]
-QuartoNotebookRunner = "=0.17.4"
+QuartoNotebookRunner = "=0.18.1"
diff --git a/src/resources/extension-subtrees/julia-engine/_extensions/julia-engine/_extension.yml b/src/resources/extension-subtrees/julia-engine/_extensions/julia-engine/_extension.yml
@@ -1,5 +1,5 @@
 title: Quarto Julia Engine Extension
-version: 0.1.0
+version: 0.2.0
 quarto-required: ">=1.9.0"
 contributes:
   engines:
diff --git a/src/resources/extension-subtrees/julia-engine/_extensions/julia-engine/julia-engine.js b/src/resources/extension-subtrees/julia-engine/_extensions/julia-engine/julia-engine.js
@@ -631,6 +631,7 @@ var kFigFormat = "fig-format";
 var kFigPos = "fig-pos";
 var kIpynbProduceSourceNotebook = "produce-source-notebook";
 var kKeepHidden = "keep-hidden";
+var kKeepIpynb = "keep-ipynb";
 
 // src/julia-engine.ts
 var isWindows2 = Deno.build.os === "windows";
@@ -749,6 +750,11 @@ var juliaEngineDiscovery = {
           language: "julia"
         };
         const assets = quarto.jupyter.assets(options.target.input, options.format.pandoc.to);
+        if (options.format.execute[kKeepIpynb]) {
+          const stem = options.target.source.replace(/\.[^.]+$/, "");
+          const ipynbPath = stem + ".ipynb";
+          Deno.writeTextFileSync(ipynbPath, JSON.stringify(nb, null, 2));
+        }
         const result = await quarto.jupyter.toMarkdown(nb, {
           executeOptions: options,
           language: nb.metadata.kernelspec.language.toLowerCase(),
diff --git a/src/resources/extension-subtrees/julia-engine/src/constants.ts b/src/resources/extension-subtrees/julia-engine/src/constants.ts
@@ -13,3 +13,4 @@ export const kFigFormat = "fig-format";
 export const kFigPos = "fig-pos";
 export const kIpynbProduceSourceNotebook = "produce-source-notebook";
 export const kKeepHidden = "keep-hidden";
+export const kKeepIpynb = "keep-ipynb";
diff --git a/src/resources/extension-subtrees/julia-engine/src/julia-engine.ts b/src/resources/extension-subtrees/julia-engine/src/julia-engine.ts
@@ -37,6 +37,7 @@ import {
   kIpynbProduceSourceNotebook,
   kJuliaEngine,
   kKeepHidden,
+  kKeepIpynb,
 } from "./constants.ts";
 
 // Platform detection
@@ -220,6 +221,14 @@ export const juliaEngineDiscovery: ExecutionEngineDiscovery = {
           options.format.pandoc.to,
         );
 
+        // Write notebook to file if keep-ipynb is set (must happen before
+        // toMarkdown which mutates nb in place)
+        if (options.format.execute[kKeepIpynb]) {
+          const stem = options.target.source.replace(/\.[^.]+$/, "");
+          const ipynbPath = stem + ".ipynb";
+          Deno.writeTextFileSync(ipynbPath, JSON.stringify(nb, null, 2));
+        }
+
         // NOTE: for perforance reasons the 'nb' is mutated in place
         // by jupyterToMarkdown (we don't want to make a copy of a
         // potentially very large notebook) so should not be relied
diff --git a/src/resources/extension-subtrees/julia-engine/tests/docs/julia-engine/.gitignore b/src/resources/extension-subtrees/julia-engine/tests/docs/julia-engine/.gitignore
@@ -4,3 +4,4 @@
 # Allow only source files
 !*/*.qmd
 !*/_quarto.yml
+!*/_metadata.yml
diff --git a/src/resources/extension-subtrees/julia-engine/tests/docs/julia-engine/engine-reordering/_metadata.yml b/src/resources/extension-subtrees/julia-engine/tests/docs/julia-engine/engine-reordering/_metadata.yml
@@ -0,0 +1 @@
+engines: ["julia"]
diff --git a/src/resources/extension-subtrees/julia-engine/tests/docs/julia-engine/engine-reordering/_quarto.yml b/src/resources/extension-subtrees/julia-engine/tests/docs/julia-engine/engine-reordering/_quarto.yml
diff --git a/src/resources/extension-subtrees/julia-engine/tests/docs/julia-engine/keep-ipynb/keep-ipynb.qmd b/src/resources/extension-subtrees/julia-engine/tests/docs/julia-engine/keep-ipynb/keep-ipynb.qmd
@@ -0,0 +1,10 @@
+---
+title: keep-ipynb test
+engine: julia
+format: html
+keep-ipynb: true
+---
+
+```{julia}
+1 + 1
+```
diff --git a/src/resources/extension-subtrees/julia-engine/tests/docs/julia-engine/keep-ipynb/no-keep-ipynb.qmd b/src/resources/extension-subtrees/julia-engine/tests/docs/julia-engine/keep-ipynb/no-keep-ipynb.qmd
@@ -0,0 +1,9 @@
+---
+title: no keep-ipynb test
+engine: julia
+format: html
+---
+
+```{julia}
+1 + 1
+```
diff --git a/src/resources/extension-subtrees/julia-engine/tests/docs/julia-engine/sleep/_quarto.yml b/src/resources/extension-subtrees/julia-engine/tests/docs/julia-engine/sleep/_quarto.yml
diff --git a/src/resources/extension-subtrees/julia-engine/tests/smoke/julia-engine/render.test.ts b/src/resources/extension-subtrees/julia-engine/tests/smoke/julia-engine/render.test.ts
@@ -44,6 +44,40 @@ Deno.test("source ranges with includes", async () => {
   try { Deno.removeSync(outputFile); } catch { /* ok */ }
 });
 
+Deno.test("keep-ipynb", async () => {
+  const dir = docs("julia-engine/keep-ipynb");
+  const input = join(dir, "keep-ipynb.qmd");
+  renderQmd(input, ["--to", "html"]);
+
+  const outputHtml = join(dir, "keep-ipynb.html");
+  assert(existsSync(outputHtml), `Output file ${outputHtml} should exist`);
+
+  const ipynbFile = join(dir, "keep-ipynb.ipynb");
+  assert(existsSync(ipynbFile), `keep-ipynb file ${ipynbFile} should exist`);
+
+  const content = await Deno.readTextFile(ipynbFile);
+  const nb = JSON.parse(content);
+  assert(nb.cells, "Notebook should have cells");
+  assert(nb.metadata, "Notebook should have metadata");
+
+  try { Deno.removeSync(outputHtml); } catch { /* ok */ }
+  try { Deno.removeSync(ipynbFile); } catch { /* ok */ }
+});
+
+Deno.test("no keep-ipynb by default", () => {
+  const dir = docs("julia-engine/keep-ipynb");
+  const input = join(dir, "no-keep-ipynb.qmd");
+  renderQmd(input, ["--to", "html"]);
+
+  const outputHtml = join(dir, "no-keep-ipynb.html");
+  assert(existsSync(outputHtml), `Output file ${outputHtml} should exist`);
+
+  const ipynbFile = join(dir, "no-keep-ipynb.ipynb");
+  assert(!existsSync(ipynbFile), `ipynb file ${ipynbFile} should NOT exist without keep-ipynb`);
+
+  try { Deno.removeSync(outputHtml); } catch { /* ok */ }
+});
+
 Deno.test("engine reordering", () => {
   const dir = docs("julia-engine/engine-reordering");
   renderQmd("notebook.qmd", ["--to", "html"], dir);
