Merge branch 'main' into jk/engine-commands

Author: jkrumbiegel

.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/actions/cache-typst/action.yml

@@ -1,10 +1,24 @@
-name: "Cache Typst package"
+name: "Restore any Typst package cache"
 description: "Configures the caching for Typst packages"
+outputs:
+  cache-hit:
+    description: "Was a cache found with primary key ?"
+    value: ${{ steps.cache-typst-restore.outputs.cache-hit }}
+  cache-primary-key:
+    description: "Key of the cache to find and save"
+    value: ${{ steps.cache-typst-restore.outputs.cache-primary-key }}
+  cache-matched-key:
+    description: "Key of the cache found and used."
+    value: ${{ steps.cache-typst-restore.outputs.cache-primary-key }}
+  cache-path:
+    description: "where is the packages cache for typst ?"
+    value: ${{ steps.cache-typst-path.outputs.TYPST_CACHE }}
 
 runs:
   using: "composite"
   steps:
     - name: Typst Cache path
+      id: cache-typst-path
       run: |
         case $RUNNER_OS in
           "Linux")
@@ -21,13 +35,14 @@ runs:
               exit 1
               ;;
         esac
+        echo "TYPST_CACHE=${TYPST_CACHE}" >> $GITHUB_OUTPUT
       shell: bash
 
     - name: Cache Typst package folder
-      uses: actions/cache@v4
+      id: cache-typst-restore
+      uses: actions/cache/restore@v4
       with:
         path: ${{ env.TYPST_CACHE }}
-        key: ${{ runner.os }}-typst-1-${{ github.run_id }}
+        key: ${{ runner.os }}-typst-1
         restore-keys: |
-          ${{ runner.os }}-typst-1-
-        save-always: true
+          ${{ runner.os }}-typst-

.github/workflows/test-smokes.yml

@@ -130,8 +130,8 @@ jobs:
           renv::restore()
           # Install dev versions for our testing
           # Use r-universe to avoid github api calls
-          try(install.packages('knitr', repos = 'https://yihui.r-universe.dev'))
-          try(install.packages('rmarkdown', repos = 'https://rstudio.r-universe.dev'))
+          try(install.packages('rmarkdown', repos = c('https://rstudio.r-universe.dev', getOption('repos'))))
+          try(install.packages('knitr', repos = c('https://yihui.r-universe.dev', getOption('repos'))))
           if ('${{ inputs.extra-r-packages }}' != '') {
             cat(sprintf("::notice::Running with the following extra R packages for pak: %s\n", "${{ inputs.extra-r-packages }}"))
             renv::install(strsplit("${{ inputs.extra-r-packages }}", split = ",")[[1]])
@@ -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"
 
@@ -161,6 +161,7 @@ jobs:
           quarto install tinytex
 
       - name: Cache Typst packages
+        id: cache-typst
         uses: ./.github/actions/cache-typst
 
       - name: Install Chrome
@@ -169,7 +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
@@ -183,7 +184,7 @@ jobs:
           export JUPYTER=$(find $(dirname $(uv run --frozen which jupyter))/ -type f -name "jupyter.exe" -o -name "jupyter")
           uv run --frozen julia --color=yes --project=. -e "import Pkg; Pkg.instantiate(); Pkg.build(\"IJulia\"); Pkg.precompile()"
           echo "Julia Jupyter:"
-          julia --project=. -e "import IJulia;println(IJulia.JUPYTER);println(IJulia.find_jupyter_subcommand(\"notebook\"))"
+          uv run julia --project=. -e "import IJulia;println(IJulia.JUPYTER);println(IJulia.find_jupyter_subcommand(\"notebook\"))"
 
       - name: Setup timing file for timed test
         if: ${{ matrix.time-test == true }}
@@ -289,6 +290,13 @@ jobs:
           name: timed test file
           path: tests/timing-for-ci.txt
 
+      - name: Save Typst cache
+        if: always()
+        uses: actions/cache/save@v4
+        with:
+          key: ${{ steps.cache-typst.outputs.cache-primary-key }}
+          path: ${{ steps.cache-typst.outputs.cache-path }}
+
       - uses: actions/upload-artifact@v4
         # PLaywright test only runs on Linux for now
         if: ${{ !cancelled() && runner.os != 'Windows' }}

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

@@ -8,6 +8,7 @@
     - Uncheck "Pre-release" (or ensure it's unchecked)
     - 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
 - [ ] update release on pypi repo
   - Goto the [quarto-cli-pypi repo](https://github.com/quarto-dev/quarto-cli-pypi)
   - Update `version.txt` to be the version you'd like to publish and commit
@@ -24,4 +25,4 @@
       - **Publishing Production**: You may elect to publish to production pypyi by checking the `Production Release` option
         - Published to: <https://pypi.org/project/quarto-cli/>
     - Take a sip of tea ☕, bask in the glory of automation.
-- [ ] Update the stable changelog by moving entries to the "in previous release"
+- [ ] Update the stable changelog by moving entries from "In this release" to the "In previous releases" section

news/changelog-1.7.md

@@ -4,24 +4,43 @@ All changes included in 1.7:
 
 - ([#11509](https://github.com/quarto-dev/quarto-cli/issues/11509)): Fix link-decoration regression in HTML formats.
 - ([#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.
 
 ## 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.
+
+## 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
+
+- ([#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.
+
 ## Lua Filters and extensions
 
 - ([#11526](https://github.com/quarto-dev/quarto-cli/pull/11526)):
   General improvements to the style and robustness of Quarto's Lua code.
   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.
 
 ## Other Fixes and Improvements
 
+- ([#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.

src/command/render/filters.ts

@@ -93,6 +93,7 @@ import { isServerShinyPython } from "../../core/render.ts";
 import { pythonExec } from "../../core/jupyter/exec.ts";
 import { kTocIndent } from "../../config/constants.ts";
 import { isWindows } from "../../deno_ral/platform.ts";
+import { tinyTexBinDir } from "../../tools/impl/tinytex-info.ts";
 
 const kQuartoParams = "quarto-params";
 
@@ -205,6 +206,7 @@ async function quartoEnvironmentParams(_options: PandocOptions) {
   return {
     "paths": {
       "Rscript": await rBinaryPath("Rscript"),
+      "TinyTexBinDir": tinyTexBinDir(), // will be undefined if no tinytex found and quarto will look in PATH
     },
   };
 }

src/command/render/pandoc.ts

@@ -594,7 +594,7 @@ export async function runPandoc(
     // or by the project as format extras
     if (extras[kNotebooks]) {
       const documentNotebooks = options.format.render[kNotebookView];
-      // False means taht the user has explicitely disabled notebooks
+      // False means that the user has explicitely disabled notebooks
       if (documentNotebooks !== false) {
         const userNotebooks = documentNotebooks === true
           ? []

src/command/render/project.ts

@@ -307,7 +307,7 @@ export async function renderProject(
       (projectRenderConfig.options.flags?.clean == true) &&
         (projType.cleanOutputDir === true))
   ) {
-    // ouptut dir
+    // output dir
     const realProjectDir = normalizePath(context.dir);
     if (existsSync(projOutputDir)) {
       const realOutputDir = normalizePath(projOutputDir);

src/core/handlers/base.ts

@@ -405,9 +405,7 @@ export async function expandIncludes(
   const newCells: MappedString[] = [];
   for (let i = 0; i < mdCells.length; ++i) {
     const cell = mdCells[i];
-    newCells.push(
-      i === 0 ? cell.sourceVerbatim : mappedConcat(["\n", cell.sourceVerbatim]),
-    );
+    newCells.push(cell.sourceVerbatim);
   }
 
   await processMarkdownIncludes(newCells, options, filename);
@@ -437,9 +435,7 @@ export async function handleLanguageCells(
 
   for (let i = 0; i < mdCells.length; ++i) {
     const cell = mdCells[i];
-    newCells.push(
-      i === 0 ? cell.sourceVerbatim : mappedConcat(["\n", cell.sourceVerbatim]),
-    );
+    newCells.push(cell.sourceVerbatim);
     if (
       cell.cell_type === "raw" ||
       cell.cell_type === "markdown"
@@ -483,7 +479,6 @@ export async function handleLanguageCells(
           (innerLanguageHandler.stage !== "any" &&
             innerLanguageHandler.stage !== options.stage)
         ) { // we're in the wrong stage, so we don't actually do anything
-          newCells[cell.index] = mappedConcat([newCells[cell.index], "\n"]);
           continue;
         }
         if (
@@ -492,7 +487,6 @@ export async function handleLanguageCells(
         ) {
           // if no handler is present (or a directive was included for something
           // that responds to cells instead), we're a no-op
-          newCells[cell.index] = mappedConcat([newCells[cell.index], "\n"]);
           continue;
         }
         if (innerLanguageHandler.directive === undefined) {