Merge branch 'main' into bugfix/typst-unitless-image-column-widths

Author: cscheid

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -29,31 +29,29 @@ body:
         You can share a Quarto document using the following syntax, _i.e._, using more backticks than you have in your document (usually four ` ```` `).
         For example with Quarto CLI >=1.5:
 
-        `````md
-        ````qmd
-        ---
-        title: "Reproducible Quarto Document"
-        format: html
-        engine: jupyter
-        ---
-
-        This is a reproducible Quarto document using `format: html`.
-        It is written in Markdown and contains embedded Python code.
-        When you run the code, it will produce a message.
-
-        ```{python}
-        print("Hello, world!")
-        ```
-
-        ![An image]({{< placeholder 600 400 >}}){#fig-placeholder}
-
-        {{< lipsum 1 >}}
-
-        A reference to @fig-placeholder.
-
-        The end.
-        ````
-        `````
+            ````qmd
+            ---
+            title: "Reproducible Quarto Document"
+            format: html
+            engine: jupyter
+            ---
+            
+            This is a reproducible Quarto document using `format: html`.
+            It is written in Markdown and contains embedded Python code.
+            When you run the code, it will produce a message.
+            
+            ```{python}
+            print("Hello, world!")
+            ```
+            
+            ![An image]({{< placeholder 600 400 >}}){#fig-placeholder}
+            
+            {{< lipsum 1 >}}
+            
+            A reference to @fig-placeholder.
+            
+            The end.
+            ````
 
   - type: textarea
     attributes:

.github/workflows/test-smokes.yml

@@ -143,7 +143,7 @@ jobs:
       - name: Install uv for Python
         uses: astral-sh/setup-uv@v3
         with:
-          version: "0.5.6"
+          version: "0.5.9"
           enable-cache: true
           cache-dependency-glob: "tests/uv.lock"
 
@@ -170,7 +170,7 @@ jobs:
       - name: Setup Julia
         uses: julia-actions/setup-julia@v2
         with:
-          version: "1.10"
+          version: "1.11"
 
       - name: Cache Julia Packages
         uses: julia-actions/cache@v2

CITATION.cff

@@ -16,8 +16,11 @@ authors:
 - family-names: "Dervieux"
   given-names: "Christophe"
   orcid: "https://orcid.org/0000-0003-4474-2498"
+- family-names: "Woodhull"
+  given-names: "Gordon"
+  orcid: "https://orcid.org/0009-0005-1809-8936"
 title: "Quarto"
-version: 1.4
+version: 1.6
 doi: 10.5281/zenodo.5960048
-date-released: 2024-02-15
+date-released: 2024-11-27
 url: "https://github.com/quarto-dev/quarto-cli"

configuration

@@ -37,9 +37,10 @@ export TIPPY_JS=6.3.7
 export PDF_JS=2.8.335
 export REVEAL_JS=5.1.0
 export REVEAL_JS_MENU=2.1.0
-# unrelease version needed for a fix with Reveal.js 5
+# unrelease version needed for fixes with Reveal.js 5
 # https://github.com/rajgoel/reveal.js-plugins/pull/180
-export REVEAL_JS_CHALKBOARD=8408d5a265abf74a042122520bbb4fd0d31feaed
+# https://github.com/rajgoel/reveal.js-plugins/pull/184
+export REVEAL_JS_CHALKBOARD=217142176341e24628db2908cae38221ef13d639
 export REVEAL_JS_PDFEXPORT=2.0.1
 export LIST_JS=2.3.1
 export DAY_JS=1.11.7

dev-docs/checklist-make-a-new-quarto-prerelease.md

@@ -0,0 +1,13 @@
+- [ ] ensure main is up to date and tests are passing on latest commit.
+- [ ] create new prerelease installers
+  - Click Actions -> Build Installers -> "Run Workflow" Dropdown Menu
+    - Select the main branch in the "Use workflow from..." dropdown
+    - Check "Pre-release" (or ensure it's checked)
+    - Check "Publish release" (or ensure it's checked)
+    - [ ] Click "Run Workflow"
+      - If workflow fails for some reason, re-run all jobs and not only failed jobs or trigger a new clean build from Actions -> Build Installers -> "Run Workflow" Dropdown Menu.
+        This is important because workflow commit an update to version.txt to main, and revert if cancelled or failure. A triggering a new workflow needs to re-run the configure step.
+- If everything went well:
+  - New release prerelease should be on Github at <https://github.com/quarto-dev/quarto-cli/releases>
+  - A new tag should be on main for the new prerelease version
+  - `version.txt` on main should have been updated by the workflow to the pre-release version just released: https://github.com/quarto-dev/quarto-cli/blob/main/version.txt

dev-docs/checklist-make-a-new-quarto-release.md

@@ -45,6 +45,7 @@
   - [ ] publish the release blog post that should exist in https://github.com/quarto-dev/quarto-web/tree/main/docs/blog/posts
         by removing the `draft: true` line in the metadata and changing the date to match the release date. Do this on a branch off of `main` to trigger our PR automation to make the corresponding change to `prerelease`.
 
+- [ ] Update https://github.com/quarto-dev/quarto-cli/blob/main/CITATION.cff
 - [ ] Packaging and package managers, etc
   - TBD winget, etc?
   - [ ] chocolatey

dev-docs/checklist-make-a-new-stable-quarto-release.md

@@ -0,0 +1,52 @@
+To perform fine-grained profiling of Pandoc Lua filters, we use custom binaries:
+
+- a patch of Lua that supports sample-based profiling
+- a custom binary of Pandoc linked against that version of Lua
+
+## Compile the custom Lua version
+
+This has currently only been tested on Macos and Linux.
+
+```
+$ git clone [email protected]:cscheid/lua-fast-profiler.git
+$ cd lua-fast-profiler
+$ git checkout feature/fast-profiler-5.4
+$ make
+```
+
+You should have `lua` and `liblua.a` in the `lua-fast-profiler` directory.
+
+This version of Lua adds a new debugging hook, "time".
+This hook triggers at specified intervals, and is enabled using the letter `t` in the `debug.sethook` call.
+The debug hook callback also supports the "alarm" hook, used when calling the `sethook` callback.
+
+Quarto ships with a custom Lua profiler that supports these hooks and performs low-overhead stack profiling.
+
+## Compile the custom Pandoc binary
+
+Clone the Pandoc repository, and then
+
+```
+$ C_INCLUDE_PATH=<path-lua-fast-profiler> LIBRARY_PATH=<path-lua-fast-profiler> cabal build pandoc-cli --constraint 'lua +system-lua'
+```
+
+## Run Quarto with profiling
+
+To get Lua profiling output from Quarto, use the `lua-profiler-output` metadata option to provide an output file name, and ensure that Quarto uses the
+`pandoc` binary you just compiled.
+
+```
+$ QUARTO_PANDOC=<path-to-built-pandoc> quarto render ...
+```
+
+The output will be written as JSON, in a format compatible with [Perfetto](https://ui.perfetto.dev).
+The default sampling interval is 5ms, but you can customize that by setting the `lua-profiler-interval-ms` metadata option.
+
+### Analyze profile
+
+The resulting profile can be visualized and analyzed as a trace file at <https://ui.perfetto.dev>.
+
+### Profiling multiple-file projects
+
+In multiple-file projects, you can get a summary of the runtime of individual filter steps by providing the `QUARTO_COMBINED_LUA_PROFILE` environment variable.
+At the end of rendering a project, the name of the file pointed to `QUARTO_COMBINED_LUA_PROFILE` will contain a CSV file with the columns `filter`, `filename`, and `time`, corresponding to an estimate of time (in microseconds) taken by each stage of Quarto's filtering pipeline.

dev-docs/performance-monitoring/pandoc-profiling.md

@@ -6,19 +6,42 @@ All changes included in 1.7:
 - ([#11532](https://github.com/quarto-dev/quarto-cli/issues/11532)): Fix regression for [#660](https://github.com/quarto-dev/quarto-cli/issues/660), which causes files to have incorrect permissions when Quarto is installed in a location not writable by the current user.
 - ([#11549](https://github.com/quarto-dev/quarto-cli/issues/11549)): Fix regression in rendering `dashboard` tabsets into cards without titles.
 - ([#11580](https://github.com/quarto-dev/quarto-cli/issues/11580)): Fix regression with documents containing `categories` fields that are not strings.
+- ([#11752](https://github.com/quarto-dev/quarto-cli/issues/11752)): Fix regression with non-alphanumeric characters in `categories` preventing correct filtering of listing.
+- ([#11561](https://github.com/quarto-dev/quarto-cli/issues/11561)): Fix a regression with `$border-color` that impacted, callouts borders, tabset borders, and table borders of the defaults themes. `$border-color` is now correctly a mixed of `$body-color` and `$body-bg` even for the default theme.
 
 ## YAML validation
 
 - ([#11654](https://github.com/quarto-dev/quarto-cli/issues/11654)): Allow `page-inset` as value in `column` key for code cells.
 
+## Website projects
+
+- ([#11701](https://github.com/quarto-dev/quarto-cli/issues/11701)): Wrap HTML emitted by EJS templates in `{=html}` blocks to avoid memory blowup issues with Pandoc's parser.
+
+## Blog projects
+
+- ([#11745](https://github.com/quarto-dev/quarto-cli/issues/11745)): Fix categories links under post title in post with url encoded path (e.g. with space or other special characters).
+
+## Book projects
+
+- ([#11520](https://github.com/quarto-dev/quarto-cli/issues/11520)): Book's cover image now escapes lightbox treatment, which was incorrectly applied to it when `lightbox: true` was set in the book's configuration.
+
 ## `quarto check`
 
 - ([#11608](https://github.com/quarto-dev/quarto-cli/pull/11608)): Do not issue error message when calling `quarto check info`.
 
-## `typst` Format
+## `html` format
+
+- ([#11860])(https://github.com/quarto-dev/quarto-cli/issues/11860)): ES6 modules that import other local JS modules in documents with `embed-resources: true` are now correctly embedded.
+
+## `pdf` format
+
+- ([#11835](https://github.com/quarto-dev/quarto-cli/issues/11835)): Take markdown structure into account when detecting minimum heading level.
+
+## `typst` format
 
 - ([#11578](https://github.com/quarto-dev/quarto-cli/issues/11578)): Typst column layout widths use fractional `fr` units instead of percent `%` units for unitless and default widths in order to fill the enclosing block and not spill outside it.
 - ([#11676](https://github.com/quarto-dev/quarto-cli/pull/11676)): Convert unitless image widths from pixels to inches for column layouts.
+- ([#11835](https://github.com/quarto-dev/quarto-cli/issues/11835)): Take markdown structure into account when detecting minimum heading level.
 
 ## Lua Filters and extensions
 
@@ -27,9 +50,20 @@ All changes included in 1.7:
   This also provides a new public function `quarto.utils.is_empty_node`
   that allows to check whether a node is empty, i.e., whether it's an
   empty list, has no child nodes, and contains no text.
+- ([#11699](https://github.com/quarto-dev/quarto-cli/issues/11699)): Fix crash with `video` shortcode inside HTML comments.
+- Expose new `quarto.paths.tinytex_bin_dir` in Quarto's Lua API. If TinyTeX is found by Quarto, this will be set to the path to the `bin` directory of the TinyTeX installation where command line tool are located (e.g., `pdflatex`, `tlmgr`, etc.). If TinyTeX is not found, this will be `nil`, meaning Quarto will use the system PATH to find the command line tools.
+- Fix `pandoc.mediabag` Lua typings so autocompletions work with the Lua LSP integration.
+
+## Engines
+
+### `julia`
+
+- ([#11659](https://github.com/quarto-dev/quarto-cli/pull/11659)): Fix escaping bug where paths containing spaces or backslashes break server startup on Windows.
 
 ## Other Fixes and Improvements
 
+- ([#7260](https://github.com/quarto-dev/quarto-cli/issues/7260)): Add support for `active` class in tabsets so the `.active` tab shows up by default.
 - ([#8613](https://github.com/quarto-dev/quarto-cli/issues/8613)): Fix `giscus` color on load to support dark mode (by @kv9898).
 - ([#11441](https://github.com/quarto-dev/quarto-cli/issues/11441)): Don't add newlines around shortcodes during processing.
 - ([#11643](https://github.com/quarto-dev/quarto-cli/issues/11643)): Improve highlighting of nested code block inside markdown code block, i.e. using ` ```{{python}} ` or ` ```python ` inside ` ````markdown` fenced code block.
+- ([fb38eb5](https://github.com/quarto-dev/quarto-cli/commit/fb38eb56c11e09f44cef58fd3b697ff24bb5a3f3)) Use the `latest` parser for Acorn when analyzing JS code imported from OJS blocks.