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‎.github/dependabot.yml‎

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# To get started with Dependabot version updates, you'll need to specify which
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# package ecosystems to update and where the package manifests are located.
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# Please see the documentation for all configuration options:
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# https://docs.github.com/code-security/dependabot/dependabot-version-updates/configuration-options-for-the-dependabot.yml-file
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version: 2
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updates:
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- package-ecosystem: "github-actions" # See documentation for possible values
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directory: "/" # Location of package manifests
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schedule:
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interval: "weekly"
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- package-ecosystem: "docker"
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directory: "/"
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schedule:
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interval: "weekly"

‎.github/renovate.json‎

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{
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"extends": [
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"config:base"
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]
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}

‎.github/workflows/R-CMD-check.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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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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name: R-CMD-check.yaml
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permissions: read-all
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
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- {os: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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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: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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with:
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upload-snapshots: true
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build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

‎.github/workflows/archive-github-pages.yml‎

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# GitHub Actions workflow for Waystation version 1.5.0.
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# Available as the file "sample-workflow.yml" from the software
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# repository at https://github.com/caltechlibrary/waystation
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name: Archive GitHub Pages
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run-name: Archive GitHub Pages in the Wayback Machine
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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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permissions:
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actions: write
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checks: write
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contents: write
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deployments: write
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id-token: write
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issues: read
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discussions: read
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packages: write
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pages: write
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pull-requests: read
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repository-projects: read
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security-events: read
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statuses: read
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jobs:
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run-waystation:
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name: Run Waystation
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runs-on: ubuntu-latest
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steps:
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- uses: caltechlibrary/waystation@main

‎.github/workflows/clear-cache.yml‎

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---
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name: Clear cache
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on:
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workflow_dispatch:
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permissions:
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actions: write
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jobs:
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clear-cache:
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runs-on: ubuntu-latest
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steps:
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- name: Clear cache
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uses: actions/github-script@v7
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with:
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script: |
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console.log("About to clear")
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const caches = await github.rest.actions.getActionsCacheList({
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owner: context.repo.owner,
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repo: context.repo.repo,
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})
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for (const cache of caches.data.actions_caches) {
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console.log(cache)
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github.rest.actions.deleteActionsCacheById({
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owner: context.repo.owner,
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repo: context.repo.repo,
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cache_id: cache.id,
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})
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}
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console.log("Clear completed")

‎.github/workflows/external-use.yaml‎

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---
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name: External Use
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on:
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push:
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branches:
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- "main"
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- "dev"
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pull_request:
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branches:
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- "main"
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- "dev"
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workflow_dispatch:
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permissions: read-all
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jobs:
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sapid-test:
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name: sapid-${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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strategy:
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matrix:
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os:
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- "ubuntu-latest"
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- "macos-latest"
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- "windows-latest"
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defaults:
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run:
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shell: bash
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steps:
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- uses: actions/checkout@v4
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- name: Get number of CPU cores
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uses: SimenB/github-actions-cpu-cores@v2
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id: cpu-cores
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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Ncpus: ${{ steps.cpu-cores.outputs.count }}
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- name: Install dependencies (Linux)
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if: matrix.os == 'ubuntu-latest'
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run: |
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sudo apt-get update && sudo apt-get install -y --no-install-recommends libcurl4-openssl-dev libfribidi-dev libharfbuzz-dev libnetcdf-dev \
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&& sudo apt-get clean \
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&& sudo rm -rf /var/lib/apt/lists/*
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- name: Install (Linux)
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if: matrix.os == 'ubuntu-latest'
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run: |
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install.packages("sapid", repos = c("https://adafede.r-universe.dev", "https://bioc.r-universe.dev", "https://cloud.r-project.org"), type = "source")
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shell: Rscript {0}
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- name: Install (MacOS and Windows)
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if: matrix.os != 'ubuntu-latest'
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run: |
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install.packages("sapid", repos = c("https://adafede.r-universe.dev", "https://bioc.r-universe.dev", "https://cloud.r-project.org"), type = "binary")
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shell: Rscript {0}
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- name: Run pipeline
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run: |
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sapid:::.packageName
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shell: Rscript {0}

‎.github/workflows/pkgdown.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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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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release:
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types: [published]
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workflow_dispatch:
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name: pkgdown
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permissions:
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actions: write
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checks: write
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contents: write
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deployments: write
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id-token: write
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issues: read
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discussions: read
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packages: write
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pages: write
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pull-requests: read
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repository-projects: read
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security-events: read
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statuses: read
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jobs:
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pkgdown:
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runs-on: ubuntu-latest
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# Only restrict concurrency for non-PR jobs
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concurrency:
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group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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permissions:
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contents: write
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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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: any::pkgdown, local::.
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needs: website
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- name: Build site
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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shell: Rscript {0}
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- name: Deploy to GitHub pages 🚀
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if: github.event_name != 'pull_request'
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uses: JamesIves/github-pages-deploy-action@v4.7.2
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with:
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clean: false
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branch: gh-pages
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folder: docs

‎.github/workflows/r-license-report.yml‎

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---
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name: License Report
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permissions: read-all
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on:
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push:
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branches-ignore:
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- "main"
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pull_request:
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branches:
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- "main"
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jobs:
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license-report:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repo
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uses: actions/checkout@v4
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- name: License Report
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uses: insightsengineering/r-license-report@v1

‎.github/workflows/remove-old-artifacts.yml‎

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---
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name: Remove old artifacts
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permissions: read-all
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on:
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schedule:
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# Every day at 1am
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- cron: "0 1 * * *"
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jobs:
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remove-old-artifacts:
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runs-on: ubuntu-latest
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timeout-minutes: 10
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steps:
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- name: Remove old artifacts
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uses: c-hive/gha-remove-artifacts@v1
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with:
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age: "1 month" # '<number> <unit>', e.g. 5 days, 2 years, 90 seconds, parsed by Moment.js
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# Optional inputs
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# skip-tags: true
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# skip-recent: 5

‎.github/workflows/test-coverage.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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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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name: test-coverage.yaml
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permissions: read-all
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jobs:
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test-coverage:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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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: any::covr, any::xml2
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needs: coverage
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- name: Test coverage
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run: |
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cov <- covr::package_coverage(
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quiet = FALSE,
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clean = FALSE,
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install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
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)
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covr::to_cobertura(cov)
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shell: Rscript {0}
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- uses: codecov/codecov-action@v5
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with:
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fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
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files: ./cobertura.xml
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plugins: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
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run: |
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## --------------------------------------------------------------------
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v4
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

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