docker-publish.yml

name: Docker

on:
  push:
    # Publish `main` as Docker `latest` image.
    branches:
      - main

    # Publish `v1.2.3` tags as releases.
    tags:
      - v*

  # Run tests for any PRs.
  pull_request:

env:
  IMAGE_NAME: bioinformatics

jobs:

  # Push image to GitHub Packages.
  # See also https://docs.docker.com/docker-hub/builds/
  push:

    runs-on: ubuntu-latest
    if: github.event_name == 'push'

    steps:
      - uses: actions/checkout@v4
        with:
          lfs: true
      - name: Checkout LFS objects
        run: git lfs checkout
      - name: Set Date
        run: echo "TODAYS_DATE=$(date +'%Y%m%d')" >> $GITHUB_ENV

      - name: Prepare tags
        id: prep
        run: |

          # Docker Registries
          GHCR_IMAGE_NAME="ghcr.io/${{ github.repository_owner }}/${{ env.IMAGE_NAME }}"
          DOCKER_HUB_IMAGE_NAME="${{ github.repository_owner }}/${{ env.IMAGE_NAME }}"

          TAGS=""
          FINAL_TAGS=""
          
          # Identify Tags
          # Type of tags:
          # 1. Scenario 1 - x.y.z.patchedYYYYMMDD
          # 2. Scenario 2 - Semver Tags x.y.z
          # 3. Scenario 3 - Main Branch
          # 4. Scenario 4 - Branches

          if [[ $GITHUB_REF == refs/tags/* ]]; then
            # If this is a tag push, use the tag name (stripping 'refs/tags/')
            FULL_TAG=${GITHUB_REF#refs/tags/}
      
            # Remove leading 'v' from tag if present
            if [[ $FULL_TAG == v* ]]; then
              FULL_TAG=${FULL_TAG#v}
            fi
      
            # Scenario 1 - x.y.z.patchedYYYYMMDD
            # Tags
            # 1. x.y.z.patchedYYYYMMDD
            # 2. x.y.z
            # 3. x.y
            # 4. x
            if [[ $FULL_TAG =~ (.*)\.patched[0-9]+ ]]; then
              # Extract the base tag without the .patched segment
              BASE_TAG=${BASH_REMATCH[1]}

              if [[ $BASE_TAG =~ ^([0-9]+)\.([0-9]+)\.([0-9]+)$ ]]; then
                MAJOR=${BASH_REMATCH[1]}
                MINOR=${BASH_REMATCH[2]}
                PATCH=${BASH_REMATCH[3]}

                TAGS="$FULL_TAG,$BASE_TAG,$MAJOR.$MINOR.$PATCH,$MAJOR.$MINOR,$MAJOR"
              fi
            else
              # Scenario 2 - Semver Tags x.y.z
              # Tags
              # 1. x.y.z
              # 2. x.y
              # 3. x
              if [[ $FULL_TAG =~ ^([0-9]+)\.([0-9]+)\.([0-9]+)$ ]]; then
                MAJOR=${BASH_REMATCH[1]}
                MINOR=${BASH_REMATCH[2]}
                PATCH=${BASH_REMATCH[3]}

                TAGS="$MAJOR.$MINOR.$PATCH,$MAJOR.$MINOR,$MAJOR"
              fi
            fi
          elif [[ $GITHUB_REF == refs/heads/main ]]; then
            # Scenario 3 - Main Branch
            # If this is a push to main, use 'latest'
            TAGS="latest"
          else
            # Scenario 4 - Branches
            # Otherwise, use the branch name, replacing non-alphanumeric characters with underscores
            TAG=$(echo ${GITHUB_REF#refs/heads/} | sed 's/[^a-zA-Z0-9]/_/g')
            TAGS=$TAG
          fi

          # For each tag, prepend the registry name and output a newline-separated list
          for tag in $(echo "$TAGS" | tr ',' '\n'); do
            FINAL_TAGS="$FINAL_TAGS $GHCR_IMAGE_NAME:$tag,"
            FINAL_TAGS="$FINAL_TAGS $DOCKER_HUB_IMAGE_NAME:$tag,"
          done

          FINAL_TAGS=${FINAL_TAGS%,}

          echo "tags=${FINAL_TAGS}" >> $GITHUB_OUTPUT

      - name: Docker meta
        id: meta
        uses: docker/metadata-action@v5
        with:
          # list of Docker images to use as base name for tags
          images: |
            ghcr.io/${{ github.repository_owner }}/${{ env.IMAGE_NAME }}
            ${{ github.repository_owner }}/${{ env.IMAGE_NAME }}
          labels: 
            org.opencontainers.image.title=${{ env.IMAGE_NAME }}
            org.opencontainers.image.description=Bioinformatics Tools
            org.opencontainers.image.vendor=Englander Institute for Precision Medicine
            maintainer=Andrea Sboner <ans2077@med.cornell.edu>
            org.opencontainers.image.authors=Andrea Sboner <ans2077@med.cornell.edu>

      - name: Set up QEMU
        uses: docker/setup-qemu-action@v3
      - name: Set up Docker Buildx
        uses: docker/setup-buildx-action@v3

      - name: Log into GitHub Container Registry
        uses: docker/login-action@v3
        with:
          registry: ghcr.io
          username: ${{ secrets.GHCR_SVC_ACCOUNT }}
          password: ${{ secrets.GHCR_TOKEN }}

      - name: Login to EIPM DockerHub
        uses: docker/login-action@v3
        with:
          username: ${{ secrets.EIPM_DOCKER_HUB_USERNAME }}
          password: ${{ secrets.EIPM_DOCKER_HUB_TOKEN }}

      - name: Build and push to Docker Hub and GitHub Container Registry
        uses: docker/build-push-action@v5
        with:
          context: .
          platforms: linux/amd64
          file: ./Dockerfile
          sbom: true
          push: true
          provenance: mode=max
          tags: ${{ steps.prep.outputs.tags }}
          labels: ${{ steps.meta.outputs.labels }}
          cache-from: type=registry,ref=ghcr.io/${{ github.repository_owner }}/${{ env.IMAGE_NAME }}:cache
          cache-to: type=registry,ref=ghcr.io/${{ github.repository_owner }}/${{ env.IMAGE_NAME }}:cache,mode=max