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First page of new autamus packages (#411)
* first page of new autamus packages * retest with public images * update docs Signed-off-by: vsoch <[email protected]> Co-authored-by: vsoch <[email protected]>
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‎.github/workflows/test-container.yml‎

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types: [labeled]
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jobs:
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test-registry:
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changes:
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if: ${{ github.event.label.name == 'container-recipe' }}
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runs-on: ubuntu-latest
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outputs:
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changed_recipes: ${{ steps.files.outputs.added_modified }}
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steps:
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- name: Find changed recipes
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id: files
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uses: jitterbit/get-changed-files@b17fbb00bdc0c0f63fcf166580804b4d2cdc2a42
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with:
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format: 'json'
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test-recipes:
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needs:
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- changes
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runs-on: ubuntu-latest
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strategy:
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# Keep going on other deployments if anything bloops
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fail-fast: false
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matrix:
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changed_recipe: ${{ fromJson(needs.changes.outputs.changed_recipes) }}
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name: Check ${{ matrix.changed_recipe }}
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steps:
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- name: Continue
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run: |
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# Continue if we have a changed recipe file
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if [[ "${{ matrix.changed_recipe }}" = registry* ]]; then
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echo "keepgoing=true" >> $GITHUB_ENV
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fi
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- name: Checkout
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if: ${{ env.keepgoing == 'true' }}
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uses: actions/checkout@v2
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- name: Make Space For Build
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if: ${{ env.keepgoing == 'true' }}
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run: |
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sudo rm -rf /usr/share/dotnet
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sudo rm -rf /opt/ghc
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- name: Install Dependencies
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if: ${{ env.keepgoing == 'true' }}
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run: |
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sudo apt-get install lua5.2 liblua5.2-dev lua-filesystem lua-posix tcl tcl-dev
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- name: Install Lmod
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if: ${{ env.keepgoing == 'true' }}
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run: |
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PKG_VERSION=8.4.27
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PKG_URL="https://github.com/TACC/Lmod/archive/${PKG_VERSION}.tar.gz"
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./configure --prefix=/usr/share && make && make install
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- uses: eWaterCycle/setup-singularity@v6
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if: ${{ env.keepgoing == 'true' }}
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name: Install Singularity
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with:
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singularity-version: 3.6.4
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- name: Derive number of commits
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run: |
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cd /opt
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branch="${{ github.head_ref }}"
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git config --global user.email "github-actions"
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git config --global user.name "[email protected]"
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git clone -b main https://github.com/singularityhub/singularity-hpc
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cd singularity-hpc
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git checkout -b $branch
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git pull origin $branch
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commits=$(git log --oneline "$branch" ^main | wc -l)
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echo "Found $commits since main"
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cd registry
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touch changes.txt
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# Note that you can also do: git diff --name-only $branch..main .
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# We show the count of commits as a sanity check to the developer
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for container_yaml in $(git diff --name-only HEAD~$commits..HEAD .); do
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echo $container_yaml >> changes.txt
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done
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cat changes.txt
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- name: Save changelist
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uses: actions/upload-artifact@v2
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with:
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name: changes.txt
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path: /opt/singularity-hpc/registry/changes.txt
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- name: Create conda environment
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if: ${{ env.keepgoing == 'true' }}
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run: conda create --quiet -c conda-forge --name shpc spython
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- uses: actions/checkout@v2
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if: ${{ env.keepgoing == 'true' }}
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- name: Install shpc
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if: ${{ env.keepgoing == 'true' }}
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run: |
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export PATH="/usr/share/miniconda/bin:$PATH"
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source activate shpc
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pip install -e .
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- name: Download changelist
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uses: actions/download-artifact@v2
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with:
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name: changes.txt
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- name: Run module tests
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if: ${{ env.keepgoing == 'true' }}
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run: |
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export PATH="/usr/share/miniconda/bin:$PATH"
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source activate shpc
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cd registry
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for container_yaml in $(cat ../changes.txt); do
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module=$(dirname $container_yaml)
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module=$(echo "${module/registry\//}")
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echo "Testing $module"
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shpc test --template ../shpc/tests/test-registry-module.sh --commands $module
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done
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container_yaml="${{ matrix.changed_recipe }}"
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module=$(dirname $container_yaml)
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module=$(echo "${module/registry\//}")
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echo "Testing $module"
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shpc test --template ../shpc/tests/test-registry-module.sh --commands $module

‎docs/getting_started/developer-guide.rst‎

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4. You should generally choose smaller images (if possible) and define aliases (entrypoints) for the commands that you think would be useful.
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A shell entrypoint for the container will be generated automatically.
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When you open a pull request, if your branch prefix starts with ``recipe`` the PR
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will test your recipe automatically. If you forget, you can ask a maintainer to apply
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the ``container-recipe`` label and it will test accordingly.
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When you open a pull request, a maintainer can apply
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the ``container-recipe`` label and it will test your new or updated recipes accordingly.
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Once your recipe is added to the repository, the versions will be automatically
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updated with a nightly run. This means that you can pull the repository to get
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updated recipes, and then check for updates (the bot to do this is not developed yet):

‎registry/ghcr.io/autamus/ed/container.yaml‎

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docker: ghcr.io/autamus/ed
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url: https://github.com/orgs/autamus/packages/container/package/ed
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maintainer: "@vsoch"
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description: "GNU ed is a line-oriented text editor used to create, display, modify and otherwise manipulate text files, both interactively and via shell scripts https://www.gnu.org/software/ed."
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latest:
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"1.4": sha256:ec791627353859a7569abd79c9b1e1f01032e2a363afc925a85849b60e5aec27
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tags:
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"1.4": sha256:ec791627353859a7569abd79c9b1e1f01032e2a363afc925a85849b60e5aec27
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aliases:
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ed: /opt/view/bin/ed
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red: /opt/view/bin/red

‎registry/ghcr.io/autamus/emacs/container.yaml‎

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docker: ghcr.io/autamus/emacs
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url: https://github.com/orgs/autamus/packages/container/package/emacs
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maintainer: "@vsoch"
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description: The Emacs programmable text editor. https://www.gnu.org/software/emacs
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latest:
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"27.2": sha256:a1fa851f9dbd3ba0474fd8f0365f23ba5cedc46095c5f6dedfa5fd433652a84a
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tags:
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"27.2": sha256:a1fa851f9dbd3ba0474fd8f0365f23ba5cedc46095c5f6dedfa5fd433652a84a
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aliases:
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ebrowse: /opt/view/bin/ebrowse
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emacs: /opt/view/bin/emacs
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emacsclient: /opt/view/bin/emacsclient
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etags: /opt/view/bin/etags

‎registry/ghcr.io/autamus/gawk/container.yaml‎

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docker: ghcr.io/autamus/gawk
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url: https://github.com/orgs/autamus/packages/container/package/gawk
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maintainer: '@vsoch'
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description: gawk is the GNU implementation of awk. The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code. https://www.gnu.org/software/gawk/
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latest:
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5.10.0: sha256:502eebe2f9a93ce7bb06fc6f97f8ce8dd76802a380ade9b4c71f0d3f15ef0a45
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tags:
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5.10.0: sha256:502eebe2f9a93ce7bb06fc6f97f8ce8dd76802a380ade9b4c71f0d3f15ef0a45
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aliases:
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gawk: /opt/view/bin/gawk

‎registry/ghcr.io/autamus/htop/container.yaml‎

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docker: ghcr.io/autamus/htop
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url: https://github.com/orgs/autamus/packages/container/package/htop
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maintainer: '@vsoch'
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description: htop is an interactive text-mode process viewer for Unix systems. https://github.com/hishamhm/htop
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latest:
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2.2.0: sha256:017e8c7e87614dddb1fd01fb1892d40947501596504bf4d27af71c677d122851
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tags:
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2.2.0: sha256:017e8c7e87614dddb1fd01fb1892d40947501596504bf4d27af71c677d122851
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aliases:
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htop: /opt/view/bin/htop

‎registry/ghcr.io/autamus/py-libensemble/container.yaml‎

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docker: ghcr.io/autamus/py-libensemble
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url: https://github.com/orgs/autamus/packages/container/package/py-libensemble
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maintainer: '@vsoch'
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description: Library for managing ensemble-like collections of computations.
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latest:
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"0.7.2": sha256:ac19eb043b9b185e299616ed642d0b9f350c2373ac8b3bb3c415439b89cc8801
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tags:
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"0.7.2": sha256:ac19eb043b9b185e299616ed642d0b9f350c2373ac8b3bb3c415439b89cc8801

‎registry/ghcr.io/autamus/py-petsc4py/container.yaml‎

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docker: ghcr.io/autamus/py-petsc4py
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url: https://github.com/orgs/autamus/packages/container/package/py-petsc4py
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maintainer: '@vsoch'
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description: This package provides Python bindings for the PETSc package.
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latest:
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"3.15.1": sha256:4a6b58e25f765f191c2ddad01ed33f4dee4de953ef7e59ff1f31e4e6d0c23f8a
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tags:
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"3.15.1": sha256:4a6b58e25f765f191c2ddad01ed33f4dee4de953ef7e59ff1f31e4e6d0c23f8a

‎registry/ghcr.io/autamus/rempi/container.yaml‎

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docker: ghcr.io/autamus/rempi
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url: https://github.com/orgs/autamus/packages/container/package/rempi
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maintainer: '@vsoch'
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description: ReMPI is a record-and-replay tool for MPI applications.
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latest:
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"1.1.0": sha256:13f3ae61146c389b0fef9e6e1f331a8f229cc15c886a215c9437249301903400
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tags:
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"1.1.0": sha256:13f3ae61146c389b0fef9e6e1f331a8f229cc15c886a215c9437249301903400
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aliases:
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rempi: /opt/view/bin/rempi
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rempi_record: /opt/view/bin/rempi_record
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rempi_replay: /opt/view/bin/rempi_replay
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reset: /opt/view/bin/reset

‎registry/ghcr.io/autamus/rsync/container.yaml‎

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docker: ghcr.io/autamus/rsync
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url: https://github.com/orgs/autamus/packages/container/package/rsync
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maintainer: '@vsoch'
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description: An open source utility that provides fast incremental file transfer. https://rsync.samba.org/
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latest:
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"3.2.2": sha256:99c4780710b1d844ca8998dea4c59b2d3b54c28ac206dc3ee580ca2c34f455d1
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tags:
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"3.2.2": sha256:99c4780710b1d844ca8998dea4c59b2d3b54c28ac206dc3ee580ca2c34f455d1
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aliases:
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rsync: /opt/view/bin/rsync
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rsync-ssl: /opt/view/bin/rsync-ssl

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