Merge pull request #7 from r-lib/main

Update
SebKrantz · Jun 25, 2024 · b0850c7 · b0850c7
2 parents a25bbfb + 34ee692
commit b0850c7
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -20,3 +20,4 @@
 ^CRAN-SUBMISSION$
 ^tools$
 ^\.lintr.R$
+^vignettes/\.quarto$
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -12,6 +12,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -28,19 +30,26 @@ jobs:
           # use 4.1 to check with rtools40's older compiler
           - {os: windows-latest, r: '4.1'}
 
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
-          - {os: ubuntu-latest,   r: 'oldrel-4'}
+          - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,  r: 'release'}
+          - {os: ubuntu-latest,  r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'oldrel-2'}
+          - {os: ubuntu-latest,  r: 'oldrel-3'}
+          - {os: ubuntu-latest,  r: 'oldrel-4'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
+
+      - uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          version: pre-release
+          tinytex: true
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -58,3 +67,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
diff --git a/.github/workflows/netlify.yaml b/.github/workflows/netlify.yaml
@@ -10,12 +10,17 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-tinytex@v2
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - name: Set up Quarto
+        uses: quarto-dev/quarto-actions/setup@v2
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true

diff --git a/.github/workflows/no-pandoc.yaml b/.github/workflows/no-pandoc.yaml
@@ -15,7 +15,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -24,9 +24,14 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          version: pre-release
+          tinytex: true
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
-      - uses: r-lib/actions/setup-tinytex@v2
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:

diff --git a/.github/workflows/pr-commands.yaml b/.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') }}
@@ -14,7 +16,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:
@@ -51,7 +53,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/pr-fetch@v2
         with:

diff --git a/.github/workflows/test-coverage.yaml b/.github/workflows/test-coverage.yaml
@@ -8,45 +8,63 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
+      - uses: quarto-dev/quarto-actions/setup@v2
+        with:
+          version: pre-release
+          tinytex: true
+        env:
+          GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
 
       - 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
         if: failure()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
diff --git a/.gitignore b/.gitignore
@@ -6,3 +6,5 @@ inst/doc
 .env
 *.tex
 docs
+
+/.quarto/
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -9,6 +9,8 @@ Authors@R: c(
     person("Maëlle", "Salmon", role = "aut",
            comment = c(ORCID = "0000-0002-2815-0399")),
     person("Olivier", "Roy", role = "aut"),
+    person("Salim", "Brüggemann", role = "aut",
+           comment = c(ORCID = "0000-0002-5329-5987")),
     person("Posit Software, PBC", role = c("cph", "fnd"))
   )
 Description: Generate an attractive and useful website from a source
@@ -26,7 +28,7 @@ Imports:
     cli (>= 3.6.1),
     desc (>= 1.4.0),
     digest,
-    downlit (>= 0.4.0),
+    downlit (>= 0.4.4),
     fontawesome,
     fs (>= 1.4.0),
     httr2 (>= 1.0.0),
@@ -44,7 +46,7 @@ Imports:
 Suggests:
     covr,
     diffviewer,
-    evaluate (>= 0.23.0.9000),
+    evaluate (>= 0.24.0),
     gert,
     gt,
     htmltools,
@@ -54,21 +56,22 @@ Suggests:
     magick,
     methods,
     pkgload (>= 1.0.2),
+    quarto,
     rsconnect,
     rstudioapi,
     rticles,
     sass,
     testthat (>= 3.1.3),
     tools
 VignetteBuilder:
-    knitr
+    knitr,
+    quarto
 Config/Needs/website: usethis, servr
 Config/potools/style: explicit
 Config/testthat/edition: 3
 Config/testthat/parallel: true
-Config/testthat/start-first: build-article, build-reference
+Config/testthat/start-first: build-article, build-quarto-article, build-reference
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
 SystemRequirements: pandoc
-Remotes: r-lib/evaluate
-Original file line number
+Diff line change
@@ Expand Up / @@ -6,3 +6,5 @@ inst/doc @@
     .env
     *.tex
     docs
+    /.quarto/