Merge branch 'main' into jk/engine-commands

Author: jkrumbiegel

.github/workflows/test-smokes.yml

@@ -170,7 +170,7 @@ jobs:
       - name: Setup Julia
         uses: julia-actions/setup-julia@v2
         with:
-          version: "1.11"
+          version: "1.11.3"
 
       - name: Cache Julia Packages
         uses: julia-actions/cache@v2

.gitignore

@@ -33,9 +33,22 @@ _manuscript
 tests/docs/luacov/luacov.report.html
 tests/docs/luacov/report.html
 
+# generated by test configuration, changes from machine to machine
+# so we don't want to track them
+tests/integration/playwright/package-lock.json
+
 # tools build files
 tools/trace-viewer/edit-distance.js
 tools/trace-viewer/trace-viewer.html
 tools/trace-viewer/trace-viewer_files
 tools/bundle-bug-finder/node_modules
-tools/bundle-bug-finder/package-lock.json
+tools/bundle-bug-finder/package-lock.json
+tools/*/*_files
+tools/*/*.html
+package/src/common/import-report/*.html
+
+# Files that are unique to specific committers of this repo
+tools/sass-variable-explainer/_publish.yml
+
+# generated by tests
+tests/docs/callouts.pdf

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-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 copy.md

@@ -0,0 +1,35 @@
+# Notes for monitoring performance on Linux
+
+Context: I've been having trouble getting consistent performance measurements on my MacBook Pro, so I decided to try my luck on an Intel Linux desktop running Ubuntu 24.
+
+## `perf` settings
+
+We'll want to monitor some performance counters that have potential security implications, so we need to disable some settings. ONLY DO THIS ON A MACHINE YOU TRUST AND THAT WILL NOT RUN POTENTIALLY-MALICIOUS THIRD-PARTY CODE!
+
+### Source `scripts/linux-perf-settings.sh`
+
+(These come from <https://easyperf.net/blog/2019/08/02/Perf-measurement-environment-on-Linux>)
+
+### `sysctl.conf` settings
+
+```
+$ cat /proc/sys/kernel/perf_event_paranoid
+```
+
+If the result isn't `-1`, then add this to `/etc/sysctl.conf`:
+
+```
+kernel.perf_event_paranoid = -1
+```
+
+```
+$ cat /proc/sys/kernel/kptr_restrict
+```
+
+If the result isn't `0`, then add this to `/etc/sysctl.conf`:
+
+```
+kernel.kptr_restrict = 0
+```
+
+After these changes, you'll need to reboot.

dev-docs/performance-monitoring/linux-performance.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

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+# This assumes intel processors!!
+
+# Intel
+echo 1 > /sys/devices/system/cpu/intel_pstate/no_turbo
+# AMD
+# echo 0 > /sys/devices/system/cpu/cpufreq/boost
+
+for i in /sys/devices/system/cpu/cpu*/cpufreq/scaling_governor
+do
+  echo performance > $i
+done
+
+echo 0 > /proc/sys/kernel/randomize_va_space
+

dev-docs/performance-monitoring/scripts/linux-perf-settings.sh

@@ -7,6 +7,7 @@ All changes included in 1.7:
 - ([#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
 
@@ -16,6 +17,10 @@ All changes included in 1.7:
 
 - ([#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.
@@ -24,9 +29,21 @@ All changes included in 1.7:
 
 - ([#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.
+- ([#11903](https://github.com/quarto-dev/quarto-cli/issues/11903)): `crossref` configuration like `fig-title` or `tbl-title` now correctly supports multi word values, e.g. `fig-title: 'Supplementary Figure'`.
+- ([#11878](https://github.com/quarto-dev/quarto-cli/issues/11878)): Correctly fixup raw LaTeX table having an unexpected table env with options (e.g `\begin{table}[c]`) to be handled as crossref table.
+
+## `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
 
@@ -39,8 +56,19 @@ All changes included in 1.7:
 - 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.
+- ([#11928](https://github.com/quarto-dev/quarto-cli/pull/11928)): Update QuartoNotebookRunner to 0.12.0.
+
 ## 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.
+- ([#10532](https://github.com/quarto-dev/quarto-cli/issues/10532)): Quarto changed default of `--headless=old` to `--headless` as [Chrome 132 has removed old headless mode](https://developer.chrome.com/blog/removing-headless-old-from-chrome) and only support new mode. For using old mode, `QUARTO_CHROMIUM` could be set to a [new `chrome-headless-shell` binary](https://developer.chrome.com/blog/chrome-headless-shell) or too an older chrome version (between 128 and 132) and `QUARTO_CHROMIUM_HEADLESS_MODE` set to `old` for using old headless mode with that compatabitle version.
+- ([#10961](https://github.com/quarto-dev/quarto-cli/issues/10961)): Add more information on which Chrome Headless will be used in `quarto check install`. This is helpful to help debug mermaid issues.