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‎.Rbuildignore‎

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^.*\.Rproj$
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^CITATION\.cff$
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^LICENSE\.md$
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^Meta$
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^README\.Rmd$
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^\.Rproj\.user$
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^\.github$
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^\.lintr$
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^\.pre-commit-config\.yaml$
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^_pkgdown\.yml$
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^codecov\.yml$
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^doc$
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^docs$
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^pkgdown$
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^tools$

‎.github/.gitignore‎

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*.html

‎.github/dependabot.yml‎

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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"

‎.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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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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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")'
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error-on: '"note"'

‎.github/workflows/lint-changed-files.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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workflow_dispatch:
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pull_request:
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branches: [main, master]
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paths:
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- '**.R'
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- '**.Rmd'
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- '**/.lintr'
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- '**/.lintr.R'
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name: lint-changed-files
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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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lint-changed-files:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: |
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any::gh
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any::lintr
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any::purrr
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any::cyclocomp
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epiverse-trace/etdev
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needs: check
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- name: Install package
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run: R CMD INSTALL .
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- name: Extract and lint files changed by this PR
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run: |
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files <- gh::gh("/repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/files")
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changed_files <- purrr::map_chr(files, "filename")
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all_files <- list.files(recursive = TRUE)
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exclusions_list <- as.list(setdiff(all_files, changed_files))
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lintr::lint_package(exclusions = exclusions_list)
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shell: Rscript {0}
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env:
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LINTR_ERROR_ON_LINT: true

‎.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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#
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# Reproduce locally by running:
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# ```r
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# pak::pak(c("any::pkgdown", "."), dependencies = "Config/Needs/website")
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# pkgdown::build_site()
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# ```
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on:
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push:
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branches: [main, master]
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paths:
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- 'README.Rmd'
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- 'README.md'
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- 'index.Rmd'
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- 'index.md'
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- 'man/**'
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- 'vignettes/**'
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- '_pkgdown.yml'
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- 'pkgdown/**'
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- 'DESCRIPTION'
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- '.Rbuildignore'
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- '.github/**'
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merge_group:
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pull_request:
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paths:
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- 'README.Rmd'
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- 'README.md'
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- 'index.Rmd'
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- 'index.md'
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- 'man/**'
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- 'vignettes/**'
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- '_pkgdown.yml'
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- 'pkgdown/**'
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- 'DESCRIPTION'
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- '.Rbuildignore'
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- '.github/**'
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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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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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jobs:
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pkgdown:
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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-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: Check website links
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uses: untitaker/hyperlink@0.1.44
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with:
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args: docs/
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- name: Deploy to GitHub pages 🚀
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if: github.event_name != 'merge_group' && github.event_name != 'pull_request'
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uses: JamesIves/github-pages-deploy-action@v4.7.3
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with:
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# We clean on releases because we want to remove old vignettes,
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# figures, etc. that have been deleted from the `main` branch.
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# But we clean ONLY on releases because we want to be able to keep
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# both the 'stable' and 'dev' websites.
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# Also discussed in https://github.com/r-lib/actions/issues/484
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clean: ${{ github.event_name == 'release' }}
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branch: gh-pages
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folder: docs

‎.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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name: test-coverage.yaml
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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: 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@v4
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with:
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# Fail if error if not on PR, or if on PR and token is given
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fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
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file: ./cobertura.xml
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plugin: 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

‎.github/workflows/update-citation-cff.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
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# The action runs when:
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# - The DESCRIPTION or inst/CITATION are modified
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# - Can be run manually
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# For customizing the triggers, visit https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
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on:
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push:
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branches:
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- main
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paths:
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- DESCRIPTION
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- inst/CITATION
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- .github/workflows/update-citation-cff.yaml
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workflow_dispatch:
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name: Update CITATION.cff
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permissions:
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contents: write
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pull-requests: write
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jobs:
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update-citation-cff:
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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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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: |
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any::cffr
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any::V8
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- name: Update CITATION.cff
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run: |
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library(cffr)
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# Customize with your own code
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# See https://docs.ropensci.org/cffr/articles/cffr.html
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# Write your own keys
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mykeys <- list()
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# Create your CITATION.cff file
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cff_write(keys = mykeys)
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shell: Rscript {0}
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- name: Create Pull Request
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uses: peter-evans/create-pull-request@v7
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with:
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commit-message: Update `CITATION.cff`
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title: Update `CITATION.cff`
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body: |
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This pull request updates the citation file, ensuring all authors are credited and there are no discrepancies.
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Please verify the changes before merging.
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branch: update-citation-cff

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