Update workflows

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

@@ -28,7 +28,7 @@ jobs:
     steps:
       - uses: actions/checkout@v6
 
-      - uses: ./.github/workflows/install
+      - uses: api2r/actions/install@v1
         with:
           use-container: "${{ matrix.config.container != '' }}"
           token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/copilot-setup-steps.yml

@@ -22,7 +22,7 @@ jobs:
     steps:
       - uses: actions/checkout@v6
 
-      - uses: ./.github/workflows/install
+      - uses: api2r/actions/install@v1
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           cache-version: copilot
@@ -45,6 +45,7 @@ jobs:
             any::testthat
             any::usethis
             any::withr
+            Gilead-BioStats/qcthat
             local::.
 
       - name: Install air

.github/workflows/pkgdown-cleanup.yaml

@@ -0,0 +1,33 @@
+# This workflow removes the pkgdown preview directory when a PR is closed.
+name: Clean up pkgdown preview
+
+on:
+  pull_request:
+    types: [closed]
+
+permissions:
+  contents: write
+
+jobs:
+  clean-pr-preview:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v6
+        with:
+          repository: ${{ github.repository }}
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ref: gh-pages
+
+      - name: Remove PR preview directory
+        run: |
+          pr_dir="pr/${{ github.event.number }}"
+          if [ -d "$pr_dir" ]; then
+            git config --local user.name "$GITHUB_ACTOR"
+            git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
+            git rm -rf "$pr_dir"
+            git commit -m "Remove preview for PR #${{ github.event.number }}"
+            git push
+          else
+            echo "Directory $pr_dir does not exist, skipping cleanup."
+          fi

.github/workflows/pkgdown.yaml

@@ -27,7 +27,7 @@ jobs:
     steps:
       - uses: actions/checkout@v6
 
-      - uses: ./.github/workflows/install
+      - uses: api2r/actions/install@v1
         with:
           use-container: "true"
           token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pr-commands.yaml

@@ -22,7 +22,7 @@ jobs:
         with:
           repo-token: ${{ secrets.GITHUB_TOKEN }}
 
-      - uses: ./.github/workflows/install
+      - uses: api2r/actions/install@v1
         with:
           use-container: "true"
           token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/qcthat.yaml

@@ -58,7 +58,7 @@ jobs:
     steps:
       - uses: actions/checkout@v6
 
-      - uses: ./.github/workflows/install
+      - uses: api2r/actions/install@v1
         with:
           use-container: "true"
           token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/test-coverage.yaml

@@ -16,7 +16,7 @@ jobs:
     steps:
       - uses: actions/checkout@v6
 
-      - uses: ./.github/workflows/install
+      - uses: api2r/actions/install@v1
         with:
           use-container: "true"
           token: ${{ secrets.GITHUB_TOKEN }}

.gitignore

@@ -7,3 +7,4 @@ inst/doc
 docs
 /.positai/
 conversation-export*.json
+.positai