quantms-rescoring AlphaPepDeep #14
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| name: QuantMS-Rescoring Containers Build and Sync | |
| on: | |
| push: | |
| branches: [ "main" ] | |
| pull_request: | |
| branches: [ "main" ] | |
| paths: | |
| - 'Dockerfile' | |
| - '.github/workflows/**' | |
| release: | |
| types: [published] | |
| workflow_dispatch: | |
| inputs: | |
| push_images: | |
| description: 'Push images to registry' | |
| required: false | |
| default: true | |
| type: 'boolean' | |
| push_release: | |
| description: 'Push as release version' | |
| required: false | |
| default: false | |
| type: boolean | |
| jobs: | |
| build-quantms-rescoring: | |
| name: Build and Push QuantMS-Rescoring Docker Images | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| env: | |
| RETRY_TIMES: 3 | |
| RETRY_DELAY: 30 | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v4 | |
| - name: Set up Docker Buildx | |
| uses: docker/setup-buildx-action@v3 | |
| - name: Log in to GitHub Container Registry | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ghcr.io | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GHCR_TOKEN }} | |
| - name: Extract version from pyproject.toml | |
| id: version | |
| run: | | |
| VERSION=$(grep '^version = ' pyproject.toml | cut -d'"' -f2) | |
| echo "VERSION=$VERSION" >> $GITHUB_OUTPUT | |
| echo "Extracted version: $VERSION" | |
| # Extract major and minor version | |
| MAJOR=$(echo $VERSION | cut -d'.' -f1) | |
| MINOR=$(echo $VERSION | cut -d'.' -f2) | |
| echo "MAJOR=$MAJOR" >> $GITHUB_OUTPUT | |
| echo "MINOR=$MINOR" >> $GITHUB_OUTPUT | |
| echo "Major.Minor: $MAJOR.$MINOR" | |
| - name: Build and Push QuantMS-Rescoring image | |
| uses: docker/build-push-action@v5 | |
| with: | |
| context: . | |
| push: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| tags: | | |
| ghcr.io/bigbio/quantms-rescoring:latest | |
| ghcr.io/bigbio/quantms-rescoring:${{ steps.version.outputs.VERSION }} | |
| cache-from: type=gha | |
| cache-to: type=gha,mode=max | |
| provenance: false | |
| # Note: Only building for linux/amd64 as pyopenms doesn't have ARM64 wheels | |
| platforms: linux/amd64 | |
| - name: Set up Singularity | |
| if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| uses: eWaterCycle/setup-singularity@v7 | |
| with: | |
| singularity-version: 3.8.7 | |
| - name: Pull Docker image for Singularity conversion | |
| if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| run: | | |
| # Pull the Docker image from GitHub Container Registry | |
| docker pull ghcr.io/bigbio/quantms-rescoring:latest | |
| # Save the Docker image to a tar file | |
| docker save ghcr.io/bigbio/quantms-rescoring:latest -o quantms-rescoring.tar | |
| - name: Convert Docker image to Singularity | |
| if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| run: | | |
| # Convert Docker tar to Singularity SIF | |
| singularity build quantms-rescoring.sif docker-archive://quantms-rescoring.tar | |
| # Verify the SIF file exists | |
| ls -la quantms-rescoring.sif | |
| - name: Login and Deploy Container | |
| if: (github.event_name != 'pull_request') | |
| env: | |
| IS_RELEASE: ${{ github.event_name == 'release' }} | |
| run: | | |
| echo ${{ secrets.GHCR_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io | |
| # Push with exact version tag | |
| singularity push quantms-rescoring.sif oras://ghcr.io/bigbio/quantms-rescoring-sif:${{ steps.version.outputs.VERSION }} | |
| # If this is a release event, also tag as latest | |
| if [[ "${{ env.IS_RELEASE }}" == "true" || "${{ github.event_name }}" == "release" ]]; then | |
| singularity push quantms-rescoring.sif oras://ghcr.io/bigbio/quantms-rescoring-sif:latest | |
| fi | |
| - name: Notify on success | |
| if: success() | |
| run: | | |
| echo "::notice::Successfully built and pushed QuantMS-Rescoring Docker and Singularity images to ghcr.io/bigbio" | |
| - name: Notify on failure | |
| if: failure() | |
| run: | | |
| echo "::error::Failed to build or push QuantMS-Rescoring images. Check the logs for details." |