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chore(syncweaver): update tracked sources from CCBR/MOSuite@v0.4.1 (#7)
Co-authored-by: ccbr-bot[bot] <258092125+ccbr-bot[bot]@users.noreply.github.com>
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‎.syncweaver-lock.json‎

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"sources": {
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"code/MOSuite": {
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"repo_url": "https://github.com/CCBR/MOSuite",
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"ref": "v0.3.2",
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"git_sha": "f4465c58a7d04f5feb41d4455a019ca4946a4ca8"
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"ref": "v0.4.1",
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"git_sha": "4e85d49ab155618d9f6beafd327b6fb87dfa8609"
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}
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}
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}

‎code/MOSuite/.Rbuildignore‎

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^renv$
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^renv\.lock$
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^_pkgdown\.yml$
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^[.]?air[.]toml$
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^\.github$
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^\.lintr$
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^\.posit$
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^\.pre-commit-config\.yaml$
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^\.prettierignore$
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^\.prettierrc$
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^\.Rproj\.user$
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^\.vscode$
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^CITATION\.cff$
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^codemeta\.json$
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^data-raw$
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^doc$
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^Dockerfile$
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^docker$
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^Dockerfile$
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^docs$
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^figures$
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^inst/quarto/report_files$
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^LICENSE\.md$
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^Meta$
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^moo_input\.rds$
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^MOSuite\.Rproj$
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^pkgdown$
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^README\.Rmd$
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^README\.html$
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^README_files$
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^Rplots\.pdf$
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^moo_input\.rds$
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^plot-volc-enh\.json$
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^volc-sum-params\.json$
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^report_files$
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^inst/quarto/report_files$
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^README.*$
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^renv\.lock$
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^renv$
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^report
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^Rplots\.pdf$
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^SECURITY\.md$
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^tests/figures$
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^vignettes/cli\.Rmd$
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^vignettes/figures/$
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^vignettes/memory\.Rmd$
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^vignettes/cli\.Rmd$
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^volc-sum-params\.json$
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VennDiagram.*\.log
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^[.]?air[.]toml$
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^\.vscode$
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^\.posit/assistant$
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^AGENTS\.md$

‎code/MOSuite/.github/CODEOWNERS‎

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* @kelly-sovacool

‎code/MOSuite/.github/workflows/R-CMD-check.yaml‎

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push:
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branches: [main, master]
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pull_request:
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branches: [main, master]
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workflow_dispatch:
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concurrency:
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fail-fast: false
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matrix:
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config:
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- { os: ubuntu-latest, r: 'release' }
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- { os: ubuntu-latest, r: 'oldrel-1' }
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- { os: ubuntu-latest, r: "release" }
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- { os: ubuntu-latest, r: "oldrel-1" }
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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env:
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- uses: actions/checkout@v6
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: '4.5'
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r-version: "4.5"
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:

‎code/MOSuite/.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: [ main, master ]
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permissions:
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contents: write
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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@v6
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- uses: actions/checkout@v7
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with:
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token: ${{ steps.generate-token.outputs.token }}
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fetch-depth: 0
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: '4.5'
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r-version: "4.5"
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: local::.
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needs: dev
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- name: update Galaxy blueprints
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shell: Rscript {0}
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run: |
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source('inst/extdata/galaxy/galaxy.R')
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write_package_json_blueprints()
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- name: render README.Rmd & docs
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shell: Rscript {0}
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run: |

‎code/MOSuite/.github/workflows/syncweaver-source-dispatch.yml‎

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name: syncweaver-source-dispatch
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on:
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release:
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types: [published]
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workflow_dispatch:
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inputs:
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source_ref:
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description: Optional source ref to dispatch (defaults to release tag for release events, or current ref for manual runs).
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required: false
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type: string
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source_repo:
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description: Optional source repository override in OWNER/REPO format (defaults to current repository).
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required: false
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type: string
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orchestrator-repo:
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description: Optional orchestrator repository override in OWNER/REPO format.
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required: false
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default: NIDAP-Community/syncweaver-orchestrator
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type: string
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permissions:
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contents: read
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jobs:
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notify-syncweaver:
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runs-on: ubuntu-latest
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env:
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SOURCE_REPOSITORY: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.source_repo || github.repository }}
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SOURCE_REF: ${{ github.event_name == 'release' && github.event.release.tag_name || github.event.inputs.source_ref || github.ref_name }}
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ORCHESTRATOR_REPO: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs['orchestrator-repo'] || vars['orchestrator-repo'] || 'NIDAP-Community/syncweaver-orchestrator' }}
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steps:
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- name: Validate dispatch payload
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shell: bash
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run: |
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set -euo pipefail
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if [[ -z "${SOURCE_REPOSITORY//[[:space:]]/}" ]]; then
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echo "Error: source repository cannot be empty." >&2
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exit 1
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fi
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if [[ -z "${SOURCE_REF//[[:space:]]/}" ]]; then
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echo "Error: source ref cannot be empty." >&2
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exit 1
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fi
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if [[ -z "${ORCHESTRATOR_REPO//[[:space:]]/}" ]]; then
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echo "Error: orchestrator repository cannot be empty." >&2
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exit 1
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fi
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if [[ "${ORCHESTRATOR_REPO}" != */* ]]; then
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echo "Error: orchestrator repository must be in OWNER/REPO format." >&2
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exit 1
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fi
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if [[ -z "${{ vars.CCBR_BOT_APP_ID }}" ]]; then
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echo "Error: vars.CCBR_BOT_APP_ID is required to generate a dispatch token." >&2
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exit 1
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fi
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if [[ -z "${{ secrets.CCBR_BOT_PRIVATE_KEY }}" ]]; then
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echo "Error: secrets.CCBR_BOT_PRIVATE_KEY is required to generate a dispatch token." >&2
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exit 1
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fi
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- name: Resolve orchestrator repository owner and name
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id: orchestrator_repo
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shell: bash
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run: |
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set -euo pipefail
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owner="${ORCHESTRATOR_REPO%%/*}"
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repo="${ORCHESTRATOR_REPO#*/}"
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if [[ -z "${owner}" || -z "${repo}" ]]; then
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echo "Error: failed to parse orchestrator repository '${ORCHESTRATOR_REPO}'." >&2
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exit 1
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fi
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echo "owner=${owner}" >> "$GITHUB_OUTPUT"
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echo "repository=${repo}" >> "$GITHUB_OUTPUT"
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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@v3
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with:
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client-id: ${{ vars.CCBR_BOT_APP_ID }}
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private-key: ${{ secrets.CCBR_BOT_PRIVATE_KEY }}
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owner: ${{ steps.orchestrator_repo.outputs.owner }}
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repositories: ${{ steps.orchestrator_repo.outputs.repository }}
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- name: Dispatch syncweaver-update-hosts workflow in orchestrator repo
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uses: peter-evans/repository-dispatch@v4
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with:
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token: ${{ steps.ccbr_bot.outputs.token }}
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repository: ${{ env.ORCHESTRATOR_REPO }}
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event-type: syncweaver-update-hosts
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client-payload: >-
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{"source_repository": ${{ toJson(env.SOURCE_REPOSITORY) }}, "ref": ${{ toJson(env.SOURCE_REF) }}}

‎code/MOSuite/.gitignore‎

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.Rproj.user
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.Rhistory
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.Rdata
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.httr-oauth
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.DS_Store
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.quarto
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docs
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inst/doc
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*_files/
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**/figures/
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/.github/plans/
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/.httr-oauth
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/.posit/
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/.quarto
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/.Rdata
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/.Rhistory
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/.Rproj.user
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/.vscode/
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/doc/
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/docs
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/inst/doc
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/Meta/
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/README.html
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**/figures/
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VennDiagram.*.log
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*_files/
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tests/testthat/Rplots.pdf
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/tests/testthat/Rplots.pdf
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/tmp
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vignettes/args*.json
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Rplots.pdf
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/vignettes/args*.json
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moo_input.rds
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plot-volc-enh.json
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Rplots.pdf
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VennDiagram.*.log
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volc-sum-params.json

‎code/MOSuite/.lintr‎

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commented_code_linter = NULL,
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object_name_linter = NULL,
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object_length_linter = object_length_linter(60L),
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object_usage_linter = NULL,
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return_linter = return_linter(
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return_style = "explicit"
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),

‎code/MOSuite/.pre-commit-config.yaml‎

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- id: trailing-whitespace
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# spell check
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- repo: https://github.com/codespell-project/codespell
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rev: v2.4.2
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rev: v2.4.3
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hooks:
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- id: codespell
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args: ["-I=.github/WORDLIST.txt"]
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# R formatting
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- repo: https://github.com/posit-dev/air-pre-commit
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rev: 0.9.0
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rev: 0.11.0
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hooks:
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- id: air-format
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- repo: https://github.com/lorenzwalthert/precommit
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rev: v0.4.3.9025
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rev: v0.4.3.9029
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hooks:
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- id: parsable-R
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- id: readme-rmd-rendered
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- id: use-tidy-description
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- id: lintr
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args: [--warn_only]

‎code/MOSuite/.vscode/extensions.json‎

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