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‎.Rbuildignore

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^.*\.Rproj$
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^\.Rproj\.user$
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^README\.Rmd$
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^\.github$
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^_pkgdown\.yml$
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^docs$
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^pkgdown$
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^LICENSE\.md$

‎.github/.gitignore

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*.html

‎.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
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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/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]
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release:
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types: [published]
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workflow_dispatch:
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name: "Deploy pkgdown site to Posit Connect"
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jobs:
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build-site:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Setup R
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uses: r-lib/actions/setup-r@v2
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with:
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r-version: 4.2.1
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- name: Setup Pandoc
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uses: r-lib/actions/setup-pandoc@v2
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- name: Install system dependencies
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run: |
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sudo apt-get update
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sudo apt-get install -y libxml2-dev libssl-dev libcurl4-openssl-dev
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- name: Install R dependencies
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: |
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any::pkgdown
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any::rsconnect
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local::.
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- name: Build site
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run: |
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Rscript -e "pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)"
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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/[email protected]
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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/test-covbadge.yaml

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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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name: test-coverage badge
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permissions: write-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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- 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, file = "coverage.xml")
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coverage_percentage <- round(covr::percent_coverage(cov), 0)
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# Export the coverage percentage as an environment variable
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cat(sprintf("COVERAGE_PERCENTAGE=%s\n", coverage_percentage), file = Sys.getenv("GITHUB_ENV"), append = TRUE)
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shell: Rscript {0}
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- name: Create Shields.io badge URL
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id: create_badge
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run: |
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coverage=$COVERAGE_PERCENTAGE
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if (( $(echo "${coverage} < 50" | bc -l) )); then
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color="red"
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elif (( $(echo "${coverage} < 80" | bc -l) )); then
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color="orange"
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else
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color="brightgreen"
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fi
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badge_url="https://img.shields.io/badge/coverage-${coverage}%25-${color}.svg"
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# Print the badge URL to the GitHub Actions log
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echo "Badge URL: ${badge_url}"
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# set badge
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echo "badge_url=${badge_url}" >> $GITHUB_ENV
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- name: Update README with coverage badge for PR
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if: github.ref_name != 'main'
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run: |
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git config --global user.name 'github-actions'
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git config --global user.email '[email protected]'
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git checkout -b ${{ github.head_ref }}
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git branch
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git pull --rebase origin ${{ github.head_ref }}
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git checkout --ours README.md || true
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sed -i 's|!\[Coverage\](https://img.shields.io/badge/coverage-[0-9]*%25-[a-z]*\.svg)|![Coverage]('"${{ env.badge_url }}"')|g' README.md
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git status
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git add README.md
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git commit -m 'Update README with coverage badge' || echo "No changes to commit"
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git push origin ${{ github.head_ref }}
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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- name: Update README with coverage badge for main branch
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if: github.ref_name == 'main'
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run: |
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git config --global user.name 'github-actions'
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git config --global user.email '[email protected]'
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git checkout main
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git branch
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git pull --rebase origin main
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git checkout --ours README.md || true
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sed -i 's|!\[Coverage\](https://img.shields.io/badge/coverage-[0-9]*%25-[a-z]*\.svg)|![Coverage]('"${{ env.badge_url }}"')|g' README.md
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git status
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git add README.md
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git commit -m 'Update README with coverage badge' || echo "No changes to commit"
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git push origin main
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

‎.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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# 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]
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pull_request:
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branches: [main]
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workflow_dispatch:
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name: test-coverage
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permissions: write-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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- 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, file = "coverage.xml")
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coverage_percentage <- round(covr::percent_coverage(cov), 0)
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writeLines(as.character(coverage_percentage), "coverage.txt")
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shell: Rscript {0}
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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@v3
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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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‎.gitignore

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.Rproj.user
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.Rhistory
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.RData
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.Ruserdata
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inst/doc
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docs
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‎DESCRIPTION

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Package: risk.assessr
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Title: Assessing package risk metrics
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Version: 1.0.0
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Authors@R: c(
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person("Edward", "Gillian", , "[email protected]", role = c("cre", "aut"), comment = c(ORCID = "0000-0003-2732-5107")),
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person("Hugo", "Bottois", , "[email protected]", role = "aut", comment = c(ORCID = "0000-0003-4674-0875")),
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person("Paulin", "Charliquart", , "[email protected]", role = "aut"),
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person("Andre", "Couturier", , "[email protected]", role = "aut"),
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person("Sanofi", role = c("cph", "fnd"))
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)
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Description: Tools for assessing R packages against a number of metrics to help validate their trustworthiness and reliability.
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License: GPL (>= 2)
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Depends: R (>= 4.1.0)
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Imports: callr, checkmate, remotes, covr, devtools, dplyr, lubridate, purrr,
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rcmdcheck, rlang, httr2, jsonlite
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Suggests: forcats, fs, glue, here, knitr, magrittr, openxlsx,
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readr, roxygen2, pkgload, testthat (>= 3.0.0), stringr (>=
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1.4.0), tibble, tidyr, tidyselect, tools, rmarkdown, utils,
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withr, mockery
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Encoding: UTF-8
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RoxygenNote: 7.3.2
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Config/testthat/edition: 3
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Config/build/clean-inst-doc: false
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VignetteBuilder: knitr
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NeedsCompilation: no
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Packaged: 2024-09-24 15:02:32 UTC; u1004798
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Author: Edward Gillian [cre, aut],
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Hugo Bottois [aut]
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Maintainer: Edward Gillian <[email protected]>

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