github action update

Author: heike

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

@@ -1,12 +1,17 @@
 # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+#
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
 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:
@@ -19,10 +24,17 @@ jobs:
       matrix:
         config:
           - {os: macos-latest,   r: 'release'}
+
           - {os: windows-latest, r: 'release'}
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
+          # use 4.0 or 4.1 to check with rtools40's older compiler
+          - {os: windows-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 }}

.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:

.github/workflows/pr-commands.yaml

@@ -0,0 +1,85 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  issue_comment:
+    types: [created]
+
+name: pr-commands.yaml
+
+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') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add \*.R
+          git commit -m 'Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.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:
@@ -23,23 +24,34 @@ 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(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