fix: update basic_checks.yaml workflow - fix deploy and update action versions

Agent-Logs-Url: https://github.com/Bioconductor/BuildABiocWorkshop/sessions/13259783-4827-44ad-a22e-79c11a5754b7

Co-authored-by: seandavi <92435+seandavi@users.noreply.github.com>

Author: Copilot

.github/workflows/basic_checks.yaml

@@ -17,7 +17,7 @@ jobs:
 
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Query dependencies and update old packages
         run: |
@@ -28,7 +28,7 @@ jobs:
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v4
+        uses: actions/cache@v5
         with:
           path: /usr/local/lib/R/site-library
           key: ${{ env.cache-version }}-${{ runner.os }}-r-${{ hashFiles('.github/depends.Rds') }}
@@ -52,12 +52,35 @@ jobs:
            PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site(".")'
 
       - name: Upload pkgdown artifact
-        uses: actions/upload-pages-artifact@v3
+        if: github.event_name == 'push'
+        uses: actions/upload-artifact@v4
         with:
+          name: pkgdown-site
           path: docs
 
+  deploy:
+    needs: r-build-and-check
+    if: github.event_name == 'push' && success()
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v6
+
+      - name: Download pkgdown artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: pkgdown-site
+          path: _site
+
+      - name: Deploy to GitHub Pages
+        uses: JamesIves/github-pages-deploy-action@v4
+        with:
+          branch: gh-pages
+          folder: _site
+
   docker-build-and-push:
-    #needs: r-build-and-check
     runs-on: ubuntu-latest
     permissions:
       contents: read
@@ -68,7 +91,7 @@ jobs:
 
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Set Environment Variables
         run: |
@@ -87,16 +110,16 @@ jobs:
       # https://github.com/sigstore/cosign-installer
       - name: Install cosign
         if: github.event_name != 'pull_request'
-        uses: sigstore/cosign-installer@v3
+        uses: sigstore/cosign-installer@v4
 
       - name: Setup Docker buildx
-        uses: docker/setup-buildx-action@v3
+        uses: docker/setup-buildx-action@v4
 
       # Login against a Docker registry except on PR
       # https://github.com/docker/login-action
       - name: Log into registry ${{ env.REGISTRY }}
         if: github.event_name != 'pull_request'
-        uses: docker/login-action@v3
+        uses: docker/login-action@v4
         with:
           registry: ${{ env.REGISTRY }}
           username: ${{ github.actor }}
@@ -106,32 +129,18 @@ jobs:
       # https://github.com/docker/metadata-action
       - name: Extract Docker metadata
         id: meta
-        uses: docker/metadata-action@v5
+        uses: docker/metadata-action@v6
         with:
           images: ${{ env.IMAGE }}
 
       # Build and push Docker image with Buildx (don't push on PR)
       # https://github.com/docker/build-push-action
       - name: Build and push Docker image
         id: build-and-push
-        uses: docker/build-push-action@v6
+        uses: docker/build-push-action@v7
         with:
           context: .
           push: ${{ github.event_name != 'pull_request' }}
           tags: |
             ${{ env.IMAGE }}:latest
-            ${{ env.IMAGE }}:${{ env.GIT_SHA }}
-
-  deploy:
-    needs: r-build-and-check
-    permissions:
-      pages: write
-      id-token: write
-    runs-on: ubuntu-24.04
-    environment:
-      name: github-pages
-      url: ${{ steps.deployment.outputs.page_url }}
-    steps:
-      - name: Deploy to GitHub Pages
-        id: deployment
-        uses: actions/deploy-pages@v4
+            ${{ env.IMAGE }}:${{ env.GIT_SHA }}