Merge branch 'main' into improve-render

Author: salim-b

.Rbuildignore

@@ -9,6 +9,7 @@
 ^doc$
 ^Meta$
 
+^vignettes/.quarto$
 ^vignettes/*_files$
 ^revdep$
 ^cran-comments\.md$

.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
@@ -24,6 +26,13 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
+      - uses: quarto-dev/quarto-actions/setup@v2
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          version: pre-release
+          tinytex: true
+
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2

.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/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.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

@@ -1,6 +1,6 @@
 Package: quarto
 Title: R Interface to 'Quarto' Markdown Publishing System
-Version: 1.4.1
+Version: 1.4.4.9003
 Authors@R: c(
     person("JJ", "Allaire", , "[email protected]", role = "aut",
            comment = c(ORCID = "0000-0003-0174-9868")),
@@ -39,6 +39,6 @@ VignetteBuilder:
 Config/testthat/edition: 3
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
-SystemRequirements: Quarto command line tools
-    (https://github.com/quarto-dev/quarto-cli).
+RoxygenNote: 7.3.2
+SystemRequirements: Quarto command line tool
+    (<https://github.com/quarto-dev/quarto-cli>).

NEWS.md

@@ -1,13 +1,31 @@
 # quarto (development version)
 
+- Add `quarto.quiet` options to allow more verbose error message when `quarto_*` function are used inside other package. 
+  For example, inside **pkgdown** for building Quarto vignettes. **pkgdown** sets `quiet = TRUE` internally for its call to `quarto_render()`, 
+  and setting `options(quarto.quiet = TRUE)` allows to overwrite this.
+  
+- `quarto_path()` now returns a normalized path with potential symlink resolved, for less confusion with `quarto_binary_sitrep()` (thanks, @jennybc).
+
+- Fix an error with interactive prompt for extension approval (thanks, @wjschne, #212).
+
+# quarto 1.4.4
+
+- `quarto_preview()` now looks at `quarto preview` log to browse to the correct url when inside RStudio viewer (thanks, @aronatkins, #167).
+
+- This package now uses the x.y.z.dev versionning scheme to indicate development, patch, minor and major versions. This follows [Tidyverse package version conventions](https://r-pkgs.org/lifecycle.html#sec-lifecycle-version-number-tidyverse).
+
+- Adapt tests for CRAN checks issues due to Quarto v1.5.54 regression (though it is fixed upstream).
+
+- Approval check in `quarto_add_extension()` and `quarto_use_template()` now works correctly (thanks, @eveyp, #172).
+
 # quarto 1.4
 
 - This version is now adapted to Quarto 1.4 latest stable release.
 
 - Add registration of vignette engine to use `quarto` as a vignette builder, and use `.qmd` file as vignette. See `vignette("hello", package = "quarto")`. (thanks, @dcnorris, #57).
 
 - New `quarto_binary_sitrep()` checks possible difference in Quarto binary used by this package, and the one used by RStudio IDE (thanks, @jthomasmock, #12).
-
+  
 - New `is_using_quarto()` to check if a directory requires using Quarto (i.e. it has a `_quarto.yml` or at least one `*.qmd` file) (thanks, @hadley, #103).
 
 - New `quarto_create_project()` calls `quarto create project <type> <name>` (thanks, @maelle, #87).

R/add.R

@@ -37,11 +37,12 @@ quarto_add_extension <- function(extension = NULL, no_prompt = FALSE, quiet = FA
   quarto_bin <- find_quarto()
 
   # This will ask for approval or stop installation
-  check_extension_approval(no_prompt, "Quarto extensions", "https://quarto.org/docs/extensions/managing.html")
+  approval <- check_extension_approval(no_prompt, "Quarto extensions", "https://quarto.org/docs/extensions/managing.html")
 
-  args <- c(extension, "--no-prompt", if (quiet) cli_arg_quiet(), quarto_args)
-
-  quarto_add(args, quarto_bin = quarto_bin, echo = TRUE)
+  if (approval) {
+    args <- c(extension, "--no-prompt", if (is_quiet(quiet)) cli_arg_quiet(), quarto_args)
+    quarto_add(args, quarto_bin = quarto_bin, echo = TRUE)
+  }
 
   invisible()
 }

R/create.R

@@ -39,7 +39,7 @@ quarto_create_project <- function(name, type = "default", dir = ".", no_prompt =
 
   quarto_bin <- find_quarto()
 
-  args <- c("project", type, name, "--no-prompt", "--no-open", if (quiet) cli_arg_quiet(), quarto_args = NULL)
+  args <- c("project", type, name, "--no-prompt", "--no-open", if (is_quiet(quiet)) cli_arg_quiet(), quarto_args = NULL)
 
   owd <- setwd(dir)
   on.exit(setwd(owd), add = TRUE, after = FALSE)