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Merge pull request #73 from almahmoud/devel
Update weekly builder GHA
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‎.github/workflows/build_containers.yaml‎

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name: Build container image for GHCR
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on:
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push: {}
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push:
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branches:
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- devel
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- RELEASE_*
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workflow_dispatch:
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schedule:
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- cron: '0 18 * * 5'

‎.github/workflows/full-rstudio-build.yml‎

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# This is a basic workflow to help you get started with Actions
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name: Full rocker & bioc build
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# Controls when the action will run. Triggers the workflow on push or pull request
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# events but only for the master branch
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on:
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workflow_dispatch:
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inputs:
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rver:
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default: "devel"
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outname:
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default: "bioconductor_docker"
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schedule:
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- cron: '0 18 * * 5'
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# A workflow run is made up of one or more jobs that can run sequentially or in parallel
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jobs:
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# This workflow contains a single job called "build"
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build:
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strategy:
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matrix:
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arch: [amd64, arm64]
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# The type of runner that the job will run on
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runs-on: ubuntu-latest
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# Steps represent a sequence of tasks that will be executed as part of the job
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steps:
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# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
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- uses: actions/checkout@v3
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- name: Free up space
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run: |
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sudo rm -rf /usr/share/dotnet
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sudo rm -rf /usr/local/lib/android
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sudo rm -rf /opt/ghc
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sudo rm -rf /opt/hostedtoolcache/*
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sudo rm -rf /usr/local/.ghcup
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sudo rm -rf /usr/lib/google-cloud-sdk
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sudo rm -rf /usr/lib/firefox
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sudo rm -rf /opt/microsoft/powershell
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sudo rm -rf /usr/lib/jvm
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sudo rm -rf /usr/local/graalvm
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sudo rm -rf /etc/skel/.rustup /home/runner/.rustup /home/runneradmin/.rustup
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sudo rm -rf /usr/lib/llvm-13
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sudo rm -rf /usr/local/julia1.8.5
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sudo rm -rf /opt/microsoft/msedge
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sudo rm -rf /usr/lib/llvm-14
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sudo rm -rf /opt/az
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- name: Set up QEMU
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uses: docker/setup-qemu-action@v2
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with:
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platforms: arm64
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if: matrix.arch == 'arm64'
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- name: Login to GHCR
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uses: docker/login-action@v2
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Login to Dockerhub
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uses: docker/login-action@v2
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with:
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username: ${{ secrets.DOCKER_USERNAME }}
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password: ${{ secrets.DOCKER_PASSWORD }}
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- name: Extract metadata for container image
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id: meta
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uses: docker/metadata-action@v4
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with:
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images: ${{ github.repository_owner }}/${{ github.event.inputs.outname }}
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tags: |
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type=raw,value=${{ github.event.inputs.rver }}-${{ matrix.arch }}
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- name: Set comma-separated list with all repository names
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id: images
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run: |
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IMG=${{ steps.meta.outputs.tags }}
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REPOLIST="docker.io/$IMG,ghcr.io/$IMG"
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echo ghcr=$(echo "ghcr.io/$IMG") >> $GITHUB_OUTPUT
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SUB="_docker"
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# Also add alternative without _docker when in name
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echo list=$(if [[ $REPOLIST == *$SUB* ]]; then echo "$REPOLIST,$(echo $REPOLIST | sed 's/_docker//g')"; else echo $REPOLIST; fi) >> $GITHUB_OUTPUT
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## git clone rocker
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git clone --depth 1 https://github.com/rocker-org/rocker-versioned2
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sed -i 's#rocker/r-ver:${{ github.event.inputs.rver }}#ghcr.io/${{ github.repository_owner }}/rocker-r-ver:${{ github.event.inputs.rver }}-${{ matrix.arch }}#g' rocker-versioned2/dockerfiles/rstudio_${{ github.event.inputs.rver }}.Dockerfile
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sed -i 's#install_quarto.sh#install_quarto.sh || true#g' rocker-versioned2/dockerfiles/rstudio_${{ github.event.inputs.rver }}.Dockerfile
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v2
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with:
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platforms: linux/${{ matrix.arch }}
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- name: Build and load r-ver
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uses: docker/build-push-action@v3
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with:
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file: rocker-versioned2/dockerfiles/r-ver_${{ github.event.inputs.rver }}.Dockerfile
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context: rocker-versioned2
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push: true
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tags: ghcr.io/${{ github.repository_owner }}/rocker-r-ver:${{ github.event.inputs.rver }}-${{ matrix.arch }}
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platforms: linux/${{ matrix.arch }}
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- name: Build and load rstudio
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uses: docker/build-push-action@v3
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with:
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file: rocker-versioned2/dockerfiles/rstudio_${{ github.event.inputs.rver }}.Dockerfile
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context: rocker-versioned2
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push: true
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tags: ghcr.io/${{ github.repository_owner }}/rocker-rstudio:${{ github.event.inputs.rver }}-${{ matrix.arch }}
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platforms: linux/${{ matrix.arch }}
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- name: Build and push container image to all repos both arm64 and amd64
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uses: docker/build-push-action@v3
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with:
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build-args: |
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BASE_IMAGE=ghcr.io/${{ github.repository_owner }}/rocker-rstudio
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arm64_tag=${{ github.event.inputs.rver }}-${{ matrix.arch }}
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amd64_tag=${{ github.event.inputs.rver }}-${{ matrix.arch }}
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file: Dockerfile
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context: .
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push: true
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tags: ${{ steps.images.outputs.list }}
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labels: ${{ steps.meta.outputs.labels }}
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platforms: linux/${{ matrix.arch }}
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test-built-containers:
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strategy:
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matrix:
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arch: [arm64, amd64]
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# The type of runner that the job will run on
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runs-on: ubuntu-latest
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needs: build
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steps:
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- name: Get image name
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id: image
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run: |
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IMG=$(echo "${{ github.repository_owner }}/${{ github.event.inputs.outname }}:${{ github.event.inputs.rver }}-${{ matrix.arch }}")
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echo name=$IMG >> $GITHUB_OUTPUT
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cat << EOF > test.Dockerfile
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FROM $IMG as test
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USER root
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RUN mkdir -p /tmp/bioc_test && \
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apt list --installed | tee /tmp/bioc_test/aptlist && \
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Rscript -e "BiocManager::install(c('SummarizedExperiment','usethis','data.table','igraph','GEOquery'))" 2>&1 | tee /tmp/bioc_test/packages_install && \
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Rscript -e "BiocManager::install('gert'); require('gert')" 2>&1 | tee /tmp/bioc_test/gert_install
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FROM scratch as export
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COPY --from=test /tmp/bioc_test /tmp
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EOF
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- name: Set up QEMU
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uses: docker/setup-qemu-action@v2
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with:
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platforms: arm64
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if: matrix.arch == 'arm64'
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- name: Set up Docker Buildx
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uses: docker/setup-buildx-action@v2
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with:
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platforms: linux/${{ matrix.arch }}
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- name: Login to GHCR
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uses: docker/login-action@v2
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with:
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registry: ghcr.io
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username: ${{ github.actor }}
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password: ${{ secrets.GITHUB_TOKEN }}
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- name: Test via build
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id: dockerbuild
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uses: docker/build-push-action@v4
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with:
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file: test.Dockerfile
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context: .
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push: false
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load: false
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outputs: type=tar,dest=/tmp/image.tar
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tags: ${{ steps.image.outputs.name }}
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- run: |
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mkdir -p /tmp/contents
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cd /tmp/contents
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tar -xvf /tmp/image.tar
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sudo ls tmp/* | xargs -i bash -c "echo 'cat {}' && cat {}"
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- name: Push patch bump
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uses: nick-fields/retry@v2
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with:
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timeout_minutes: 10
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max_attempts: 50
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shell: bash
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command: |
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set -x
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git config --global --add safe.directory "$GITHUB_WORKSPACE"
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git config user.name github-actions
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git config user.email github-actions@github.com
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git pull origin main || git reset --hard origin/main
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sed -r -i 's/(^ARG BIOCONDUCTOR_PATCH=)([0-9]+)$/echo "\1$((\2+1))"/ge' Dockerfile
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git add Dockerfile
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git commit -m "Bump BIOCONDUCTOR_PATCH"
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git push
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‎.github/workflows/image-scan.yml‎

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schedule:
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- cron: "0 0 * * *"
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push:
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branches: master
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branches:
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- devel
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- RELEASE_*
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env:
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IMAGE_NAME: bioconductor/bioconductor_docker
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DEVEL_TAG: devel
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RELEASE_TAG: RELEASE_3_14
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jobs:
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scan-devel:
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scan-images:
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name: devel vulnerability scan
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runs-on: ubuntu-latest
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steps:
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- uses: azure/container-scan@v0
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name: devel scan
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with:
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image-name: ${{ env.IMAGE_NAME }}:${{ env.DEVEL_TAG }}
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- name: Extract branch name
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id: branch
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run: echo "name=$(echo ${GITHUB_REF#refs/heads/})" >> $GITHUB_OUTPUT
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scan-release:
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name: release vulnerability scan
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runs-on: ubuntu-latest
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steps:
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- uses: azure/container-scan@v0
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name: release scan
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name: devel scan
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with:
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image-name: ${{ env.IMAGE_NAME }}:${{ env.RELEASE_TAG }}
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image-name: ${{ env.IMAGE_NAME }}:${{ steps.branch.outputs.name }}

‎.github/workflows/test-images.yaml‎

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‎.github/workflows/weekly-devel-builder.yml‎

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‎.scripts/weekly_build.sh‎

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