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kelly-sovacoolgithub-actions[bot]
kelly-sovacool
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feat: set up Syncweaver + mosuite v0.3.2 (#3)
* Squashed 'code/MOSuite/' content from commit c09ee39 git-subtree-dir: code/MOSuite git-subtree-split: c09ee39f9b282237f13d88dcf4cdfed965209c68 * refactor: load local MOSuite * feat: intialize syncweaver & mosuite v0.3.2 * chore: remove dupe * chore: use mosuite-minimal v0.3.2 * `air format` (GitHub Actions) * ci: update workflows from template * ci(tests): limit permissions --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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‎.codeocean/environment.json‎

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{
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"version": 1,
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"base_image": "codeocean/mosuite:v0.3.0",
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"post_install": true,
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"base_image": "codeocean/mosuite-minimal:v0.3.2",
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"options": {
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"registry_host_arg": true,
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"git_ask_pass": true,

‎.gitattributes‎

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/code/MOSuite linguist-vendored

‎.github/WORDLIST.txt‎

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‎.github/workflows/auto-format.yml‎

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on:
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workflow_dispatch:
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pull_request:
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branches: [dev, main]
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env:
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GH_TOKEN: ${{ github.token }}
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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permissions:
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contents: write
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pull-requests: write
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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auto-format:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v4
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if: github.event_name == 'pull_request'
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- name: Generate a token
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id: generate-token
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uses: actions/create-github-app-token@v2
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with:
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fetch-depth: 0
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ref: ${{ github.head_ref }}
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- uses: actions/checkout@v4
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if: github.event_name != 'pull_request'
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app-id: ${{ vars.CCBR_BOT_APP_ID }}
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private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
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owner: ${{ github.repository_owner }}
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- uses: actions/checkout@v7
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with:
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fetch-depth: 0
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ref: ${{ github.ref_name }}
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token: ${{ steps.generate-token.outputs.token }}
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ref: ${{ github.event_name == 'pull_request' && github.head_ref || github.ref_name }}
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- name: git config
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run: |
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git config --global user.name "github-actions[bot]"
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git config --global user.email "41898282+github-actions[bot]@users.noreply.github.com"
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- name: Format R code with air
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uses: rstudio/shiny-workflows/format-r-code@v1
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git config --global user.name "CCBR-bot"
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git config --global user.email "258092125+ccbr-bot@users.noreply.github.com"
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- name: format
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uses: pre-commit/action@v3.0.1
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continue-on-error: true
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- name: commit & push
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if: ${{ github.event_name == 'pull_request' }}
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run: |
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git add .
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git commit -m "ci: 🤖 auto-format" || echo "nothing to commit"
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git commit -m "ci: 🤖 auto-format with pre-commit" || echo "nothing to commit"
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git push || echo "nothing to push"

‎.github/workflows/syncweaver-host-contribute-patch.yml‎

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name: syncweaver-contribute-patch
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on:
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workflow_dispatch:
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inputs:
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source_path:
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description: Optional tracked source path override; if omitted, source_path is resolved from lockfile.
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required: false
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type: string
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repo_url:
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description: Optional source repository identifier (URL or OWNER/REPO) used to resolve source_path from lockfile.
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required: false
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type: string
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source_repository:
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description: Optional source repository in OWNER/REPO format; if omitted, derives from lockfile repo_url.
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required: false
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type: string
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lockfile:
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description: Path to the syncweaver lockfile.
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required: false
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default: .syncweaver-lock.json
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type: string
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patch_path:
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description: Optional patch path override; if omitted, uses source entry patch value from lockfile.
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required: false
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type: string
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source_base_ref:
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description: Optional source repository base branch for PR; if omitted, uses source entry ref from lockfile.
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required: false
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type: string
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syncweaver-version:
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description: syncweaver version/ref to install (e.g. version tag, branch name, or commit SHA). Will use docker image if available.
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required: false
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type: string
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default: main
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permissions:
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contents: read
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jobs:
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resolve-patch-metadata:
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runs-on: ubuntu-latest
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outputs:
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source_path: ${{ steps.resolve.outputs.source_path }}
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repo_url: ${{ steps.resolve.outputs.repo_url }}
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source_repository: ${{ steps.resolve.outputs.source_repository }}
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patch_path: ${{ steps.resolve.outputs.patch_path }}
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source_base_ref: ${{ steps.resolve.outputs.source_base_ref }}
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lockfile: ${{ env.LOCKFILE }}
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env:
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SOURCE_PATH: ${{ github.event.inputs.source_path || '' }}
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REPO_URL: ${{ github.event.inputs.repo_url || '' }}
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SOURCE_REPOSITORY: ${{ github.event.inputs.source_repository || '' }}
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LOCKFILE: ${{ github.event.inputs.lockfile || '.syncweaver-lock.json' }}
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PATCH_PATH: ${{ github.event.inputs.patch_path || '' }}
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SOURCE_BASE_REF: ${{ github.event.inputs.source_base_ref || '' }}
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SYNCWEAVER_VERSION: ${{ github.event.inputs['syncweaver-version'] || github.event.client_payload['syncweaver-version'] || 'main' }}
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steps:
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- name: Checkout host repository
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uses: actions/checkout@v6
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- name: Setup syncweaver
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uses: CCBR/syncweaver/actions/setup-syncweaver@main
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with:
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syncweaver-version: ${{ env.SYNCWEAVER_VERSION }}
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- name: Resolve source and patch metadata
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id: resolve
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shell: bash
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env:
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SOURCE_PATH_INPUT: ${{ env.SOURCE_PATH }}
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REPO_URL_INPUT: ${{ env.REPO_URL }}
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SOURCE_REPOSITORY_INPUT: ${{ env.SOURCE_REPOSITORY }}
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LOCKFILE_PATH: ${{ env.LOCKFILE }}
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PATCH_PATH_INPUT: ${{ env.PATCH_PATH }}
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SOURCE_BASE_REF_INPUT: ${{ env.SOURCE_BASE_REF }}
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SYNCWEAVER_HOST_CWD: ${{ github.workspace }}
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run: |
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set -euo pipefail
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syncweaver-python -m syncweaver.contribute_patch
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- name: Print resolved metadata
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shell: bash
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run: |
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set -euo pipefail
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echo "source_path=${{ steps.resolve.outputs.source_path }}"
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echo "repo_url=${{ steps.resolve.outputs.repo_url }}"
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echo "source_repository=${{ steps.resolve.outputs.source_repository }}"
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echo "patch_path=${{ steps.resolve.outputs.patch_path }}"
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echo "source_base_ref=${{ steps.resolve.outputs.source_base_ref }}"
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contribute-patch:
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runs-on: ubuntu-latest
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needs: resolve-patch-metadata
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permissions:
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contents: read
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env:
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SOURCE_PATH: ${{ needs.resolve-patch-metadata.outputs.source_path }}
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REPO_URL: ${{ needs.resolve-patch-metadata.outputs.repo_url }}
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SOURCE_REPOSITORY: ${{ needs.resolve-patch-metadata.outputs.source_repository }}
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PATCH_PATH: ${{ needs.resolve-patch-metadata.outputs.patch_path }}
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SOURCE_BASE_REF: ${{ needs.resolve-patch-metadata.outputs.source_base_ref }}
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LOCKFILE: ${{ needs.resolve-patch-metadata.outputs.lockfile }}
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steps:
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- name: Generate CCBR-bot token
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id: ccbr_bot
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uses: actions/create-github-app-token@v1
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with:
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app-id: ${{ secrets.CCBR_BOT_APP_ID }}
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private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
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- name: Checkout host repository
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uses: actions/checkout@v6
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with:
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path: host
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- name: Checkout source repository
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uses: actions/checkout@v6
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with:
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repository: ${{ env.SOURCE_REPOSITORY }}
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ref: ${{ env.SOURCE_BASE_REF }}
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token: ${{ steps.ccbr_bot.outputs.token }}
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path: source
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- name: Apply patch to source repository
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id: apply_patch
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shell: bash
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run: |
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set -euo pipefail
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patch_file="$GITHUB_WORKSPACE/host/${PATCH_PATH}"
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if [[ ! -f "$patch_file" ]]; then
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echo "Error: patch file not found in host repository: ${PATCH_PATH}" >&2
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exit 1
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fi
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branch_stub=$(printf '%s' "$SOURCE_PATH" | tr '/ ' '--' | tr -cd '[:alnum:]._-')
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if [[ -z "$branch_stub" ]]; then
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branch_stub="patch"
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fi
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branch_name="syncweaver/contribute-patch/${branch_stub}-${GITHUB_RUN_ID}"
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cd "$GITHUB_WORKSPACE/source"
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git config user.name "github-actions[bot]"
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git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
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git switch -c "$branch_name"
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if ! git apply --3way --whitespace=nowarn "$patch_file"; then
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echo "Error: patch failed to apply cleanly to ${SOURCE_REPOSITORY}@${SOURCE_BASE_REF}" >&2
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exit 1
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fi
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if git diff --quiet; then
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echo "has_changes=false" >> "$GITHUB_OUTPUT"
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else
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echo "has_changes=true" >> "$GITHUB_OUTPUT"
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fi
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echo "branch_name=$branch_name" >> "$GITHUB_OUTPUT"
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- name: Open pull request in source repository
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if: steps.apply_patch.outputs.has_changes == 'true'
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uses: peter-evans/create-pull-request@v7
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with:
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token: ${{ steps.ccbr_bot.outputs.token }}
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path: source
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base: ${{ env.SOURCE_BASE_REF }}
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branch: ${{ steps.apply_patch.outputs.branch_name }}
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delete-branch: true
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commit-message: "chore(syncweaver): apply host patch for ${{ env.SOURCE_PATH }}"
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title: "chore(syncweaver): apply host patch for ${{ env.SOURCE_PATH }}"
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body: |
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Automated patch contribution from host repository workflow dispatch.
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Inputs used:
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- source_path: ${{ env.SOURCE_PATH }}
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- repo_url: ${{ env.REPO_URL }}
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- source_repository: ${{ env.SOURCE_REPOSITORY }}
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- source_base_ref: ${{ env.SOURCE_BASE_REF }}
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- patch_path: ${{ env.PATCH_PATH }}
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- lockfile: ${{ env.LOCKFILE }}
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Trigger context:
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- host_repository: ${{ github.repository }}
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- workflow_run: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
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- name: Print no-op summary
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if: steps.apply_patch.outputs.has_changes == 'false'
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shell: bash
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run: |
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set -euo pipefail
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echo "Patch applied cleanly but introduced no source changes. No PR created."

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