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Merge pull request #1 from uc-cdis/feat/init
Feat/init
2 parents 1ee3010 + b44b53b commit 52063cc

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‎.dockerignore‎

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# Ignore unnecessary files inside allowed directories
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# This should go after the allowed directories
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**/*.pyc
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**/*.egg-info
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**/__pycache__

‎.github/workflows/automation.yml‎

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# push will run on every pushed commit to any branch (so this will rerun the tests
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# once a branch gets merged to main in addition to any new commits on any branch)
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on: push
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name: Automation
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concurrency:
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group: '${{ github.workflow }} @ ${{ github.event.pull_request.head.label || github.head_ref || github.ref }}'
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cancel-in-progress: true
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jobs:
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post-commit-check:
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name: Post-Commit Validation of Pre-Commit Checks (Includes Linting)
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uses: uc-cdis/.github/.github/workflows/pre_commit.yaml@fix/linting
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with:
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UV_VERSION: '0.10.9'
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JUST_VERSION: '1.46.0'
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secrets: inherit
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security:
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name: Security Pipeline
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uses: uc-cdis/.github/.github/workflows/securitypipeline.yaml@master
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with:
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python-poetry: 'true'
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secrets: inherit
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unit-test:
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name: Python Unit Test
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# TODO: enable when security and post-commit work reliably
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# needs: [ security, post-commit-check ]
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runs-on: ubuntu-latest
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env:
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UV_VERSION: '0.10.9'
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JUST_VERSION: '1.46.0'
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PYTHON_VERSION: '3.13'
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PGHOST: 'localhost'
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PGPORT: 5432
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PGUSER: 'postgres'
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steps:
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- name: Check out code
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uses: actions/checkout@v6
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with:
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persist-credentials: false
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- name: Set up python
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uses: actions/setup-python@v6
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with:
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python-version: ${{ env.PYTHON_VERSION }}
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- name: python info
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run: python --version
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- name: Install uv
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run: |
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curl -LsSf https://astral.sh/uv/${{ env.UV_VERSION }}/install.sh | sh
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- uses: taiki-e/install-action@v2
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with:
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tool: just@${{ env.JUST_VERSION }}
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- name: just setup
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run: |
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just setup
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- name: just install
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run: |
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just install
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- name: just test
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run: |
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just test
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image-build-push-1:
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name: Build Image and Push - Gen3 Embeddings
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uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@fix/linting
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needs: [post-commit-check, security, unit-test]
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with:
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BUILD_PLATFORMS: "linux/amd64"
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DOCKERFILE_BUILD_CONTEXT: '.'
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BUILD_ARGS: SERVICE_NAME=gen3_embeddings
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OVERRIDE_REPO_NAME: gen3_embeddings
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secrets:
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ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
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ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}
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QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }}
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QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }}
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image-build-push-2:
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name: Build Image and Push - Gen3 Inference
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uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@fix/linting
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needs: [post-commit-check, security, unit-test]
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with:
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BUILD_PLATFORMS: "linux/amd64"
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DOCKERFILE_BUILD_CONTEXT: '.'
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BUILD_ARGS: SERVICE_NAME=gen3_inference
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OVERRIDE_REPO_NAME: gen3_inference
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secrets:
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ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
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ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}
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QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }}
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QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }}
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image-build-push-3:
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name: Build Image and Push - Gen3 AI Model Repo
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uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@fix/linting
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needs: [post-commit-check, security, unit-test]
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with:
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BUILD_PLATFORMS: "linux/amd64"
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DOCKERFILE_BUILD_CONTEXT: '.'
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BUILD_ARGS: SERVICE_NAME=gen3_ai_model_repo
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OVERRIDE_REPO_NAME: gen3_ai_model_repo
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secrets:
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ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }}
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ECR_AWS_SECRET_ACCESS_KEY: ${{ secrets.ECR_AWS_SECRET_ACCESS_KEY }}
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QUAY_USERNAME: ${{ secrets.QUAY_USERNAME }}
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QUAY_ROBOT_TOKEN: ${{ secrets.QUAY_ROBOT_TOKEN }}

‎.github/workflows/markdown_validation.yml‎

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name: Markdown validation
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on:
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pull_request:
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types:
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- opened
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- reopened
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- synchronize
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paths:
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- .github/workflows/validate_markdown.yaml
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- "**.md"
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jobs:
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markdown_validation:
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name: Markdown validation
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uses: uc-cdis/.github/.github/workflows/validate_markdown.yaml@master

‎.gitignore‎

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.abstra/
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# Visual Studio Code
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# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
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# Visual Studio Code specific template is maintained in a separate VisualStudioCode.gitignore
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# that can be found at https://github.com/github/gitignore/blob/main/Global/VisualStudioCode.gitignore
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# and can be added to the global gitignore or merged into this file. However, if you prefer,
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# and can be added to the global gitignore or merged into this file. However, if you prefer,
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# you could uncomment the following to ignore the entire vscode folder
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# .vscode/
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marimo/_static/
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marimo/_lsp/
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__marimo__/
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# Other
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.DS_Store

‎.justfile_helpers.bash‎

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# setup some color to help differentiate between services and tool runs
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# should default to normal colors if terminal doesn't support
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is_tty() { [[ -t 1 ]] && [[ -t 0 ]]; }
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if is_tty; then
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RED=$(tput setaf 1)
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GREEN=$(tput setaf 2)
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YELLOW=$(tput setaf 3)
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BLUE=$(tput setaf 4)
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PURPLE=$(tput setaf 5)
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CYAN=$(tput setaf 6)
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RESET=$(tput sgr0)
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else
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RED='' GREEN='' YELLOW='' BLUE='' PURPLE='' CYAN='' RESET=''
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fi
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# utility for adding color and a border to a message
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print_header() {
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local command=$1
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local message_left=$2
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local service=$3
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local message_right=$4
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local type=${5:-default}
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local color
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case "$type" in
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error) color="${RED}" ;;
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success) color="${GREEN}" ;;
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# anything else (default)
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*) color="${PURPLE}" ;;
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# I hate bash syntax. esac...
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esac
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# fallback width
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local cols=$(tput cols 2>/dev/null || echo 100)
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if (( cols <= 0 )); then cols=100; fi
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local visible_length=$(
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echo -ne "$command$message_left$service$message_right" |
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sed -r 's/\x1b\[[0-9;]*m//g' |
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wc -c)
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# dashes on each side
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local left_dashes=$(( (cols - visible_length) / 2 ))
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local message_right_dashes=$(( cols - visible_length - left_dashes ))
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# print the dashes, the coloured parts, then the message_right-side dashes
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printf '%b' "${color}"
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printf '%*s' "$left_dashes" '' | tr ' ' '-'
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printf '%b' " ${BLUE}$command ${color}$message_left ${CYAN}$service ${color}$message_right "
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printf '%*s\n' "$message_right_dashes" '' | tr ' ' '-'
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printf '%b' "${RESET}"
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}
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print_message() {
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local message=$1
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local type=${2:-info}
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# Choose color based on type
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local color
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case "$type" in
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error) color="${RED}" ;;
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*) color="${GREEN}" ;; # anything else (info, success, etc.)
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esac
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# fallback width
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local cols=$(tput cols 2>/dev/null || echo 100)
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if (( cols <= 0 )); then cols=100; fi
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local visible_length=$(
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echo -ne "$message" |
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sed -r 's/\x1b\[[0-9;]*m//g' |
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wc -c
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)
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local left_spaces=$(( (cols - visible_length) / 2 ))
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local right_spaces=$(( cols - visible_length - left_spaces ))
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printf '%b' "${color}"
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printf '%*s' "$left_spaces" '' | tr ' ' ' '
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printf '%b' " ** $message ** "
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printf '%*s\n' "$right_spaces" '' | tr ' ' ' '
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printf '%b' "${RESET}"
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echo
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}
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report_error_or_success() {
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local status=$1
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local command=$2
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local message_left=$3
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local service=$4
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local message_right=$5
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echo
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if [ $status -ne 0 ]; then
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print_header "$command" "ERROR: $message_left" "$service" "$message_right" "error"
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else
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print_header "$command" "SUCCESS: $message_left" "$service" "$message_right" "success"
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fi
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echo
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}
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report_error_if_failed() {
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local status=$1
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local command=$2
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local message_left=$3
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local service=$4
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local message_right=$5
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if [ $status -ne 0 ]; then
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echo
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print_header "$command" "ERROR: $message_left" "$service" "$message_right" "error"
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echo
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fi
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}

‎.pre-commit-config.yaml‎

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repos:
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- repo: https://github.com/Yelp/detect-secrets
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rev: v1.5.0
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hooks:
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- id: detect-secrets
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args: ["--baseline", ".secrets.baseline"]
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exclude: poetry.lock
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v6.0.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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- id: no-commit-to-branch
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args: [--branch, develop, --branch, master, --branch, main, --pattern, release/.*]
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- repo: local
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hooks:
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- id: lint
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name: lint
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entry: uv run just lint
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language: python
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types: [python]
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pass_filenames: false

‎.python-version‎

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3.13

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