fixed fasta filepaths #156
Workflow file for this run
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| name: Docker Build | |
| on: | |
| push: | |
| branches: ['**'] | |
| tags: ['**'] | |
| pull_request: | |
| branches: [main] | |
| merge_group: | |
| delete: # Trigger cleanup when branches are deleted | |
| env: | |
| REGISTRY: ghcr.io | |
| IMAGE_NAME: ${{ github.repository }} | |
| jobs: | |
| build-amd64: | |
| if: github.event_name != 'delete' | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| outputs: | |
| digest: ${{ steps.build.outputs.digest }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: docker/setup-buildx-action@v3 | |
| - name: Log in to Container Registry | |
| if: github.event_name == 'push' | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Generate tag suffix | |
| id: tag | |
| run: | | |
| # Sanitize ref_name: replace / with - for valid Docker tags | |
| echo "suffix=$(echo '${{ github.ref_name }}' | tr '/' '-')" >> $GITHUB_OUTPUT | |
| - name: Build and push (amd64) | |
| id: build | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| platforms: linux/amd64 | |
| push: ${{ github.event_name == 'push' }} | |
| tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.tag.outputs.suffix }}-amd64 | |
| provenance: false | |
| sbom: false | |
| cache-from: | | |
| type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:buildcache-amd64 | |
| type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:main-amd64 | |
| cache-to: ${{ github.event_name == 'push' && format('type=registry,ref={0}/{1}:buildcache-amd64,mode=max', env.REGISTRY, env.IMAGE_NAME) || '' }} | |
| build-arm64: | |
| if: github.event_name != 'delete' | |
| runs-on: ubuntu-24.04-arm | |
| permissions: | |
| contents: read | |
| packages: write | |
| outputs: | |
| digest: ${{ steps.build.outputs.digest }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: docker/setup-buildx-action@v3 | |
| - name: Log in to Container Registry | |
| if: github.event_name == 'push' | |
| uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Generate tag suffix | |
| id: tag | |
| run: | | |
| # Sanitize ref_name: replace / with - for valid Docker tags | |
| echo "suffix=$(echo '${{ github.ref_name }}' | tr '/' '-')" >> $GITHUB_OUTPUT | |
| - name: Build and push (arm64) | |
| id: build | |
| uses: docker/build-push-action@v6 | |
| with: | |
| context: . | |
| platforms: linux/arm64 | |
| push: ${{ github.event_name == 'push' }} | |
| tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ steps.tag.outputs.suffix }}-arm64 | |
| provenance: false | |
| sbom: false | |
| cache-from: | | |
| type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:buildcache-arm64 | |
| type=registry,ref=${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:main-arm64 | |
| cache-to: ${{ github.event_name == 'push' && format('type=registry,ref={0}/{1}:buildcache-arm64,mode=max', env.REGISTRY, env.IMAGE_NAME) || '' }} | |
| create-manifest: | |
| if: github.event_name == 'push' | |
| needs: [build-amd64, build-arm64] | |
| runs-on: ubuntu-latest | |
| permissions: | |
| contents: read | |
| packages: write | |
| steps: | |
| - uses: docker/login-action@v3 | |
| with: | |
| registry: ${{ env.REGISTRY }} | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| - name: Generate tag suffix | |
| id: tag | |
| run: | | |
| # Sanitize ref_name: replace / with - for valid Docker tags | |
| echo "suffix=$(echo '${{ github.ref_name }}' | tr '/' '-')" >> $GITHUB_OUTPUT | |
| - name: Extract metadata | |
| id: meta | |
| uses: docker/metadata-action@v5 | |
| with: | |
| images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }} | |
| tags: | | |
| type=ref,event=branch | |
| type=ref,event=tag | |
| type=raw,value=latest,enable={{is_default_branch}} | |
| - name: Create and push manifest | |
| env: | |
| TAGS: ${{ steps.meta.outputs.tags }} | |
| SUFFIX: ${{ steps.tag.outputs.suffix }} | |
| run: | | |
| # Iterate over multi-line tags properly | |
| echo "$TAGS" | while IFS= read -r tag; do | |
| [ -z "$tag" ] && continue | |
| echo "Creating manifest for: $tag" | |
| docker buildx imagetools create \ | |
| --annotation "index:org.opencontainers.image.description=ML-guided qPCR primer design with off-target minimization" \ | |
| --annotation "index:org.opencontainers.image.source=https://github.com/broadinstitute/qprimer_designer" \ | |
| --annotation "index:org.opencontainers.image.licenses=MIT" \ | |
| -t "$tag" \ | |
| "${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${SUFFIX}-amd64" \ | |
| "${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${SUFFIX}-arm64" | |
| done | |
| cleanup-untagged: | |
| if: github.event_name == 'push' && github.ref == 'refs/heads/main' | |
| needs: [create-manifest] | |
| runs-on: ubuntu-latest | |
| permissions: | |
| packages: write | |
| steps: | |
| - uses: actions/delete-package-versions@v5 | |
| with: | |
| package-name: qprimer_designer | |
| package-type: container | |
| min-versions-to-keep: 5 | |
| delete-only-untagged-versions: true | |
| cleanup-branch-images: | |
| if: github.event_name == 'delete' && github.event.ref_type == 'branch' | |
| runs-on: ubuntu-latest | |
| permissions: | |
| packages: write | |
| steps: | |
| - name: Delete branch images from ghcr.io | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| run: | | |
| # Sanitize branch name (same logic as build jobs) | |
| SUFFIX=$(echo '${{ github.event.ref }}' | tr '/' '-') | |
| # Delete multi-arch manifest and arch-specific images | |
| for TAG in "${SUFFIX}" "${SUFFIX}-amd64" "${SUFFIX}-arm64"; do | |
| echo "Looking for tag: $TAG" | |
| # Get version IDs for this tag (may return multiple lines) | |
| # Use index() for exact match instead of contains() which does substring matching | |
| VERSION_IDS=$(gh api \ | |
| "orgs/${{ github.repository_owner }}/packages/container/qprimer_designer/versions" \ | |
| --jq ".[] | select(.metadata.container.tags | index(\"$TAG\")) | .id" \ | |
| 2>/dev/null || true) | |
| if [ -n "$VERSION_IDS" ]; then | |
| echo "$VERSION_IDS" | while read -r VERSION_ID; do | |
| [ -z "$VERSION_ID" ] && continue | |
| gh api --method DELETE \ | |
| "orgs/${{ github.repository_owner }}/packages/container/qprimer_designer/versions/$VERSION_ID" | |
| echo "Deleted version $VERSION_ID (tag: $TAG)" | |
| done | |
| else | |
| echo "Tag $TAG not found, skipping" | |
| fi | |
| done |