bioconda-utils-build-env-cos7.yml

name: 'Build & Push: bioconda-utils-build-env-cos7'
on:
  push:
    branches:
    - test-push
    paths:
    - images/bioconda-utils-build-env-cos7/**
    - .github/workflows/bioconda-utils-build-env-cos7.yml
  pull_request:
    paths:
    - images/bioconda-utils-build-env-cos7/**
    - .github/workflows/bioconda-utils-build-env-cos7.yml

jobs:
  build:
    name: Build & Push
    runs-on: ubuntu-22.04
    env:
      # The base image is not intended to change often and should be used with
      # version tags or checksum IDs, but not via "latest".
      MAJOR_VERSION: 3
      MINOR_VERSION: 1

      # Used for testing -- set to something like 'tmp-' or 'test-' to prefix
      # images with this name during testing
      IMAGE_PREFIX: "tmp-"
      IMAGE_NAME: bioconda-utils-build-env-cos7

    steps:
    - name: Checkout bioconda-containers
      uses: actions/checkout@v4
      with:
        fetch-depth: 0

    - name: Checkout bioconda-utils
      uses: actions/checkout@v4
      with:
        fetch-depth: 0
        repository: 'bioconda/bioconda-utils'
        path: 'images/bioconda-utils-build-env-cos7/bioconda-utils'

    - name: Set up QEMU
      uses: docker/setup-qemu-action@v3
      with:
        platforms: arm64

    - name: Build
      id: build
      run: |
        set -xeu

        image_name='${{ env.IMAGE_PREFIX }}${{ env.IMAGE_NAME }}'
        image_dir='images/${{ env.IMAGE_NAME }}'
        tags='
          ${{ env.MAJOR_VERSION }}
          ${{ env.MAJOR_VERSION }}.${{ env.MINOR_VERSION }}
          latest
        '
        # Adds image and tags to outputs which can be used in later steps.
        printf %s\\n \
          "image_dir=${image_dir}" \
          "image_name=${image_name}" \
          "tags=$( echo ${tags} )" \
          >> $GITHUB_OUTPUT

        cd 'images/${{ env.IMAGE_NAME }}'

        # Create manifest (which is considered arch-independent)
        for tag in ${tags} ; do
          buildah manifest create "${image_name}:${tag}"
        done

        # Due to different nomenclature used by conda-forge and buildah, we
        # need to map archs to base images.
        for arch_and_image in \
          "amd64=quay.io/condaforge/linux-anvil-cos7-x86_64" \
          "arm64=quay.io/condaforge/linux-anvil-aarch64";
        do
          # Unpack archs and base images
          arch=$(echo $arch_and_image | cut -f1 -d "=")
          base_image=$(echo $arch_and_image | cut -f2 -d "=")

          # --iidfile prints the built image ID to the specified file. This is
          # used so we can refer to the image in later steps.
          iidfile="$( mktemp )"
          buildah bud \
            --arch="${arch}" \
            --iidfile="${iidfile}" \
            --build-arg=base_image="$base_image"
          image_id="$( cat "${iidfile}" )"
          rm "${iidfile}"

          # Extract various package info and version info to store as labels
          container="$( buildah from "${image_id}" )"
          run() { buildah run "${container}" "${@}" ; }
          deb_list="$( run cat /.deb.lst | tr '\n' '|' | sed 's/|$//' )"
          pkg_list="$( run cat /.pkg.lst | tr '\n' '|' | sed 's/|$//' )"
          glibc="$( run sh -c 'exec "$( find -xdev -name libc.so.6 -print -quit )"' | sed '1!d' )"
          bash="$( run bash --version | sed '1!d' )"
          bioconda_utils="$( run sh -c '. /opt/conda/etc/profile.d/conda.sh && conda activate base && bioconda-utils --version' | rev | cut -f1 -d " " | rev )"
          buildah rm "${container}"

          # Store package/version info as labels for the image
          container="$( buildah from "${image_id}" )"
          buildah config \
            --label=glibc="${glibc}" \
            --label=bash="${bash}" \
            --label=deb-list="${deb_list}" \
            --label=pkg-list="${pkg_list}" \
            --label=bioconda-utils="${bioconda_utils}" \
            "${container}"

          # Store the new image (now with labels)
          image_id="$( buildah commit "${container}" )"
          buildah rm "${container}"

          # image tag includes arch; then added to manifest which does not include arch
          for tag in ${tags} ; do
            buildah tag \
              "${image_id}" \
              "${image_name}:${tag}-${arch}"
            buildah manifest add \
              "${image_name}:${tag}" \
              "${image_id}"
          done
        done

    - name: Test
      run: |
        image_name='${{ steps.build.outputs.image_name }}'
        image_dir='${{ steps.build.outputs.image_dir }}'

        # Extract image ids from manifest to test.
        ids="$(
          for tag in ${{ steps.build.outputs.tags }} ; do
            buildah manifest inspect "${image}:${tag}" \
              | jq -r '.manifests[]|.digest' \
              | while read id ; do
                  buildah images --format '{{.ID}}{{.Digest}}' \
                  | sed -n "s/${id}//p"
                done
          done
          )"

        # See Dockerfile.test for actual tests run
        ids="$( printf %s "${ids}" | sort -u )"
        for id in ${ids} ; do
          podman history "${id}"
          buildah bud \
            --build-arg=base="${id}" \
            --file=Dockerfile.test \
            "${image_dir}"
        done
        buildah rmi --prune || true

    - name: Check Tags
      run: |
        # FIX upstream: Quay.io does not support immutable images currently.
        #               => Try to use the REST API to check for duplicate tags and exit if they exist
        response="$(
          curl -sL \
            'https://quay.io/api/v1/repository/bioconda/${{ steps.build.outputs.image_name }}/tag/'
          )"

        # This might be the first time making this image (e.g., will likely
        # happen when using a test prefix), in which case there will be no
        # available images.
        if [ "$(echo "${response}" | jq -r '.error_message')" == "Requires authentication" ]; then
          exit 0
        fi

        existing_tags="$(
          printf %s "${response}" \
            | jq -r '.tags[]|select(.end_ts == null or .end_ts >= now)|.name'
          )" \
          || {
            printf %s\\n \
              'Could not get list of image tags.' \
              'Does the repository exist on Quay.io?' \
              'Quay.io REST API response was:' \
              "${response}"
            exit 1
          }
        for tag in ${{ steps.build.outputs.tags }} ; do
          case "${tag}" in
            latest | '${{ env.MAJOR_VERSION }}' ) ;;
            * )
              if printf %s "${existing_tags}" | grep -qxF "${tag}" ; then
                printf 'Tag %s already exists!\n' "${tag}"
                exit 1
              fi
          esac
        done

    - if: ${{ github.ref == 'refs/heads/test-push' }}
      name: Push
      uses: redhat-actions/push-to-registry@v2
      with:
        image: ${{ steps.build.outputs.image_name }}
        tags: ${{ steps.build.outputs.tags }}
        registry: quay.io/bioconda
        username: ${{ secrets.QUAY_BIOCONDA_USERNAME }}
        password: ${{ secrets.QUAY_BIOCONDA_TOKEN }}

    - if: ${{ github.ref == 'refs/heads/test-push' }}
      name: Test Pushed
      run: |

        image_name='${{ steps.build.outputs.image_name }}'
        image_dir='${{ steps.build.outputs.image_dir }}'
        ids="$(
          for tag in ${{ steps.build.outputs.tags }} ; do
            buildah manifest inspect "${image_name}:${tag}" \
              | jq -r '.manifests[]|.digest' \
              | while read id ; do
                  buildah images --format '{{.ID}}{{.Digest}}' \
                  | sed -n "s/${id}//p"
                done
          done
          )"
        ids="$( printf %s "${ids}" | sort -u )"
        for id in ${ids} ; do
          podman history "${id}"
          buildah bud \
            --build-arg=base="${id}" \
            --file=Dockerfile.test \
            "${image_dir}"
        done
        buildah rmi --prune || true