Workflow updates

.github/workflows/basic_checks.yaml

@@ -13,15 +13,16 @@ jobs:
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: TRUE
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-      CRAN: https://packagemanager.posit.co/cran/__linux__/jammy/latest
+      CRAN: https://packagemanager.posit.co/cran/__linux__/noble/latest
 
     steps:
       - name: Checkout Repository
         uses: actions/checkout@v4
 
       - name: Query dependencies and update old packages
         run: |
-          BiocManager::install(ask=FALSE)
+          options(repos = c(CRAN = Sys.getenv("CRAN")))
+          BiocManager::install(c("remotes", "rcmdcheck"), ask = FALSE)
           saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
         shell: Rscript {0}
 
@@ -35,9 +36,9 @@ jobs:
 
       - name: Install dependencies
         run: |
-          BiocManager::repositories()
+          options(repos = c(CRAN = Sys.getenv("CRAN")))
           remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories())
-          remotes::install_cran("rcmdcheck")
+          BiocManager::install(ask = FALSE, update = TRUE)
         shell: Rscript {0}
 
       - name: Check
@@ -50,18 +51,10 @@ jobs:
         run: |
            PATH=$PATH:$HOME/bin/ Rscript -e 'pkgdown::build_site(".")'
 
-      # deploy needs rsync? Seems so.
-      - name: Install deploy dependencies
-        run: |
-          apt-get update
-          apt-get -y install rsync
-
-      - name: Deploy 🚀
-        uses: JamesIves/github-pages-deploy-action@v4
+      - name: Upload pkgdown artifact
+        uses: actions/upload-pages-artifact@v3
         with:
-          TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          BRANCH: gh-pages # The branch the action should deploy to.
-          FOLDER: docs # The folder the action should deploy.
+          path: docs
 
   docker-build-and-push:
     #needs: r-build-and-check
@@ -121,10 +114,22 @@ jobs:
       # https://github.com/docker/build-push-action
       - name: Build and push Docker image
         id: build-and-push
-        uses: docker/build-push-action@v5
+        uses: docker/build-push-action@v6
         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
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
+