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kaitejohnsonkaitejohnson
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Merge pull request #2 from epiforecasts/1-add-repo-skeleton
Issue 1: add repo skeleton
2 parents 1556061 + cc0698a commit 59d6ea6

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‎.Rbuildignore‎

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^LICENSE\.md$
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^\.devcontainer$
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^data-raw$
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^README\.Rmd$
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^\.github$
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^\.pre-commit-config\.yaml$
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^\.lintr$
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^\.Rprofile
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^_pkgdown\.yml$
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^docs$
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^pkgdown$
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^vignettes/cache$
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^.*\.Rproj$
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^\.Rproj\.user$
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^codemeta\.json$
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^inst/make_hexsticker\.R$
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^inst/scripts$
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^vignettes/precompile\.R$
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^vignettes/chunks$
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^doc$
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^Meta$
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^\.vscode$
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^CITATION\.cff$
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^vignettes/using-stan-tools\.Rmd$
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^touchstone$
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^cran-comments\.md$
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^CRAN-SUBMISSION$
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^[\.]?air\.toml$

‎.github/.gitignore‎

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*.html

‎.github/workflows/R-CMD-check.yaml‎

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# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
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# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
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on:
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push:
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branches:
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- main
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schedule:
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- cron: '5 4 * * 1'
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pull_request:
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branches:
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- main
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merge_group:
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workflow_dispatch:
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name: R-CMD-check
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concurrency:
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group: ${{ github.workflow }}-${{ github.head_ref }}
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cancel-in-progress: true
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jobs:
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R-CMD-check:
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if: "! contains(github.event.head_commit.message, '[ci skip]')"
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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: ubuntu-latest, r: 'release'}
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- {os: ubuntu-latest, r: 'oldrel-1'}
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- {os: macos-latest, r: 'release'}
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- {os: windows-latest, r: 'release'}
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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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NOT_CRAN: true
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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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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, any::testthat
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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

‎.github/workflows/codemeta.yaml‎

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on:
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push:
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paths:
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- DESCRIPTION
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- .github/workflows/codemeta.yaml
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workflow_dispatch:
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name: Render codemeta
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jobs:
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render:
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runs-on: ubuntu-latest
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if: "!contains(github.event.head_commit.message, 'cm-skip')"
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::codemetar
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needs: codemeta
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- name: Render codemeta
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run: codemetar::write_codemeta()
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shell: Rscript {0}
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- name: Create Pull Request
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if: github.ref == 'refs/heads/main'
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uses: peter-evans/create-pull-request@v7
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with:
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commit-message: "Update codemeta.json"
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title: "Update codemeta.json"
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body: "This is an automated pull request to update the codemeta.json file."
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branch: "update-codemeta-${{ github.run_number }}"
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labels: "metadata"
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reviewers: seabbs
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add-paths: |
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codemeta.json
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token: ${{ secrets.GITHUB_TOKEN }}

‎.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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pull_request:
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branches:
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- main
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workflow_dispatch:
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name: lint-changed-files
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jobs:
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lint-changed-files:
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runs-on: ubuntu-latest
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if: "! contains(github.event.head_commit.message, '[ci skip]')"
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: |
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any::gh
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any::lintr
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any::purrr
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any::cyclocomp
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needs: check
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- name: Add lintr options
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run: |
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cat('\noptions(lintr.linter_file = ".lintr")\n', file = "~/.Rprofile", append = TRUE)
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shell: Rscript {0}
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- name: Install package
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run: R CMD INSTALL .
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- name: Extract and lint files changed by this PR
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run: |
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files <- gh::gh("GET https://api.github.com/repos/${{ 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/pr-commands.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/master/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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issue_comment:
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types: [created]
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name: Commands
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jobs:
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document:
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if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER' || github.event.comment.author_association == 'COLLABORATOR') && startsWith(github.event.comment.body, '/document') }}
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name: document
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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/pr-fetch@v2
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: roxygen2
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- name: Document
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run: Rscript -e 'roxygen2::roxygenise()'
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- name: commit
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run: |
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git config --local user.name "$GITHUB_ACTOR"
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git config --local user.email "[email protected]"
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git add man/\* NAMESPACE
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git commit -m 'Document'
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- uses: r-lib/actions/pr-push@v2
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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style:
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if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER' || github.event.comment.author_association == 'COLLABORATOR') && startsWith(github.event.comment.body, '/style') }}
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name: style
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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/pr-fetch@v2
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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- uses: r-lib/actions/setup-r@v2
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- name: Install dependencies
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run: Rscript -e 'install.packages(c("styler", "roxygen2"))'
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- name: Style
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run: Rscript -e 'styler::style_pkg()'
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- name: Install Air
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uses: posit-dev/setup-air@v1
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- name: Check
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run: air format . --check
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- name: commit
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run: |
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git config --local user.name "$GITHUB_ACTOR"
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git config --local user.email "[email protected]"
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git add \*.R
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git commit -m 'Style'
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- uses: r-lib/actions/pr-push@v2
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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update_wordlist:
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if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER' || github.event.comment.author_association == 'COLLABORATOR') && startsWith(github.event.comment.body, '/update_wordlist') }}
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name: update_wordlist
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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/pr-fetch@v2
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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- uses: r-lib/actions/setup-r@v2
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- name: Install dependencies
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run: |
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install.packages(c("spelling"))
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shell: Rscript {0}
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- name: Update wordlist
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run: |
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spelling::update_wordlist(confirm = TRUE)
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shell: Rscript {0}
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- name: Commit changes
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run: |
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git config --local user.name "$GITHUB_ACTOR"
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git config --local user.email "[email protected]"
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git add inst/WORDLIST
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git commit -m 'Update wordlist' || echo "No changes to commit"
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- uses: r-lib/actions/pr-push@v2
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with:
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repo-token: ${{ secrets.GITHUB_TOKEN }}

‎.github/workflows/test-coverage.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/master/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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merge_group:
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concurrency:
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group: ${{ github.workflow }}-${{ github.head_ref }}
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cancel-in-progress: true
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name: test-coverage
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jobs:
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test-coverage:
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runs-on: ubuntu-latest
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if: "! contains(github.event.head_commit.message, '[ci skip]')"
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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NOT_CRAN: true
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steps:
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- uses: actions/checkout@v4
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::covr
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needs: coverage
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- name: Test coverage
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run: covr::codecov(quiet = FALSE, token = "${{ secrets.CODECOV_TOKEN }}")
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shell: Rscript {0}

‎.gitignore‎

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*.xlsx
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output
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*.rds
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inst/doc
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*.tex
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*.log
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_targets
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docs
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cache
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.DS_Store
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.Rproj.user
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*.Rproj
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!inst/extdata/*.rds
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/doc/
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/Meta/
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*.Rhistory
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.vscode
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/figures/
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/vignettes/*_cache/
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.here
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*.pdf
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*.html
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CRAN-SUBMISSION

‎.lintr‎

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linters: all_linters(
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packages = "lintr",
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implicit_integer_linter = NULL,
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undesirable_function_linter = NULL,
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function_argument_linter = NULL,
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indentation_linter = NULL,
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object_name_linter = NULL,
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return_linter(return_style = "explicit"),
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cyclocomp_linter(25L)
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)
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exclusions: list(
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"inst",
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"tests/testthat.R" = list(
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unused_import_linter = Inf
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)
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)

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