Singularity to apptainer

Author: almahmoud

.github/workflows/build_singularity.yaml

@@ -1,4 +1,4 @@
-name: Build Singularity Images
+name: Build Apptainer Images
 
 on:
   workflow_run:
@@ -7,23 +7,20 @@ on:
       - completed
 
 jobs:
-  build-singularity:
+  build-apptainer:
     runs-on: ubuntu-latest
     strategy:
       matrix:
         base:
           - {image: 'ghcr.io/bioconductor/r-ver', outname: 'r-ver'}
           - {image: 'ghcr.io/bioconductor/bioconductor', outname: 'bioconductor'}
           - {image: 'ghcr.io/bioconductor/tidyverse', outname: 'tidyverse'}
-          - {image: 'ghcr.io/bioconductor/cuda', outname: 'cuda'}
-          - {image: 'ghcr.io/bioconductor/ml', outname: 'ml'}
-          - {image: 'ghcr.io/bioconductor/ml-verse', outname: 'ml-verse'}
           - {image: 'ghcr.io/bioconductor/shiny', outname: 'shiny'}
     steps:
       - name: Checkout code
         uses: actions/checkout@v4
 
-      - name: Setup Singularity deps
+      - name: Install Apptainer dependencies
         run: |
           sudo apt-get update
           sudo apt-get install -y \
@@ -50,18 +47,18 @@ jobs:
         with:
           go-version: 1.24.1
 
-      - name: Setup Singularity
+      - name: Install Apptainer
         run: |
-          export VERSION=4.3.0 && # adjust this as necessary \
-          wget https://github.com/sylabs/singularity/releases/download/v${VERSION}/singularity-ce-${VERSION}.tar.gz && \
-          tar -xzf singularity-ce-${VERSION}.tar.gz && \
-          cd singularity-ce-${VERSION}
-          ./mconfig && \
-          make -C ./builddir && \
+          export VERSION=1.3.6  # Latest Apptainer version as of 2025-04
+          wget https://github.com/apptainer/apptainer/releases/download/v${VERSION}/apptainer-${VERSION}.tar.gz
+          tar -xzf apptainer-${VERSION}.tar.gz
+          cd apptainer-${VERSION}
+          ./mconfig
+          make -C ./builddir
           sudo make -C ./builddir install
-          
-      - name: Singularity build config
-        run: singularity buildcfg
+
+      - name: Verify Apptainer config
+        run: apptainer buildcfg
 
       - name: Get branch name
         id: vars
@@ -78,14 +75,14 @@ jobs:
           echo "origbranch=$BRANCH_NAME" >> $GITHUB_OUTPUT
           echo "procbranch=$PROCESSED_NAME" >> $GITHUB_OUTPUT
 
-      - name: Build Singularity Image
+      - name: Build Apptainer Image
         run: |
-          singularity build --fakeroot \
+          apptainer build \
             "${{matrix.base.outname}}-$(date +%s).sif" \
             docker://${{ matrix.base.image }}:${{steps.vars.origbranch}}
 
       - name: Push to GitHub Packages
         run: |
-          echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ github.actor }} --password-stdin oras://ghcr.io
-          singularity push *.sif oras://ghcr.io/${{github.repository_owner}}/${{matrix.base.outname}}:${{steps.vars.origbranch}}
-          singularity push *.sif oras://ghcr.io/${{github.repository_owner}}/${{matrix.base.outname}}:${{steps.vars.procbranch}}
+          echo ${{ secrets.GITHUB_TOKEN }} | apptainer remote login -u ${{ github.actor }} --password-stdin oras://ghcr.io
+          apptainer push *.sif oras://ghcr.io/${{github.repository_owner}}/${{matrix.base.outname}}:${{steps.vars.origbranch}}
+          apptainer push *.sif oras://ghcr.io/${{github.repository_owner}}/${{matrix.base.outname}}:${{steps.vars.procbranch}}