Merge remote-tracking branch 'upstream/main'

Author: ‘topepo’

.github/workflows/R-CMD-check.yaml

@@ -5,13 +5,16 @@
 # check-standard.yaml is likely a better choice.
 # usethis::use_github_action("check-standard") will install it.
 on:
+  workflow_dispatch:
   push:
     branches: [main, master]
   pull_request:
     branches: [main, master]
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -27,8 +30,6 @@ jobs:
 
           - {os: windows-latest, r: 'release'}
           - {os: windows-latest, r: 'release', quarto: 'pre-release'}
-          # Use 3.6 to trigger usage of RTools35
-          - {os: windows-latest, r: '3.6'}
           # use 4.1 to check with rtools40's older compiler
           - {os: windows-latest, r: '4.1'}
 
@@ -48,6 +49,8 @@ jobs:
       - uses: actions/checkout@v4
 
       - uses: quarto-dev/quarto-actions/setup@v2
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           version: ${{ matrix.config.quarto || 'release' }}
           tinytex: true
@@ -71,3 +74,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/pkgdown.yaml

@@ -11,6 +11,8 @@ on:
 
 name: pkgdown
 
+permissions: read-all
+
 jobs:
   pkgdown:
     runs-on: ubuntu-latest

.github/workflows/pr-commands.yaml

@@ -6,6 +6,8 @@ on:
 
 name: Commands
 
+permissions: read-all
+
 jobs:
   document:
     if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}

.github/workflows/test-coverage.yaml

@@ -8,6 +8,8 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
@@ -28,23 +30,32 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
             install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results

DESCRIPTION

@@ -41,6 +41,6 @@ VignetteBuilder:
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 SystemRequirements: Quarto command line tools
     (https://github.com/quarto-dev/quarto-cli).

R/render.R

@@ -6,7 +6,7 @@
 #'
 #' @param input The input file or project directory to be rendered (defaults
 #'   to rendering the project in the current working directory).
-#' @param output_format Target output format (defaults to "html"). The option
+#' @param output_format Target output format (defaults to `"html"`). The option
 #'   `"all"` will render all formats defined within the file or project.
 #' @param output_file The name of the output file. If using `NULL`, the output
 #'   filename will be based on the filename for the input file. `output_file` is
@@ -46,7 +46,7 @@
 #'   advanced usage and useful for CLI arguments which are not yet mirrored in a
 #'   dedicated parameter of this \R function. See `quarto render --help` for options.
 #' @param pandoc_args Additional command line arguments to pass on to Pandoc.
-#' @param as_job Render as an RStudio background job. Default is "auto",
+#' @param as_job Render as an RStudio background job. Default is `"auto"`,
 #'   which will render individual documents normally and projects as
 #'   background jobs. Use the `quarto.render_as_job` \R option to control
 #'   the default globally.

R/run.R

@@ -2,9 +2,9 @@
 #'
 #' Serve a Shiny interactive document. By default, the document will
 #' be rendered first and then served If you have previously rendered
-#' the document, pass `render - FALSE` to skip rendering.
+#' the document, pass `render = FALSE` to skip rendering.
 #'
-#' @param input The input file to run Should be a file with
+#' @param input The input file to run. Should be a file with
 #'   a `server: shiny` entry in its YAML front-matter.
 #' @param render Render the document before serving it.
 #'

man/quarto_render.Rd

@@ -42,21 +42,22 @@ format:
     css: custom.css
 ```
 
-All those configurations are set in way that they can't be override by YAML header in the vignette source file. Only new configuration can be set, e.g adding a Table Of Content: 
+All those configurations are set in way that they can't be overriden by the YAML header in the vignette source file and only new configurations can be set. Typical examples for such configurations are adding a [table of contents](https://quarto.org/docs/reference/formats/html.html#table-of-contents) or enabling the rendering of mathematical notation in the [format options](https://quarto.org/docs/reference/formats/html.html#format-options), e.g., by MathJax. Specifically, these two options can be set in the following way:
 
 ````yaml
 format: 
   html:
     toc: true
+    html-math-method: mathjax
 vignette: >
   %\VignetteIndexEntry{Vignette's Title}
   %\VignetteEngine{quarto::html}
   %\VignetteEncoding{UTF-8}
 ````
 
-This is one limitation of the current implementation of the vignette engine. This is to insure HTML vignette produced are reasonable in size and can be published on CRAN without problem.
+The minimal default format is a deliberate limitation of the current implementation of the vignette engine. It ensures that the HTML vignettes produced are reasonable in size and can be published on CRAN without problems.
 
-The other limitation concerns the interactive rendering. If you render your vignette `.qmd` file using `quarto render` or any other function, the output will be based on default HTML format from Quarto and not the vignette engine one. Only building the vignette will produce the real results. More about building vignette in the [R Packages (2e)](https://r-pkgs.org/vignettes.html#sec-vignettes-how-built-checked) book.
+Another limitation concerns the interactive rendering. If you render your vignette `.qmd` file using `quarto render` or any other function, the output will be based on the default HTML format from Quarto and not the vignette engine one. Only building the vignette will produce the real results. More details about building vignettes are available in the [R Packages (2e)](https://r-pkgs.org/vignettes.html#sec-vignettes-how-built-checked) book.
 
 Intermediates resources that would be created by an authoring workflow that would `quarto render` with default `format: html` should be ignored in package sources.