ci: publish singularity image to registry (#4)

AllenNeuralDynamics · Mar 18, 2024 · 9633ebd · 9633ebd
1 parent 7567d1b
commit 9633ebd
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diff --git a/.github/workflows/tag_and_publish.yml b/.github/workflows/tag_and_publish.yml
@@ -17,7 +17,7 @@ jobs:
     - name: Set up Python 3.10
       uses: actions/setup-python@v3
       with:
-        python-version: 3.10
+        python-version: '3.10'
     - name: Install dependencies
       run: | 
         python -m pip install -e .[dev] --no-cache-dir
@@ -63,3 +63,49 @@ jobs:
     uses: AllenNeuralDynamics/aind-github-actions/.github/workflows/tag.yml@main
     secrets:
       SERVICE_TOKEN: ${{ secrets.SERVICE_TOKEN }}
+  publish:
+    runs-on: ubuntu-latest
+    needs: tag
+    steps:
+      - uses: actions/checkout@v3
+      - name: Pull latest changes
+        run: git pull origin main
+      - name: Set up Go 1.14
+        uses: actions/setup-go@v1
+        with:
+          go-version: 1.14
+        id: go
+      - name: Install Dependencies
+        run: |
+          sudo apt-get update && sudo apt-get install -y \
+            build-essential \
+            libssl-dev \
+            uuid-dev \
+            libgpgme11-dev \
+            squashfs-tools \
+            libseccomp-dev \
+            pkg-config
+      - name: Install Singularity
+        env:
+          SINGULARITY_VERSION: 3.7.0
+          GOPATH: /tmp/go
+        run: |
+          mkdir -p $GOPATH
+          sudo mkdir -p /usr/local/var/singularity/mnt && \
+          mkdir -p $GOPATH/src/github.com/sylabs && \
+          cd $GOPATH/src/github.com/sylabs && \
+          wget -qO- https://github.com/sylabs/singularity/releases/download/v${SINGULARITY_VERSION}/singularity-ce-${SINGULARITY_VERSION}.tar.gz | \
+          tar xzv && \
+          cd singularity-ce-${SINGULARITY_VERSION} && \
+          ./mconfig -p /usr/local && \
+          make -C builddir && \
+          sudo make -C builddir install
+      - name: Build sif container
+        run: |
+          mkdir sudo aind-data-transformation/build
+          sudo -E singularity build aind-data-transformation/build/container.sif aind-data-transformation/scripts/singularity_build.def
+      - name: Login and Deploy Container
+        run: |
+          echo ${{ secrets.GITHUB_TOKEN }} | singularity remote login -u ${{ github.actor }} --password-stdin oras://ghcr.io
+          singularity push aind-data-transformation/build/container.sif oras://ghcr.io/${GITHUB_REPOSITORY}:${{ needs.tag.outputs.new_version }}
+          singularity push aind-data-transformation/build/container.sif oras://ghcr.io/${GITHUB_REPOSITORY}:latest
diff --git a/scripts/singularity_build.def b/scripts/singularity_build.def
@@ -0,0 +1,12 @@
+Bootstrap: docker
+From: python:3.10-bullseye
+Stage: build
+
+%setup
+    # Copy project directory into container
+    cp -R aind-data-transformation ${SINGULARITY_ROOTFS}/aind-data-transformation
+
+%post
+    cd ${SINGULARITY_ROOTFS}/aind-data-transformation
+    pip install .[ephys] --no-cache-dir
+    rm -rf ${SINGULARITY_ROOTFS}/aind-data-transformation