Merge branch 'main' into fix/issue10251

Author: mcanouil

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -6,22 +6,22 @@ body:
   - type: markdown
     attributes:
       value: |
-        Welcome to the quarto GitHub repository!
+        Welcome to the Quarto CLI GitHub repository!
         We are always happy to hear feedback from our users.
 
         This is the repository for the command-line program `quarto`:
 
         - If you're reporting an issue with the VS Code extension, please visit https://github.com/quarto-dev/quarto
         - If you're reporting an issue inside RStudio, please visit https://github.com/rstudio/rstudio
+        - If you're reporting an issue inside **Positron**, please visit https://github.com/posit-dev/positron
+        - If you want to ask for a feature, please use the [Feature Requests GitHub Discussions](https://github.com/quarto-dev/quarto-cli/discussions/categories/feature-requests).
+        - If you want to ask for help, please use the [Q&A GitHub Discussions](https://github.com/quarto-dev/quarto-cli/discussions/categories/q-a).
 
         Quarto is under active development!
         If convenient, we'd appreciate if you could check that the issue persists on the [latest pre-release](https://github.com/quarto-dev/quarto-cli/releases).
 
         Finally, so that we can get the most out of your bug report, consider reading our ["Bug Reports" guide](https://quarto.org/bug-reports.html).
 
-        If you want to ask for a feature, please use the [Feature Requests GitHub Discussions](https://github.com/quarto-dev/quarto-cli/discussions/categories/feature-requests).
-        If you want to ask for help, please use the [Q&A GitHub Discussions](https://github.com/quarto-dev/quarto-cli/discussions/categories/q-a).
-
         Thank you for using Quarto!
 
         ---
@@ -96,13 +96,13 @@ body:
 
   - type: textarea
     attributes:
-      label: Expected behavior
-      description: Tell us what should happen.
+      label: Actual behavior
+      description: Tell us what happens instead.
 
   - type: textarea
     attributes:
-      label: Actual behavior
-      description: Tell us what happens instead.
+      label: Expected behavior
+      description: Tell us what should happen.
 
   - type: textarea
     attributes:

.github/actions/cache-typst/action.yml

@@ -9,7 +9,7 @@ outputs:
     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 }}
+    value: ${{ steps.cache-typst-restore.outputs.cache-matched-key }}
   cache-path:
     description: "where is the packages cache for typst ?"
     value: ${{ steps.cache-typst-path.outputs.TYPST_CACHE }}
@@ -22,20 +22,21 @@ runs:
       run: |
         case $RUNNER_OS in
           "Linux")
-              echo "TYPST_CACHE=${XDG_CACHE_HOME:-~/.cache}/typst/packages/" >> $GITHUB_ENV
+              typst_cache="${XDG_CACHE_HOME:-~/.cache}/typst/packages/"
               ;;
           "macOS")
-              echo "TYPST_CACHE=~/Library/Caches/typst/packages/" >> $GITHUB_ENV
+              typst_cache="~/Library/Caches/typst/packages/"
               ;;
           "Windows")
-              echo "TYPST_CACHE=$LOCALAPPDATA/typst/packages/" >> $GITHUB_ENV
+              typst_cache="$LOCALAPPDATA/typst/packages/"
               ;;
             *)
               echo "$RUNNER_OS not supported"
               exit 1
               ;;
         esac
-        echo "TYPST_CACHE=${TYPST_CACHE}" >> $GITHUB_OUTPUT
+        echo "TYPST_CACHE=${typst_cache}" >> $GITHUB_ENV
+        echo "TYPST_CACHE=${typst_cache}" >> $GITHUB_OUTPUT
       shell: bash
 
     - name: Cache Typst package folder

.github/workflows/test-smokes.yml

@@ -105,14 +105,16 @@ jobs:
           cat("r-version=", R.Version()$version.string, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE)
         shell: Rscript {0}
 
-      - name: Cache R packages
-        uses: actions/cache@v4
+      - name: Restore Renv package cache
+        id: cache-renv-packages-restore
+        uses: actions/cache/restore@v4
         with:
-          path: ${{ env.RENV_PATHS_ROOT }}
-          key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-renv-2-${{ hashFiles('tests/renv.lock') }}
+          path: |
+            ${{ env.RENV_PATHS_ROOT }}
+            renv/library
+          key: ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-renv-3-${{ hashFiles('tests/renv.lock') }}
           restore-keys: |
-            ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-renv-2-
-          save-always: ${{ inputs.extra-r-packages == '' }} # don't save cache if we have extra R packages
+            ${{ steps.get-version.outputs.os-version }}-${{ steps.get-version.outputs.r-version }}-renv-3-
 
       - name: Install missing system deps
         if: runner.os == 'Linux'
@@ -291,15 +293,25 @@ jobs:
           path: tests/timing-for-ci.txt
 
       - name: Save Typst cache
-        if: always()
+        if: always() && steps.cache-typst.outputs.cache-hit != 'true'
         uses: actions/cache/save@v4
         with:
           key: ${{ steps.cache-typst.outputs.cache-primary-key }}
           path: ${{ steps.cache-typst.outputs.cache-path }}
 
+      - name: Save Renv package cache
+        # don't save cache if we have extra R packages
+        if: ${{ always() && steps.cache-renv-packages-restore.outputs.cache-hit != 'true' && inputs.extra-r-packages == '' }}
+        uses: actions/cache/save@v4
+        with:
+          path: |
+            ${{ env.RENV_PATHS_ROOT }}
+            renv/library
+          key: ${{ steps.cache-renv-packages-restore.outputs.cache-primary-key }}
+
       - uses: actions/upload-artifact@v4
-        # PLaywright test only runs on Linux for now
-        if: ${{ !cancelled() && runner.os != 'Windows' }}
+        # Upload pLaywright test report if they exists (playwright is only running on Linux for now)
+        if: ${{ !cancelled() && runner.os != 'Windows' && hashFiles('tests/integration/playwright/playwright-report/**/*') != '' }}
         with:
           name: playwright-report
           path: ./tests/integration/playwright/playwright-report/

CONTRIBUTING.md

@@ -3,7 +3,7 @@
 You can contribute to Quarto in many ways:
 
 - By opening issues to provide feedback and share ideas.
-- By submitting Pull Request (PR) to fix opened issues
+- By submitting Pull Request (PR) to fix open issues
 - By submitting Pull Request (PR) to suggest new features (it is considered good practice to open an issue for discussion before working on a pull request for a new feature).
 
 Please be mindful of our [code of conduct](https://github.com/quarto-dev/quarto-cli/blob/main/.github/CODE_OF_CONDUCT.md) as you interact with other community members.
@@ -26,8 +26,8 @@ Pull requests are very welcome! Here's how to contribute via PR:
     $ git checkout -b feature/newthing
     ```
 
-2.  For significant changes (e.g more than small bug fixes), ensure that you have signed the [individual](https://posit.co/wp-content/uploads/2023/04/2023-03-13_TC_Indiv_contrib_agreement.pdf) or [corporate](https://posit.co/wp-content/uploads/2023/04/2023-03-13_TC_Corp_contrib_agreement.pdf) contributor agreement as appropriate. You can send the signed copy to [jj\@rstudio.com](mailto:[email protected]){.email}.
+2.  For significant changes (e.g., more than small bug fixes), ensure that you have signed the [individual](https://posit.co/wp-content/uploads/2023/04/2023-03-13_TC_Indiv_contrib_agreement.pdf) or [corporate](https://posit.co/wp-content/uploads/2023/04/2023-03-13_TC_Corp_contrib_agreement.pdf) contributor agreement as appropriate. You can send the signed copy to [jj\@rstudio.com](mailto:[email protected]){.email}.
 
-3.  Submit the [pull request](https://help.github.com/articles/using-pull-requests). It is ok to submit as draft in your are still working on it but would like some feedback from us. It always good to share in the open that you are working on it.
+3.  Submit the [pull request](https://help.github.com/articles/using-pull-requests). It is ok to submit as draft if your are still working on it but would like some feedback from us. It is always good to share in the open that you are working on it.
 
 We'll try to be as responsive as possible in reviewing and accepting pull requests.

README.md

@@ -2,25 +2,25 @@
 
 # Quarto
 
-Quarto is an open-source scientific and technical publishing system built on [Pandoc](https://pandoc.org). Quarto documents are authored using [markdown](https://en.wikipedia.org/wiki/Markdown), an easy to write plain text format.
+Quarto is an open-source scientific and technical publishing system built on [Pandoc](https://pandoc.org). Quarto documents are authored using [Markdown](https://en.wikipedia.org/wiki/Markdown), an easy to write plain text format.
 
 In addition to the core capabilities of Pandoc, Quarto includes:
 
 1.  Embedding code and output from Python, R, Julia, and JavaScript via integration with [Jupyter](https://jupyter.org/), [Knitr](https://yihui.org/knitr/), and [Observable](https://github.com/observablehq/).
 
-2.  A variety of extensions to Pandoc markdown useful for technical writing including cross-references, sub-figures, layout panels, hoverable citations and footnotes, callouts, and more.
+2.  A variety of extensions to Pandoc Markdown useful for technical writing including cross-references, sub-figures, layout panels, hoverable citations and footnotes, callouts, and more.
 
 3.  A project system for rendering groups of documents at once, sharing options across documents, and producing aggregate output like [websites](https://quarto.org/docs/websites/) and [books](https://quarto.org/docs/books/).
 
 4.  Authoring using a wide variety of editors and notebooks including [JupyterLab](https://quarto.org/docs/tools/jupyter-lab.html), [RStudio](https://quarto.org/docs/tools/rstudio.html), and [VS Code](https://quarto.org/docs/tools/vscode.html).
 
-5.  A [visual markdown editor](https://quarto.org/docs/visual-editor/) that provides a productive writing interface for composing long-form documents.
+5.  A [visual Markdown editor](https://quarto.org/docs/visual-editor/) that provides a productive writing interface for composing long-form documents.
 
 Learn more about Quarto at <https://quarto.org>.
 
 ## Development Version
 
-To install the development version of the Quarto CLI, clone the quarto-cli repository then run the configure script for your platform (`configure.sh` for Linux/macOS or `configure.cmd` for Windows). For example:
+To install the development version of the Quarto CLI, clone the `quarto-cli` repository then run the configure script for your platform (`configure.sh` for Linux/macOS or `configure.cmd` for Windows). For example:
 
 ```bash
 git clone https://github.com/quarto-dev/quarto-cli

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

@@ -0,0 +1,27 @@
+- [ ] ensure tests pass on stable branch
+  - Actions -> Parallel Smokes Tests -> Run Workflow ->
+    - Select the current stable branch in the "Use workflow from... v1.x" dropdown
+    - [ ] Click "Run Workflow"
+- [ ] create new stable installers
+  - Click Actions -> Build Installers -> "Run Workflow" Dropdown Menu
+    - Select the current stable branch in the "Use workflow from..." dropdown
+    - Uncheck "Pre-release" (or ensure it's unchecked)
+    - Check "Publish release" (or ensure it's checked)
+    - [ ] Click "Run Workflow"
+- [ ] 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
+  - Go to actions
+    - Select 'Publish Quarto PyPi'
+    - [ ] Click "Run Workflow"
+      - **Publishing Test**: You may elect to publish to test.pypi first by _unchecking_ the `Production Release` option
+        - Once complete, trest using
+          ```bash
+          python3 -m pip install --index-url https://test.pypi.org/ --extra-index-url https://pypi.org/ quarto-cli
+          ```
+        - You may have to run this command twice as the first time may report the package not found and cause cache invalidation. The next try should succeed.
+        - Published to: <https://test.pypi.org/project/quarto-cli/>
+      - **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"

news/changelog-1.7.md

@@ -14,10 +14,13 @@ All changes included in 1.7:
 
 - ([#11654](https://github.com/quarto-dev/quarto-cli/issues/11654)): Allow `page-inset` as value in `column` key for code cells.
 - ([#10251](https://github.com/quarto-dev/quarto-cli/issues/10251)): EJS template for website now uses proper object to get alt text for logo in sidebar.
+- ([#12151](https://github.com/quarto-dev/quarto-cli/issues/12151)): Fix YAML validation in computations cell on Windows.
+- ([#12151](https://github.com/quarto-dev/quarto-cli/pull/12151)): Basic YAML validation is now active in cell for document using Julia engine.
 
 ## 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.
+- ([#12134](https://github.com/quarto-dev/quarto-cli/issues/12134)): Forward `logo.small` images in `_brand.yml` files to a website `favicon`.
 
 ## Blog projects
 
@@ -26,20 +29,21 @@ All changes included in 1.7:
 ## 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.
+- ([#12134](https://github.com/quarto-dev/quarto-cli/issues/12134)): Forward `logo.small` images in `_brand.yml` files to the `favicon` of the book's website.
 
 ## `quarto check`
 
 - ([#11608](https://github.com/quarto-dev/quarto-cli/pull/11608)): Do not issue error message when calling `quarto check info`.
 
 ## `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.
+- ([#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.
+- ([#11878](https://github.com/quarto-dev/quarto-cli/issues/11878), [#12085](https://github.com/quarto-dev/quarto-cli/issues/12085)): Correctly fixup raw LaTeX table having an unexpected table env with options (e.g `\begin{table}[!ht]`) to be handled as crossref table.
 
 ## `typst` format
 
@@ -48,6 +52,14 @@ All changes included in 1.7:
 - ([#11835](https://github.com/quarto-dev/quarto-cli/issues/11835)): Take markdown structure into account when detecting minimum heading level.
 - ([#11964](https://github.com/quarto-dev/quarto-cli/issues/11964)): Using panel layout without a crossref label now correctly do not add an empty `#block[]` that was leading to an unnecessary space in output.
 
+## `revealjs` format
+
+- ([#12147](https://github.com/quarto-dev/quarto-cli/issues/12147)): `serif` and `simple` themes defaults back to have their heading color (`$presentation-heading-color`) to be the same as the body color (`$body-color`) as in Quarto 1.5.
+
+## Interactive Shiny Document
+
+- ([#12059](https://github.com/quarto-dev/quarto-cli/issues/12059)): `quarto preview` now correctly run on Windows an interactive Quarto doc with Jupyter engine and py-shiny, when using a `*.py` file as resource.
+
 ## Lua Filters and extensions
 
 - ([#11526](https://github.com/quarto-dev/quarto-cli/pull/11526)):
@@ -58,13 +70,20 @@ All changes included in 1.7:
 - ([#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.
+- ([#11896](https://github.com/quarto-dev/quarto-cli/pull/11896)): fix `\f` (`{{< pagebreak >}}`) form feed character not valid in PowerPoint (`pptx`).
+- ([#11664](https://github.com/quarto-dev/quarto-cli/issues/11664)): `lipsum` shortcode is no longer randomly generated by default, use `{{< lipsum random=true >}}` to restore randomness.
 
 ## 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.
+- ([#12121](https://github.com/quarto-dev/quarto-cli/pull/12121)): Update QuartoNotebookRunner to 0.13.1. Support for evaluating Python cells via [PythonCall.jl](https://github.com/JuliaPy/PythonCall.jl) added.
+- ([#12151](https://github.com/quarto-dev/quarto-cli/pull/12151)): Basic YAML validation is now active for document using Julia engine.
+
+### `jupyter`
+
+- ([#12114](https://github.com/quarto-dev/quarto-cli/issues/12114)): `JUPYTERCACHE` environment variable from [Jupyter cache CLI](https://jupyter-cache.readthedocs.io/en/latest/using/cli.html) is now respected by Quarto when `cache: true` is used. This environment variable allows to change the path of the cache directory.
 
 ## Other Fixes and Improvements
 
@@ -75,3 +94,5 @@ All changes included in 1.7:
 - ([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.
+- ([#11951](https://github.com/quarto-dev/quarto-cli/issues/11951)): Raw LaTeX table without `tbl-` prefix label for using Quarto crossref are now correctly passed through unmodified.
+- ([#12117](https://github.com/quarto-dev/quarto-cli/issues/12117)): Color output to stdout and stderr is now correctly rendered for `html` format in the Jupyter and Julia engines.

package/src/common/patches/revealjs-theme-0001-simple.patch

@@ -28,7 +28,7 @@ index f0472d7b9..3b1e3cbdc 100644
 +$font-family-sans-serif: "Lato", sans-serif !default;
 +$body-color: #000 !default;
 +$presentation-heading-font: "News Cycle", sans-serif !default;
-+$presentation-heading-color: #000 !default;
++$presentation-heading-color: $body-color !default;
 +$presentation-heading-text-shadow: none !default;
 +$presentation-heading-text-transform: none !default;
 +$body-bg: #fff !default;