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Diann 2.1.0 available
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‎.github/workflows/quantms-containers.yml‎

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name: QuantMS Containers Build and Sync
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on:
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push:
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branches: [ "main" ]
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pull_request:
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branches: [ "main" ]
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paths:
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- 'diann-*/Dockerfile'
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- '.github/workflows/**'
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release:
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types: [published]
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workflow_dispatch:
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inputs:
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push_images:
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description: 'Push images to registry'
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required: false
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default: true
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type: 'boolean'
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push_release:
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description: 'Push as release version'
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required: false
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default: false
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type: boolean
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jobs:
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build-diann:
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name: Build and Push DiaNN Docker Images
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runs-on: ubuntu-latest
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permissions:
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contents: read
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packages: write
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env:
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RETRY_TIMES: 3
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RETRY_DELAY: 30
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Log in to GitHub Container Registry
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GHCR_TOKEN }}
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- name: Extract metadata for Docker
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id: meta
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uses: docker/metadata-action@v5
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with:
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images: ghcr.io/bigbio/diann
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tags: |
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type=raw,value=latest,enable={{is_default_branch}}
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type=raw,value={{date 'YYYY.MM.DD'}}
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- name: Set date tag
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id: date
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run: echo "DATE_TAG=$(date +'%Y.%m.%d')" >> $GITHUB_OUTPUT
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- name: Build and Push DiaNN 2.1.0 image (Latest)
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uses: docker/build-push-action@v5
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with:
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context: ./diann-2.1.0
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push: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }}
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tags: |
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ghcr.io/bigbio/diann:2.1.0
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ghcr.io/bigbio/diann:latest
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cache-from: type=gha
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cache-to: type=gha,mode=max
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provenance: false
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- name: Set up Singularity
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if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }}
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uses: eWaterCycle/setup-singularity@v7
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with:
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singularity-version: 3.8.7
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- name: Pull Docker image for Singularity conversion
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if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }}
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run: |
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# Pull the Docker image from GitHub Container Registry
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docker pull ghcr.io/bigbio/diann:2.1.0
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# Save the Docker image to a tar file
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docker save ghcr.io/bigbio/diann:2.1.0 -o diann-2.1.0.tar
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- name: Convert Docker image to Singularity
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if: ${{ (github.event.inputs.push_images == true || github.event.inputs.push_images == '') }}
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run: |
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# Convert Docker tar to Singularity SIF
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singularity build diann-2.1.0.sif docker-archive://diann-2.1.0.tar
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# Verify the SIF file exists
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ls -la diann-2.1.0.sif
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- name: Login and Deploy Container
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if: (github.event_name != 'pull_request')
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env:
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IS_RELEASE: ${{ github.event_name == 'release' }}
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run: |
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echo ${{ secrets.GHCR_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io
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# Push with version tag
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singularity push diann-2.1.0.sif oras://bigbio/diann-sif:2.1.0
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# Push with date tag
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singularity push diann-2.1.0.sif oras://bigbio/diann-sif:2.1.0-${{ steps.date.outputs.DATE_TAG }}
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# If this is a release event, also tag as latest
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if [[ "${{ env.IS_RELEASE }}" == "true" || "${{ github.event_name }}" == "release" ]]; then
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singularity push diann-2.1.0.sif oras://bigbio/diann-sif:latest
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fi
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- name: Notify on success
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if: success()
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run: |
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echo "::notice::Successfully built and pushed DiaNN Docker and Singularity images to ghcr.io/bigbio"
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- name: Notify on failure
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if: failure()
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run: |
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echo "::error::Failed to build or push DiaNN images. Check the logs for details."
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sync-openms:
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name: Sync OpenMS Containers
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needs: build-diann
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runs-on: ubuntu-latest
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permissions:
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contents: read
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packages: write
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v3
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- name: Log in to GitHub Container Registry
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uses: docker/login-action@v3
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GHCR_TOKEN }}
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- name: Set date tag
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id: date
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run: echo "DATE_TAG=$(date +'%Y.%m.%d')" >> $GITHUB_OUTPUT
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- name: Pull OpenMS Docker container
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id: pull_docker
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uses: nick-fields/retry@v2
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with:
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timeout_minutes: 10
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max_attempts: 3
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retry_wait_seconds: 30
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command: docker pull ghcr.io/openms/openms-tools-thirdparty:latest
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- name: Tag and push OpenMS Docker container
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if: steps.pull_docker.outcome == 'success'
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run: |
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# Set container names
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SOURCE_CONTAINER="ghcr.io/openms/openms-tools-thirdparty:latest"
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TARGET_CONTAINER="ghcr.io/bigbio/openms-tools-thirdparty:${{ steps.date.outputs.DATE_TAG }}"
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echo "Tagging as $TARGET_CONTAINER"
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docker tag $SOURCE_CONTAINER $TARGET_CONTAINER
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echo "Pushing $TARGET_CONTAINER"
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docker push $TARGET_CONTAINER || {
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echo "Failed to push $TARGET_CONTAINER, retrying..."
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sleep 30
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docker push $TARGET_CONTAINER
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}
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# If this is a release push or a GitHub release event, also tag as latest
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if [[ "${{ github.event.inputs.push_release }}" == "true" || "${{ github.event_name }}" == "release" ]]; then
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LATEST_IMAGE="ghcr.io/bigbio/openms-tools-thirdparty:latest"
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docker tag $SOURCE_CONTAINER $LATEST_IMAGE
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docker push $LATEST_IMAGE || {
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echo "Failed to push $LATEST_IMAGE, retrying..."
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sleep 30
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docker push $LATEST_IMAGE
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}
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echo "Pushed release version as $LATEST_IMAGE"
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fi
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- name: Set up Singularity
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if: success()
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uses: eWaterCycle/setup-singularity@v7
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with:
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singularity-version: 3.8.7
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- name: Configure Singularity for GitHub Container Registry
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if: success()
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run: |
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# Create Singularity remote endpoint for GitHub Container Registry
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singularity remote add --no-login GithubContainer oras://ghcr.io
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# Login to GitHub Container Registry
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echo "${{ secrets.GHCR_TOKEN }}" | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin GithubContainer
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- name: Pull OpenMS SIF container
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id: pull_sif
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if: success()
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uses: nick-fields/retry@v2
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with:
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timeout_minutes: 15
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max_attempts: 3
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retry_wait_seconds: 60
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command: singularity pull --force openms-tools-thirdparty.sif oras://ghcr.io/openms/openms-tools-thirdparty-sif:latest
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- name: Login and Push OpenMS SIF container
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if: steps.pull_sif.outcome == 'success'
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env:
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keepgoing: true
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run: |
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# Login to GitHub Container Registry
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echo ${{ secrets.GHCR_TOKEN }} | singularity remote login -u ${{ secrets.GHCR_USERNAME }} --password-stdin oras://ghcr.io
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# Set SIF paths and push with date tag
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echo "Pushing OpenMS SIF with date tag"
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singularity push openms-tools-thirdparty.sif oras://bigbio/openms-tools-thirdparty-sif:${{ steps.date.outputs.DATE_TAG }} || {
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echo "Failed to push with date tag, retrying..."
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sleep 60
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singularity push openms-tools-thirdparty.sif oras://bigbio/openms-tools-thirdparty-sif:${{ steps.date.outputs.DATE_TAG }}
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}
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# If this is a release push or a GitHub release event, also tag as latest
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if [[ "${{ github.event.inputs.push_release }}" == "true" || "${{ github.event_name }}" == "release" ]]; then
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echo "Pushing OpenMS SIF as latest"
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singularity push openms-tools-thirdparty.sif oras://bigbio/openms-tools-thirdparty-sif:latest || {
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echo "Failed to push as latest, retrying..."
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sleep 60
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singularity push openms-tools-thirdparty.sif oras://bigbio/openms-tools-thirdparty-sif:latest
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}
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fi
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- name: Notify on success
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if: success()
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run: |
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echo "::notice::Successfully synced OpenMS containers to BigBio repositories"
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- name: Notify on failure
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if: failure()
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run: |
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echo "::error::Failed to sync OpenMS containers. Check the logs for details."

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