Amend R CMD check based on r-lib/actions

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

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: R-CMD-check
+name: R-CMD-check.yaml
+
+permissions: read-all
 
 jobs:
   R-CMD-check:
@@ -33,7 +34,7 @@ jobs:
       _R_CHECK_DEPENDS_ONLY_TESTS_: ${{ matrix.config.depends_only }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -51,3 +52,4 @@ 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

@@ -4,12 +4,13 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: pkgdown
+name: pkgdown.yaml
+
+permissions: read-all
 
 jobs:
   pkgdown:
@@ -19,8 +20,10 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -37,24 +40,10 @@ jobs:
         run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
         shell: Rscript {0}
 
-      - name: Upload artifact
-        uses: actions/upload-pages-artifact@v1
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
         with:
-          path: ./docs
-
-  # Deployment job
-  deploy:
-    if: github.event_name != 'pull_request'
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-    runs-on: ubuntu-latest
-    needs: pkgdown
-    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
-    permissions:
-      pages: write      # to deploy to Pages
-      id-token: write   # to verify the deployment originates from an appropriate source
-    steps:
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v1
+          clean: false
+          branch: gh-pages
+          folder: docs

.github/workflows/test-coverage.yaml

@@ -4,9 +4,10 @@ on:
   push:
     branches: [main, master]
   pull_request:
-    branches: [main, master]
 
-name: test-coverage
+name: test-coverage.yaml
+
+permissions: read-all
 
 jobs:
   test-coverage:
@@ -15,37 +16,47 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - 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,
-            function_exclusions = c("\\.onLoad", "release_bullets"),
-            install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package")
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          print(cov)
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v5
+        with:
+          # Fail if error if not on PR, or if on PR and token is given
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
+          files: ./cobertura.xml
+          plugins: 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

.github/workflows/touchstone-comment.yaml

@@ -21,6 +21,6 @@ jobs:
     if: >
       ${{ github.event.workflow_run.event == 'pull_request' }}
     steps:
-      - uses: lorenzwalthert/touchstone/actions/comment@v1
-        with: 
+      - uses: lorenzwalthert/touchstone/actions/comment@main
+        with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/touchstone-receive.yaml

@@ -4,27 +4,27 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref }}
   cancel-in-progress: true
 
-on: 
+on:
   pull_request:
 
 permissions:
   contents: read
 
 jobs:
   prepare:
-    runs-on: ubuntu-latest 
+    runs-on: ubuntu-latest
     if:
       true &&
       (
         github.event.pull_request.author_association == 'OWNER' ||
         github.event.pull_request.author_association == 'MEMBER' ||
-        github.event.pull_request.author_association == 'COLLABORATOR' 
+        github.event.pull_request.author_association == 'COLLABORATOR'
       )
     outputs:
       config: ${{ steps.read_touchstone_config.outputs.config }}
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           fetch-depth: 0
 
@@ -50,10 +50,10 @@ jobs:
       RSPM: ${{ matrix.config.rspm }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: lorenzwalthert/touchstone/actions/receive@v1
+      - uses: lorenzwalthert/touchstone/actions/receive@main
         with:
           cache-version: 1
           benchmarking_repo: ${{ matrix.config.benchmarking_repo }}
           benchmarking_ref: ${{ matrix.config.benchmarking_ref }}
-          benchmarking_path: ${{ matrix.config.benchmarking_path }} 
+          benchmarking_path: ${{ matrix.config.benchmarking_path }}
           force_upstream: true