build-images.yml

# Build all container images.
#
name: Build images
concurrency:
  group: ${{ github.workflow }}-${{ github.ref }}
  cancel-in-progress: true

on:
  pull_request:
    paths-ignore:
    - '.circleci/**'
    - 'docs/**'
    - 'test/**'
env:
  # Used to override BIOCONDA_UTILS_VERSION in images/versions.sh
  BIOCONDA_UTILS_VERSION: ${{ github.event.release && github.event.release.tag_name || github.head_ref || github.ref_name }}

jobs:

  # JOBS FOR BUILDING IMAGES
  # ----------------------------------------------------------------------
  # These jobs will build images for archs, put them into a manifest, and push
  # that to GitHub Container Registry. Later, the testing jobs will test and
  # push to quay.io.

  build-base-debian:
    name: Build base-debian
    runs-on: ubuntu-22.04
    outputs:
      # A note on these TAG_EXISTS_* outputs: these allow subsequent jobs to
      # change behavior (e.g., skip building or skip pushing to ghcr) depending
      # on whether an image has already been created.
      TAG_EXISTS_base-debian: ${{ steps.base-debian.outputs.TAG_EXISTS_base-debian }}
    steps:

    - uses: actions/checkout@v4
      with:
        fetch-depth: 0

    - name: Install qemu dependency
      run: |
        sudo apt-get update
        sudo apt-get install -y qemu-user-static

    - name: base-debian
      id: base-debian
      run: |
        source images/versions.sh
        if [ $(tag_exists $BASE_DEBIAN_IMAGE_NAME $BASE_TAG) ]; then
          echo "TAG_EXISTS_base-debian=true" >> $GITHUB_OUTPUT
        else
          cd images && bash build.sh base-glibc-debian-bash
        fi

    - name: push to ghcr
      if: '${{ ! steps.base-debian.outputs.TAG_EXISTS_base-debian }}'
      run: |
        echo '${{ secrets.GITHUB_TOKEN }}' | podman login ghcr.io -u '${{ github.actor }}' --password-stdin
        source images/versions.sh
        push_to_ghcr $BASE_DEBIAN_IMAGE_NAME $BASE_TAG

  build-base-busybox:
    name: Build base-busybox
    runs-on: ubuntu-22.04
    outputs:
      TAG_EXISTS_base-busybox: ${{ steps.base-busybox.outputs.TAG_EXISTS_base-busybox }}
    steps:

    - uses: actions/checkout@v4
      with:
        fetch-depth: 0

    - name: Install qemu dependency
      run: |
        sudo apt-get update
        sudo apt-get install -y qemu-user-static

    - name: base-busybox
      id: base-busybox
      run: |
        source images/versions.sh
        if [ $(tag_exists $BASE_BUSYBOX_IMAGE_NAME $BASE_TAG) ]; then
          echo "TAG_EXISTS_base-busybox=true" >> $GITHUB_OUTPUT
        else
          cd images && bash build.sh base-glibc-busybox-bash
        fi

    - name: push to ghcr
      if: '${{ ! steps.base-busybox.outputs.TAG_EXISTS_base-busybox }}'
      run: |
        echo '${{ secrets.GITHUB_TOKEN }}' | podman login ghcr.io -u '${{ github.actor }}' --password-stdin
        source images/versions.sh
        push_to_ghcr $BASE_BUSYBOX_IMAGE_NAME $BASE_TAG

  build-build-env:
    name: Build build-env
    outputs:
      TAG_EXISTS_build-env: ${{ steps.build-env.outputs.TAG_EXISTS_build-env }}
    runs-on: ubuntu-22.04
    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0

    - name: Install qemu dependency
      run: |
        sudo apt-get update
        sudo apt-get install -y qemu-user-static

    - name: build-env
      id: build-env
      run: |
        source images/versions.sh
        if [ $(tag_exists $BUILD_ENV_IMAGE_NAME $BIOCONDA_IMAGE_TAG) ]; then
          echo "TAG_EXISTS_build-env=true" >> $GITHUB_OUTPUT
        else
          cd images && bash build.sh bioconda-utils-build-env-cos7
        fi

    - name: push to ghcr
      if: '${{ ! steps.build-env.outputs.TAG_EXISTS_build-env }}'
      run: |
        echo '${{ secrets.GITHUB_TOKEN }}' | podman login ghcr.io -u '${{ github.actor }}' --password-stdin
        source images/versions.sh
        push_to_ghcr $BUILD_ENV_IMAGE_NAME $BIOCONDA_IMAGE_TAG

  build-create-env:
    name: Build create-env
    needs: [build-build-env, build-base-busybox]
    outputs:
      TAG_EXISTS_create-env: ${{ steps.create-env.outputs.TAG_EXISTS_create-env }}
    runs-on: ubuntu-22.04
    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0

    - name: Install qemu dependency
      run: |
        sudo apt-get update
        sudo apt-get install -y qemu-user-static

    - name: Build create-env
      id: create-env
      run: |
        source images/versions.sh
        echo '${{ secrets.GITHUB_TOKEN }}' | podman login ghcr.io -u '${{ github.actor }}' --password-stdin
        if [ $(tag_exists $CREATE_ENV_IMAGE_NAME $BIOCONDA_IMAGE_TAG) ]; then
          echo "TAG_EXISTS_create-env=true" >> $GITHUB_OUTPUT
        else
          cd images && bash build.sh create-env
        fi

    - name: push to ghcr
      if: '${{ ! steps.create-env.outputs.TAG_EXISTS_create-env }}'
      run: |
        echo '${{ secrets.GITHUB_TOKEN }}' | podman login ghcr.io -u '${{ github.actor }}' --password-stdin
        source images/versions.sh
        push_to_ghcr $CREATE_ENV_IMAGE_NAME $BIOCONDA_IMAGE_TAG


  # END OF BUILDING IMAGES
  # ----------------------------------------------------------------------
  # START TESTING
  # These testing jobs will run the respective Dockerfile.test in each image
  # directory.

  test:
    name: test bioconda-utils with images
    runs-on: ubuntu-20.04
    needs: [build-base-debian, build-base-busybox, build-build-env, build-create-env]
    steps:

    - uses: actions/checkout@v4
      with:
        fetch-depth: 0

    # Clone bioconda-recipes to use as part of the tests.
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0
        repository: bioconda/bioconda-recipes
        path: recipes

    - name: set path
      run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH

    - name: Install bioconda-utils
      run: |
        export BIOCONDA_DISABLE_BUILD_PREP=1
        wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
        bash install-and-set-up-conda.sh
        eval "$(conda shell.bash hook)"
        mamba create -n bioconda -y --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
        conda activate bioconda
        python setup.py install

    - name: test
      run: |
        eval "$(conda shell.bash hook)"
        conda activate bioconda

        source images/versions.sh

        # Figure out which registry to use for each image, based on what was built.
        [ ${{ needs.build-build-env.outputs.TAG_EXISTS_build-env }} ] && BUILD_ENV_REGISTRY='quay.io/bioconda' || BUILD_ENV_REGISTRY="ghcr.io/bioconda"
        [ ${{ needs.build-create-env.outputs.TAG_EXISTS_create-env }} ] && CREATE_ENV_REGISTRY='quay.io/bioconda' || CREATE_ENV_REGISTRY="ghcr.io/bioconda"
        [ ${{ needs.build-base-busybox.outputs.TAG_EXISTS_base_busybox }} ] && DEST_BASE_IMAGE_REGISTRY='quay.io/bioconda' || DEST_BASE_REGISTRY="ghcr.io/bioconda"

        # Tell mulled-build which image to use
        export DEST_BASE_IMAGE="${DEST_BASE_IMAGE_REGISTRY}/${BASE_BUSYBOX_IMAGE_NAME}:${BASE_TAG}"

        # Build a package with containers.
        cd recipes
        bioconda-utils build \
        --docker-base-image "${BUILD_ENV_REGISTRY}/${BUILD_ENV_IMAGE_NAME}:${BIOCONDA_IMAGE_TAG}" \
        --mulled-conda-image "${CREATE_ENV_REGISTRY}/${CREATE_ENV_IMAGE_NAME}:${BIOCONDA_IMAGE_TAG}" \
        --packages seqtk \
        --docker \
        --mulled-test \
        --force

    # END TESTING
    # ------------------------------------------------------------------------
    # START PUSHING IMAGES

    # For these push steps, a repository must first exist on quay.io/bioconda
    # AND that repository must also be configured to allow write access for the
    # appropriate service account. This must be done by a user with admin
    # access to quay.io/bioconda.
    #
    # This uses the TAG_EXISTS_* outputs from previous jobs to determine if
    # a push to quay.io should happen.

  push:
    name: push images
    runs-on: ubuntu-20.04
    needs: [build-base-debian, build-base-busybox, build-build-env, build-create-env, test]
    steps:

    - uses: actions/checkout@v4
      with:
        fetch-depth: 0

    - name: push base-debian
      if: ${{ ! needs.base-debian.outputs.TAG_EXISTS_base-debian }}
      run: |
        echo '${{ secrets.QUAY_BIOCONDA_TOKEN }}' | podman login quay.io -u '${{ secrets.QUAY_BIOCONDA_USERNAME }}' --password-stdin
        source images/versions.sh
        move_from_ghcr_to_quay ${BASE_DEBIAN_IMAGE_NAME} ${BASE_TAG}


    - name: push base-busybox
      if: ${{ ! needs.base-busybox.outputs.TAG_EXISTS_base-busybox }}
      run: |
        echo '${{ secrets.QUAY_BIOCONDA_TOKEN }}' | podman login quay.io -u '${{ secrets.QUAY_BIOCONDA_USERNAME }}' --password-stdin
        source images/versions.sh
        move_from_ghcr_to_quay ${BASE_BUSYBOX_IMAGE_NAME} ${BASE_TAG}

    - name: push create-env
      if: ${{ ! needs.create-env.outputs.TAG_EXISTS_create-env }}
      run: |
        echo '${{ secrets.QUAY_BIOCONDA_TOKEN }}' | podman login quay.io -u '${{ secrets.QUAY_BIOCONDA_USERNAME }}' --password-stdin
        source images/versions.sh
        move_from_ghcr_to_quay ${CREATE_ENV_IMAGE_NAME} ${BIOCONDA_IMAGE_TAG}

    - name: push build-env
      if: ${{ ! needs.build-env.outputs.TAG_EXISTS_build-env }}
      run: |
        echo '${{ secrets.QUAY_BIOCONDA_TOKEN }}' | podman login quay.io -u '${{ secrets.QUAY_BIOCONDA_USERNAME }}' --password-stdin
        source images/versions.sh
        move_from_ghcr_to_quay ${BUILD_ENV_IMAGE_NAME} ${BIOCONDA_IMAGE_TAG}