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| # 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: | ||
| BIOCONDA_UTILS_VERSION: ${{ github.event.release && github.event.release.tag_name || github.head_ref || github.ref_name }} | ||
| jobs: | ||
| # JOBS FOR BUILDING IMAGES | ||
| # ---------------------------------------------------------------------- | ||
| # Build images for all archs, upload as artifacts. | ||
| demo: | ||
| name: demo | ||
| runs-on: ubuntu-24.04 | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
| - name: export env vars | ||
| run: | | ||
| source images/versions.sh | ||
| for var in $(grep "# GITHUB_ENV$" $HERE | cut -f1 -d "="); do | ||
| echo "$var=\"${!var}\"" >> $GITHUB_ENV | ||
| done | ||
| - name: check env vars | ||
| run: | | ||
| set -x | ||
| echo $ARCHS | ||
| echo $BASE_BUSYBOX_IMAGE_NAME | ||
| echo $BIOCONDA_IMAGE_TAG | ||
| mkdir -p image-artifacts | ||
| echo hi > image-artifacts/$BASE_BUSYBOX_IMAGE_NAME | ||
| - name: Upload artifact | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: demo | ||
| path: | | ||
| image-artifacts/${{ env.BASE_BUSYBOX_IMAGE_NAME }} | ||
| next: | ||
| - name: Download artifacts | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| pattern: demo | ||
| - name: show | ||
| run: | | ||
| cat image-artifacts/$BASE_BUSYBOX_IMAGE_NAME | ||
| exit 1 | ||
| build-base-busybox: | ||
| name: Build base-busybox | ||
| runs-on: ubuntu-24.04 | ||
| container: | ||
| # travier/podman-action contains newer podman/buildah versions. | ||
| image: quay.io/travier/podman-action | ||
| options: --privileged | ||
| outputs: | ||
| TAG_EXISTS_base-busybox: ${{ steps.base-busybox.outputs.TAG_EXISTS_base-busybox }} | ||
| steps: | ||
| - uses: actions/checkout@v4 | ||
| with: | ||
| fetch-depth: 0 | ||
| - name: Set up QEMU | ||
| run: | | ||
| podman run --rm --privileged \ | ||
| docker.io/tonistiigi/binfmt --install arm64 | ||
| - name: Install Tools | ||
| run: | | ||
| set -eu | ||
| # jq nor git are not installed in travier/podman-action | ||
| dnf install -qy \ | ||
| jq | ||
| rpm -q \ | ||
| buildah podman \ | ||
| coreutils findutils sed \ | ||
| curl jq \ | ||
| | ( | ||
| while read -r line ; do | ||
| printf %s\\n "${line}" | ||
| case "${line}" in (*' not installed'*) | ||
| err=1 ;; | ||
| esac | ||
| done | ||
| exit "${err-0}" | ||
| ) | ||
| - name: export env vars | ||
| run: | | ||
| source images/versions.sh | ||
| for var in $(grep "# GITHUB_ENV$" $HERE | cut -f1 -d "="); do | ||
| echo "$var=\"${!var}\"" >> $GITHUB_ENV | ||
| done | ||
| - 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" >> $GITHUB_OUTPUT | ||
| else | ||
| cd images && bash build.sh base-glibc-busybox-bash | ||
| fi | ||
| - name: Upload artifact | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: base-busybox | ||
| path: | | ||
| image-artifacts/${{ env.BASE_BUSYBOX_IMAGE_NAME }}*.tar | ||
| build-build-env: | ||
| name: Build build-env | ||
| needs: build-base-busybox | ||
| 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: Download artifacts | ||
| uses: actions/download-artifact@v4 | ||
| with: | ||
| pattern: base-busybox | ||
| - name: Install qemu dependency | ||
| run: | | ||
| sudo apt-get update | ||
| sudo apt-get install -y qemu-user-static | ||
| - name: Load images | ||
| run: | | ||
| for image in image-artifacts/*.tar; do | ||
| podman load -i $image | ||
| done | ||
| - 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 build-env | ||
| fi | ||
| - name: Upload artifact | ||
| uses: actions/upload-artifact@v4 | ||
| with: | ||
| name: build-env | ||
| path: | | ||
| image-artifacts/tmp-build-env-*.tar | ||
| # build-create-env: | ||
| # name: Build create-env | ||
| # needs: [build-build-env, build-base-busybox] | ||
| # outputs: | ||
| # TAG_EXISTS_create-env: ${{ steps.create-env.outputs.TAG_EXISTS_create-env }} | ||
| # runs-on: ubuntu-24.04 | ||
| # container: | ||
| # # travier/podman-action contains newer podman/buildah versions. | ||
| # image: quay.io/travier/podman-action | ||
| # options: --privileged | ||
| # steps: | ||
| # - uses: actions/checkout@v4 | ||
| # with: | ||
| # fetch-depth: 0 | ||
| # - name: Set up QEMU | ||
| # run: | | ||
| # podman run --rm --privileged \ | ||
| # docker.io/tonistiigi/binfmt --install arm64 | ||
| # - name: Install Tools | ||
| # run: | | ||
| # set -eu | ||
| # # jq is not installed in travier/podman-action | ||
| # dnf install -qy \ | ||
| # jq | ||
| # rpm -q \ | ||
| # buildah podman \ | ||
| # coreutils findutils sed \ | ||
| # curl jq \ | ||
| # | ( | ||
| # while read -r line ; do | ||
| # printf %s\\n "${line}" | ||
| # case "${line}" in (*' not installed'*) | ||
| # err=1 ;; | ||
| # esac | ||
| # done | ||
| # exit "${err-0}" | ||
| # ) | ||
| # - 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 $BIOCONDA_IMAGE_TAG | ||
| # # END OF BUILDING IMAGES | ||
| # # ---------------------------------------------------------------------- | ||
| # # START TESTING | ||
| # # These testing jobs will run the respective Dockerfile.test in each image | ||
| # # directory. | ||
| # test: | ||
| # name: test bioconda-utils with images | ||
| # runs-on: ubuntu-24.04 | ||
| # needs: [build-base-debian, build-base-busybox, build-build-env, build-create-env] | ||
| # steps: | ||
| # - uses: actions/checkout@v4 | ||
| # with: | ||
| # fetch-depth: 0 | ||
| # - name: Install bioconda-utils | ||
| # run: | | ||
| # export BIOCONDA_DISABLE_BUILD_PREP=1 | ||
| # BRANCH=simplify-unify-containers | ||
| # wget https://raw.githubusercontent.com/bioconda/bioconda-common/${BRANCH}/{common,install-and-set-up-conda,configure-conda}.sh | ||
| # source images/versions.sh | ||
| # # Ensure install-and-set-up-conda uses same version as in the container | ||
| # # (which uses images/versions.sh | ||
| # export BIOCONDA_UTILS_TAG=$BIOCONDA_UTILS_VERSION | ||
| # bash install-and-set-up-conda.sh | ||
| # eval "$(conda shell.bash hook)" | ||
| # conda 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. If we built an image | ||
| # # during this workflow run, it was pushed to ghcr.io as a staging area. | ||
| # # If it was not built during this run, then we use the exissting one on | ||
| # # quay.io. | ||
| # [ ${{ 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_REGISTRY='quay.io/bioconda' || DEST_BASE_REGISTRY="ghcr.io/bioconda" | ||
| # [ ${{ needs.build-base-debian.outputs.TAG_EXISTS_base_debian }} ] && DEST_EXTENDED_BASE_REGISTRY='quay.io/bioconda' || DEST_EXTENDED_BASE_REGISTRY="ghcr.io/bioconda" | ||
| # # Tell mulled-build which image to use | ||
| # # | ||
| # # DEST_BASE_IMAGE, DEFAULT_BASE_IMAGE, and DEFAULT_EXTENDED_BASE_IMAGE | ||
| # # are hard-coded by mulled-build, e.g. | ||
| # # https://github.com/galaxyproject/galaxy/blob/957f6f5475f8f96c6af110be10791b5acab3a0df/lib/galaxy/tool_util/deps/mulled/mulled_build.py#L62-L71 | ||
| # # We keep DEST_BASE_IMAGE unset so it defaults to DEFAULT_BASE_IMAGE or | ||
| # # DEFAULT_EXTENDED_BASE_IMAGE. | ||
| # export DEFAULT_BASE_IMAGE="${DEST_BASE_REGISTRY}/${BASE_BUSYBOX_IMAGE_NAME}:${BASE_TAG}" | ||
| # export DEFAULT_EXTENDED_BASE_IMAGE="${DEST_EXTENDED_BASE_REGISTRY}/${BASE_DEBIAN_IMAGE_NAME}:${BASE_TAG}" | ||
| # export BUILD_ENV_IMAGE="${BUILD_ENV_REGISTRY}/${BUILD_ENV_IMAGE_NAME}:${BIOCONDA_IMAGE_TAG}" | ||
| # export CREATE_ENV_IMAGE="${CREATE_ENV_REGISTRY}/${CREATE_ENV_IMAGE_NAME}:${BIOCONDA_IMAGE_TAG}" | ||
| # source images/env_var_inventory.sh | ||
| # [ command -v podman > /dev/null ] && podman images | ||
| # [ command -v docker > /dev/null ] && docker images | ||
| # py.test --durations=0 test/ -v --log-level=DEBUG -k "docker" --tb=native | ||
| # # 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 | ||
| # if: github.ref == 'refs/heads/master' | ||
| # runs-on: ubuntu-24.04 | ||
| # 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} | ||
