Merge branch 'main' of github.com:poissonconsulting/chk

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

@@ -27,8 +27,6 @@ jobs:
           token: ${{ secrets.GITHUB_TOKEN }}
 
       - uses: r-lib/actions/setup-r@v2
-        with:
-          install-r: false
 
       - id: set-matrix
         uses: ./.github/workflows/dep-matrix
@@ -70,7 +68,6 @@ jobs:
 
       - uses: ./.github/workflows/install
         with:
-          install-r: false
           cache-version: rcc-dev-base-1
           needs: check
           extra-packages: "any::rcmdcheck any::remotes ."
@@ -118,7 +115,6 @@ jobs:
 
       - uses: ./.github/workflows/install
         with:
-          install-r: false
           cache-version: rcc-dev-${{ matrix.package }}-1
           needs: check
           extra-packages: "any::rcmdcheck any::remotes ."

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

@@ -12,7 +12,7 @@ name: rcc-status
 
 jobs:
   rcc-status:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
 
     name: "Update commit status"
 

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

@@ -43,7 +43,7 @@ name: rcc
 
 jobs:
   rcc-smoke:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     outputs:
       sha: ${{ steps.commit.outputs.sha }}
       versions-matrix: ${{ steps.versions-matrix.outputs.matrix }}
@@ -106,7 +106,7 @@ jobs:
           cache-version: rcc-smoke-2
           needs: check, website
           # Beware of using dev pkgdown here, has brought in dev dependencies in the past
-          extra-packages: any::rcmdcheck r-lib/roxygen2 any::decor r-lib/styler r-lib/pkgdown@f-readme-tweak deps::.
+          extra-packages: any::rcmdcheck r-lib/roxygen2 any::decor r-lib/styler r-lib/pkgdown deps::.
 
       - name: Install package
         run: |
@@ -205,7 +205,7 @@ jobs:
         shell: bash
 
   rcc-smoke-check-matrix:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
 
     name: "Check matrix"
 
@@ -267,6 +267,8 @@ jobs:
         with:
           results: ${{ runner.os }}-r${{ matrix.r }}
 
+# The status update is taken care of by R-CMD-check-status.yaml
+
   rcc-suggests:
     needs:
       - rcc-smoke
@@ -292,7 +294,6 @@ jobs:
 
       - uses: ./.github/workflows/install
         with:
-          install-r: false
           cache-version: rcc-dev-${{ matrix.package }}-1
           needs: check
           extra-packages: "any::rcmdcheck any::remotes ."
@@ -340,3 +341,5 @@ jobs:
       - uses: ./.github/workflows/check
         with:
           results: ${{ matrix.package }}
+
+# The status update is taken care of by R-CMD-check-status.yaml

.github/workflows/fledge.yaml

@@ -19,7 +19,7 @@ concurrency:
 
 jobs:
   check_fork:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     outputs:
       is_forked: ${{ steps.check.outputs.is_forked }}
     steps:
@@ -33,7 +33,7 @@ jobs:
         shell: bash
 
   fledge:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     needs: check_fork
     if: needs.check_fork.outputs.is_forked == 'false'
     permissions:
@@ -43,9 +43,10 @@ jobs:
     env:
       FLEDGE_GHA_CI: true
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+          fetch-tags: true
 
       - name: Configure Git identity
         run: |
@@ -61,7 +62,6 @@ jobs:
 
       - uses: r-lib/actions/setup-r@v2
         with:
-          install-r: false
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
@@ -72,8 +72,18 @@ jobs:
           packages: cynkra/fledge
           cache-version: fledge-1
 
+      - name: Count rulesets
+        # Assume that branch is protected if ruleset exists
+        id: rulesets
+        env:
+          GH_TOKEN: ${{ github.token }}
+        run: |
+          n_rulesets=$(gh api repos/${{ github.repository }}/rulesets -q length)
+          echo "count=${n_rulesets}" >> $GITHUB_OUTPUT
+        shell: bash
+
       - name: Switch to branch if branch protection is enabled
-        if: github.ref_protected == 'true' || inputs.pr == 'true'
+        if: github.ref_protected == 'true' || inputs.pr == 'true' || steps.rulesets.outputs.count > 0
         run: |
           git checkout -b fledge
           git push -f -u origin HEAD
@@ -83,21 +93,25 @@ jobs:
         env:
           GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          check_default_branch <- ("${{ github.ref_protected == 'true' || inputs.pr == 'true' }}" != "true")
+          check_default_branch <- ("${{ github.ref_protected == 'true' || inputs.pr == 'true' || steps.rulesets.outputs.count > 0 }}" != "true")
           if (fledge::bump_version(which = "dev", no_change_behavior = "noop", check_default_branch = check_default_branch)) {
             fledge::finalize_version(push = TRUE)
           }
         shell: Rscript {0}
 
       - name: Create and merge PR if branch protection is enabled
-        if: github.ref_protected == 'true' || inputs.pr == 'true'
+        if: github.ref_protected == 'true' || inputs.pr == 'true' || steps.rulesets.outputs.count > 0
         env:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: |
-          set -x
-          gh pr create --base main --head fledge --fill-first
-          gh workflow run rcc -f ref=$(git rev-parse HEAD)
-          gh pr merge --merge --auto
+          set -ex
+          if [ -n "$(git diff main --numstat)" ]; then
+            gh pr create --base main --head fledge --fill-first
+            gh workflow run rcc -f ref=$(git rev-parse HEAD)
+            gh pr merge --squash --auto
+          else
+            echo "No changes."
+          fi
         shell: bash
 
       - name: Check release

.github/workflows/install/action.yml

@@ -56,6 +56,9 @@ runs:
         echo "_R_CHECK_UNDOC_USE_ALL_NAMES_=true" | tee -a $GITHUB_ENV
         echo "_R_CHECK_URLS_SHOW_301_STATUS_=true" | tee -a $GITHUB_ENV
         echo "_R_CXX_USE_NO_REMAP_=true" | tee -a $GITHUB_ENV
+        # There is no way to disable recency and frequency checks when the incoming checks are run
+        # echo "_R_CHECK_CRAN_INCOMING_=true" | tee -a $GITHUB_ENV
+        echo "_R_CHECK_CRAN_INCOMING_SKIP_LARGE_VERSION_=true" | tee -a $GITHUB_ENV
       shell: bash
 
     - name: Set environment variables (non-Windows only)
@@ -72,6 +75,12 @@ runs:
         echo "_R_CHECK_CRAN_INCOMING_USE_ASPELL_=true" | tee -a $GITHUB_ENV
       shell: bash
 
+    - name: Remove [email protected]
+      if: runner.os == 'macOS'
+      run: |
+        brew uninstall [email protected] || true
+      shell: bash
+
     - uses: r-lib/actions/setup-pandoc@v2
 
     - uses: r-lib/actions/setup-r@v2
@@ -92,7 +101,7 @@ runs:
       env:
         GITHUB_PAT: ${{ inputs.token }}
       with:
-        pak-version: devel
+        pak-version: stable
         needs: ${{ inputs.needs }}
         packages: ${{ inputs.packages }}
         extra-packages: ${{ inputs.extra-packages }} ${{ ( matrix.config.covr && 'any::covr' ) || '' }} ${{ steps.get-extra.outputs.packages }}

.github/workflows/lock.yaml

@@ -1,14 +1,18 @@
 name: "Lock threads"
-
+permissions:
+  issues: write
+  pull-requests: write
+  discussions: write
 on:
+  workflow_dispatch:
   schedule:
     - cron: "37 2 * * *"
 
 jobs:
   lock:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
     steps:
-      - uses: dessant/lock-threads@v5
+      - uses: krlmlr/lock-threads@patch-1
         with:
           github-token: ${{ github.token }}
           issue-inactive-days: "365"

.github/workflows/pkgdown.yaml

@@ -16,7 +16,7 @@ concurrency:
 
 jobs:
   pkgdown:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-24.04
 
     name: "pkgdown"
 
@@ -39,10 +39,9 @@ jobs:
       - uses: ./.github/workflows/install
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
-          install-r: false
           cache-version: pkgdown-2
           needs: website
-          extra-packages: r-lib/pkgdown@f-readme-tweak local::.
+          extra-packages: r-lib/pkgdown local::.
 
       - uses: ./.github/workflows/custom/after-install
         if: hashFiles('.github/workflows/custom/after-install/action.yml') != ''

.github/workflows/pr-commands.yaml

@@ -16,8 +16,6 @@ jobs:
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
       - uses: r-lib/actions/setup-r@v2
-        with:
-          install-r: false
       - name: Configure Git identity
         run: |
           env | sort
@@ -55,8 +53,6 @@ jobs:
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
       - uses: r-lib/actions/setup-r@v2
-        with:
-          install-r: false
       - name: Configure Git identity
         run: |
           env | sort

DESCRIPTION

@@ -44,4 +44,4 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.2.9000