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ZoeLeibowitzZoeLeibowitz
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misc: Merge main into petsc branch
2 parents f5b60f2 + c71560b commit d0d0486

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‎.deploy_key.enc‎

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‎.github/actionlint.yaml‎

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self-hosted-runner:
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labels:
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- asv
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- amdgpu
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- nvidiagpu

‎.github/actions/docker-build/action.yaml‎

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name: Docker build action
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description: Composite action for building Devito Docker containers
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author: "Devito"
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inputs:
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# The only supported GHA input type is string
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file:
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description: "Dockerfile containing build instructions"
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required: true
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default: Dockerfile
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tag:
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description: "Tag to add to the built image"
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required: true
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base:
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description: "Base docker image to build on top of"
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default: ""
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args:
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description: "Arguments to pass to `docker build`"
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required: true
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default: ""
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outputs:
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unique:
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description: "Unique identifier for the CI run"
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value: ${{ steps.uniquetag.outputs.unique }}
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runs:
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using: "composite"
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steps:
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- id: uniquetag
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name: "Generate unique CI tag"
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shell: bash
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run: |
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UNIQUE=$(echo "${GITHUB_RUN_ID}_${GITHUB_RUN_ATTEMPT}" | cksum | cut -f 1 -d " ")
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echo "Unique ID: ${UNIQUE}"
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echo "unique=${UNIQUE}" >> "$GITHUB_OUTPUT"
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- id: dockerbuild
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name: "Build docker container"
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shell: bash
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env:
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BASE: ${{ inputs.base }}
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run: |
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docker build \
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--pull \
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--file ${{ inputs.file }} \
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--tag ${{ inputs.tag }}_${{ steps.uniquetag.outputs.unique }} \
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${BASE:+--build-arg base=$BASE} \
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${{ inputs.args }} \
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.

‎.github/actions/docker-clean/action.yaml‎

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name: Docker cleanup action
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description: Composite action for removing Docker images
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author: "Devito"
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inputs:
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# The only supported GHA input type is string
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uid:
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description: "Unique identifier output from docker-build action"
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required: true
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tag:
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description: "Tag of the built image to use"
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required: true
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runs:
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using: "composite"
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steps:
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- id: dockerclean
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name: "Cleanup docker image"
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shell: bash
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run: |
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docker image rm -f "${{ inputs.tag }}_${{ inputs.uid }}"

‎.github/actions/docker-run/action.yaml‎

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name: Docker run action
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description: Composite action for running commands in Docker containers
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author: "Devito"
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inputs:
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# The only supported GHA input type is string
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uid:
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description: "Unique identifier output from docker-build action"
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required: true
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tag:
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description: "Tag of the built image to use"
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required: true
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name:
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description: "Name substring for docker to use when running the command"
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default: ""
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args:
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description: "Arguments to pass to `docker run`, `--init -t --rm` are always added"
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required: true
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default: ""
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env:
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description: "Environment variables to set inside the docker container, one environment variable per line"
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required: true
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default: ""
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command:
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description: "Command to execute inside of the docker container"
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required: true
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runs:
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using: "composite"
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steps:
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- id: processenv
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name: Process environment variable list
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shell: bash
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env:
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ENV_INPUT: ${{ inputs.env }}
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run: |
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ENV_STRING=""
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# Read line by line with here string, safely handling spaces within the values
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while IFS= read -r LINE; do
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if [[ -n "$LINE" ]]; then
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ENV_STRING="$ENV_STRING --env $LINE"
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fi
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done <<< "$ENV_INPUT"
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# Remove the leading space from the first concatenation
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ENV_STRING="${ENV_STRING# }"
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echo "docker_environment_args=$ENV_STRING" >> "$GITHUB_OUTPUT"
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- id: dockerrun
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name: "Run command ${{ inputs.command }} in ${{ inputs.tag }} docker container"
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shell: bash
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env:
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NAME: ${{ inputs.name }}
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run: |
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docker run \
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--init -t --rm \
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${{ inputs.args }} \
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--name "ci-${NAME:-${{ inputs.tag }}}-${{ inputs.uid }}" \
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--env-file=docker/coverage.env \
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${{ steps.processenv.outputs.docker_environment_args }} \
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"${{ inputs.tag }}_${{ inputs.uid }}" \
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${{ inputs.command }}

‎.github/actions/readme.md‎

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# Devito Actions
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The Devito actions can either be used from the Github interface:
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```yaml
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uses: devitocodes/devito/.github/actions/docker-build@main
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```
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Or internally from within the repository:
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```yaml
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uses: ./.github/actions/docker-run
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```
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## `docker-build`
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Inputs:
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- `file`: Dockerfile containing build instructions (default: `Dockerfile`)
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- `tag`: Tag to add to the built image
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- `base`: Base docker image to build on top of
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- `args`: Arguments to pass to `docker build`
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Outputs:
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- `unique`: Unique identifier for the CI run (ie: `${{ steps.build.outputs.unique }}`)
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Example:
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```yaml
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jobs:
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test:
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steps:
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- id: build
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name: Build docker image for Devito
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uses: ./.github/actions/docker-build
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with:
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file: docker/Dockerfile.devito
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tag: tag-related-to-test-config
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base: base-image-to-build-from
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args: "--more-docker-build-args"
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```
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## `docker-run`
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Inputs:
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- `uid`: Unique identifier output from docker-build action
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- `tag`: Tag of the built image to use
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- `name`: Name substring for docker to use when running the command (optional)
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- `args`: Arguments to pass to `docker run`, `--init -t --rm` are always added
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- `env`: Environment variables to set inside the docker container, one environment variable per line
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-command: Command to execute inside of the docker container
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### Notes
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- The UID must be unique, easily obtained from build action
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- The tag must match built image, easily obtained from build action
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- If you provide a custom name `foo` the container name will be `ci-foo-UUUUUUUUUU` where UUUUUUUUUU is the UID
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- The default args `--init -t --rm` are _always_ added
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- Environment variables must be passed a single environment variable per line, best achieved with the (`|`) syntax in yaml
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- Only a single command is executed, not a list of commands. Using `;` or `&&` will result in subsequent commands being executed outside of the docker environment
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Example:
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```yaml
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jobs:
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test:
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steps:
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- name: Run a command in a previously built Docker container
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uses: ./.github/actions/docker-run
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with:
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uid: ${{ steps.build.outputs.unique }}
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tag: tag-related-to-test-config
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name: completely-optional-name
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args: "--more-docker-run-args"
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env: |
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FOO=value1
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BAR=value2
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command: |
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mpiexec -n 4 \
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python \
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my_complicated_script.py --arg1 -v
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```
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## `docker-clean`
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Inputs:
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- `uid`: Unique identifier output from docker-build action
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- `tag`: Tag of the built image to use
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### Notes
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- UID must be unique, easily obtained from build action
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- Tag must match built image, easily obtained from build action
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- Use `if: always()` to always clean up the image, even if the workflow fails
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Example:
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```yaml
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jobs:
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test:
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steps:
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- name: Cleanup Docker image
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if: always()
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uses: ./.github/actions/docker-clean
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with:
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uid: ${{ steps.build.outputs.unique }}
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tag: tag-related-to-test-config
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```

.github/dependabot.yml renamed to .github/dependabot.yaml

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directory: "/" # Location of package manifests
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schedule:
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interval: "daily"
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# Use the widen strategy to update requirements to avoid lower bound bump
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versioning-strategy: "widen"
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# Add assignees
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assignees:
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- "mloubout"

.github/release-drafter.yml renamed to .github/release-drafter.yaml

File renamed without changes.

.github/workflows/asv.yml renamed to .github/workflows/asv.yaml

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- name: Set VIRTUAL_ENV
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run: |
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echo "VIRTUAL_ENV=$ENVHOME/asv" >> $GITHUB_ENV
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echo "PATH=$VIRTUAL_ENV/bin:$PATH" >> $GITHUB_ENV
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echo "VIRTUAL_ENV=$ENVHOME/asv" >> "$GITHUB_ENV"
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echo "PATH=$VIRTUAL_ENV/bin:$PATH" >> "$GITHUB_ENV"
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- name: Set PATH
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run: |
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echo "PATH=$VIRTUAL_ENV/bin:$PATH" >> $GITHUB_ENV
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echo "PATH=$VIRTUAL_ENV/bin:$PATH" >> "$GITHUB_ENV"
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- name: Install dependencies
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run: |

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