Replace ML stack with shiny for rocker builds

Author: almahmoud

.github/workflows/rocker-builds.yaml

@@ -220,11 +220,12 @@ jobs:
         tags: ${{ steps.defs.outputs.rockerintermediateprefix }}-tidyverse:${{ steps.defs.outputs.rver }}-${{ matrix.build.arch }}
         platforms: linux/${{ matrix.build.arch }}
 
-  mlbuild:
+  buildshiny:
     strategy:
       matrix:
         build:
           - { arch: 'amd64', runner: 'ubuntu-latest' }
+          - { arch: 'arm64', runner: 'ubuntu-latest-arm64' }
     runs-on: ${{ matrix.build.runner }}
     steps:
     - uses: actions/checkout@v3
@@ -250,55 +251,18 @@ jobs:
         password: ${{ secrets.GITHUB_TOKEN }}
 
     - name: Prep rocker rocker files
-      run: |
-        ## git clone rocker
-        git clone --depth 1 https://github.com/rocker-org/rocker-versioned2
-        sed -i 's#11.8.0-cudnn8-devel-ubuntu22.04#12.6.2-cudnn-devel-ubuntu24.04#g' rocker-versioned2/dockerfiles/cuda_${{ steps.defs.outputs.rver }}.Dockerfile
-        sed -i 's#11.8.0-cudnn8-devel-ubuntu22.04#12.6.2-cudnn-devel-ubuntu24.04#g' rocker-versioned2/dockerfiles/ml_${{ steps.defs.outputs.rver }}.Dockerfile
-        sed -i 's#11.8.0-cudnn8-devel-ubuntu22.04#12.6.2-cudnn-devel-ubuntu24.04#g' rocker-versioned2/dockerfiles/ml-verse_${{ steps.defs.outputs.rver }}.Dockerfile
-
-        # Package archived from CRAN
-        sed -i '/rmdshower/d' rocker-versioned2/scripts/install_verse.sh
-
-        sed -i 's#rocker/cuda:${{ steps.defs.outputs.rver }}#${{ steps.defs.outputs.rockerintermediateprefix }}-cuda:${{ steps.defs.outputs.rver }}-${{ matrix.build.arch }}#g' rocker-versioned2/dockerfiles/ml_${{ steps.defs.outputs.rver }}.Dockerfile
-        sed -i 's#rocker/ml:${{ steps.defs.outputs.rver }}#${{ steps.defs.outputs.rockerintermediateprefix }}-ml:${{ steps.defs.outputs.rver }}-${{ matrix.build.arch }}#g' rocker-versioned2/dockerfiles/ml-verse_${{ steps.defs.outputs.rver }}.Dockerfile
-
-        echo "Bioconductor Version: ${{ steps.defs.outputs.biocver }}"
-        if [ "${{ steps.defs.outputs.rver }}" == "devel" ]; then
-          bash .github/scripts/devel_or_patched_rversion.sh "${{ steps.defs.outputs.biocver }}" "rocker-versioned2/dockerfiles/cuda_${{ steps.defs.outputs.rver }}.Dockerfile"
-          bash .github/scripts/devel_or_patched_rversion.sh "${{ steps.defs.outputs.biocver }}" "rocker-versioned2/dockerfiles/ml_${{ steps.defs.outputs.rver }}.Dockerfile"
-          bash .github/scripts/devel_or_patched_rversion.sh "${{ steps.defs.outputs.biocver }}" "rocker-versioned2/dockerfiles/ml-verse_${{ steps.defs.outputs.rver }}.Dockerfile"
-        fi
+      run: bash .github/scripts/rocker_prep.sh ${{ steps.defs.outputs.rver }} ${{ steps.defs.outputs.biocver }} ${{ steps.defs.outputs.rockerintermediateprefix }} ${{ matrix.build.arch }}
 
     - name: Set up Docker Buildx
       uses: docker/setup-buildx-action@v2
       with:
         platforms: linux/${{ matrix.build.arch }}
 
-    - name: Build and load cuda
+    - name: Build and push shiny
       uses: docker/build-push-action@v3
       with:
-        file: rocker-versioned2/dockerfiles/cuda_${{ steps.defs.outputs.rver }}.Dockerfile
+        file: rocker-versioned2/dockerfiles/shiny_${{ steps.defs.outputs.rver }}.Dockerfile
         context: rocker-versioned2
         push: true
-        tags: ${{ steps.defs.outputs.rockerintermediateprefix }}-cuda:${{ steps.defs.outputs.rver }}-${{ matrix.build.arch }}
+        tags: ${{ steps.defs.outputs.rockerintermediateprefix }}-shiny:${{ steps.defs.outputs.rver }}-${{ matrix.build.arch }}
         platforms: linux/${{ matrix.build.arch }}
-
-    - name: Build and load ml
-      uses: docker/build-push-action@v3
-      with:
-        file: rocker-versioned2/dockerfiles/ml_${{ steps.defs.outputs.rver }}.Dockerfile
-        context: rocker-versioned2
-        push: true
-        tags: ${{ steps.defs.outputs.rockerintermediateprefix }}-ml:${{ steps.defs.outputs.rver }}-${{ matrix.build.arch }}
-        platforms: linux/${{ matrix.build.arch }}
-
-    - name: Build and load ml-verse
-      uses: docker/build-push-action@v3
-      with:
-        file: rocker-versioned2/dockerfiles/ml-verse_${{ steps.defs.outputs.rver }}.Dockerfile
-        context: rocker-versioned2
-        push: true
-        tags: ${{ steps.defs.outputs.rockerintermediateprefix }}-ml-verse:${{ steps.defs.outputs.rver }}-${{ matrix.build.arch }}
-        platforms: linux/${{ matrix.build.arch }}
-