Merge branch 'main' into bugfix/9832

Author: cscheid

.air.toml

@@ -0,0 +1,8 @@
+[format]
+line-width = 80
+indent-width = 2
+indent-style = "space"
+line-ending = "auto"
+persistent-line-breaks = true
+exclude = []
+default-exclude = true

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -6,54 +6,52 @@ 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!
 
         ---
 
         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:
@@ -98,13 +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

@@ -1,33 +1,49 @@
-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-matched-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 $RUNNER_OS in
           "Linux")
-              echo "TYPST_CACHE=${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}" >> $GITHUB_ENV
+        echo "TYPST_CACHE=${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

@@ -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'
@@ -130,8 +132,8 @@ 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 +145,7 @@ 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 +163,7 @@ jobs:
           quarto install tinytex
 
       - name: Cache Typst packages
+        id: cache-typst
         uses: ./.github/actions/cache-typst
 
       - name: Install Chrome
@@ -169,7 +172,7 @@ jobs:
       - name: Setup Julia
         uses: julia-actions/setup-julia@v2
         with:
-          version: "1.10"
+          version: "1.11.3"
 
       - name: Cache Julia Packages
         uses: julia-actions/cache@v2
@@ -183,7 +186,7 @@ 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 }}
@@ -289,9 +292,26 @@ jobs:
           name: timed test file
           path: tests/timing-for-ci.txt
 
+      - name: Save Typst cache
+        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/

.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

.vscode/extensions.json

@@ -3,6 +3,7 @@
     "denoland.vscode-deno",
     "esbenp.prettier-vscode",
     "sumneko.lua",
-    "nvarner.typst-lsp"
+    "nvarner.typst-lsp",
+    "Posit.air-vscode"
   ]
 }

.vscode/settings.json

@@ -3,8 +3,12 @@
     "editor.defaultFormatter": "denoland.vscode-deno"
   },
   "[r]": {
-    "editor.formatOnSave": false,
-    "editor.defaultFormatter": "REditorSupport.r"
+    "editor.formatOnSave": true,
+    "editor.defaultFormatter": "Posit.air-vscode"
+  },
+  "[quarto]": {
+    "editor.formatOnSave": true,
+    "editor.defaultFormatter": "quarto.quarto"
   },
   "[html]": {
     "editor.formatOnSave": false
@@ -16,5 +20,7 @@
   "deno.lint": true,
   "deno.unstable": true,
   "deno.importMap": "./src/import_map.json",
-  "deno.disablePaths": ["tests/integration/playwright/"]
+  "deno.disablePaths": ["tests/integration/playwright/"],
+  // opt-out lintr as we use air formatter
+  "r.lsp.diagnostics": false
 }

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: 1.7
 doi: 10.5281/zenodo.5960048
-date-released: 2024-02-15
+date-released: 2025-04-28
 url: "https://github.com/quarto-dev/quarto-cli"

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