Merge pull request #33 from daichengxin/dev #30
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # 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 | |
| # SINGULARITY_TMPDIR: ${{ github.workspace }}/.singularity-tmp | |
| # SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| # SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| # steps: | |
| # - name: Free up disk space before build | |
| # run: | | |
| # sudo rm -rf /usr/share/dotnet /usr/local/lib/android /opt/ghc | |
| # docker system prune -af || true | |
| # sudo apt-get clean | |
| # sudo rm -rf /var/lib/apt/lists/* | |
| # - 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: Free up disk space after build | |
| # run: | | |
| # docker system prune -af || true | |
| # sudo apt-get clean | |
| # sudo rm -rf /var/lib/apt/lists/* | |
| # - 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: | | |
| # docker pull ghcr.io/bigbio/quantms-rescoring:latest | |
| # docker save ghcr.io/bigbio/quantms-rescoring:latest -o quantms-rescoring.tar | |
| # - name: Remove Docker image to free up space | |
| # if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| # run: | | |
| # docker rmi ghcr.io/bigbio/quantms-rescoring:latest || true | |
| # docker system prune -af || true | |
| # df -h | |
| # - name: Prepare Singularity temp dir | |
| # run: mkdir -p ${{ github.workspace }}/.singularity-tmp | |
| # - name: Convert Docker image to Singularity | |
| # if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }} | |
| # run: | | |
| # singularity build quantms-rescoring.sif docker-archive://quantms-rescoring.tar | |
| # 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 ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io | |
| # singularity push quantms-rescoring.sif oras://ghcr.io/bigbio/quantms-rescoring-sif:${{ steps.version.outputs.VERSION }} | |
| # 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." |