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Merge pull request #425 from cmu-delphi/ds/ci
ci: add document, lint, style like epidatr
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‎.github/pull_request_template.md

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(backwards-incompatible changes to the documented interface) are noted.
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Collect the changes under the next release number (e.g. if you are on
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1.7.2, then write your changes under the 1.8 heading).
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- See [DEVELOPMENT.md](DEVELOPMENT.md) for more information on the development
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process.
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### Change explanations for reviewer
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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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#
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# Created with usethis + edited to run on PRs to dev, use API key.
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# Modifications:
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# - API key secrets.SECRET_EPIPROCESS_GHACTIONS_DELPHI_EPIDATA_KEY
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on:
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push:
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branches: [main, dev]

‎.github/workflows/document.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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# Modifications:
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# - devtools::build_readme()
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# - workflow_dispatch added to allow manual triggering of the workflow
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# - trigger branches changed
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# - API key secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY
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on:
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push:
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paths: ["R/**", "README.Rmd"]
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workflow_dispatch:
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name: Document
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jobs:
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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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DELPHI_EPIDATA_KEY: ${{ secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY }}
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steps:
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- name: Checkout repo
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uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- name: Setup R
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uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- name: Install dependencies
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: |
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any::devtools
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any::roxygen2
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needs: |
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devtools
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roxygen2
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- name: Document
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run: roxygen2::roxygenise()
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shell: Rscript {0}
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- name: Build README.md from README.Rmd
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run: Rscript -e 'devtools::build_readme()'
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- name: Commit and push changes
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run: |
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git config --local user.name "$GITHUB_ACTOR"
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git config --local user.email "[email protected]"
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git add README.md
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git add man/\* NAMESPACE DESCRIPTION
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git commit -m "docs: document (GHA)" || echo "No changes to commit"
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git pull --rebase
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git push origin

‎.github/workflows/lint.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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# Modifications:
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# * workflow_dispatch added to allow manual triggering of the workflow
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# * trigger branches changed
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# * API key secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY
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on:
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push:
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branches: [main, dev]
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pull_request:
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branches: [main, dev]
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workflow_dispatch:
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name: Lint
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jobs:
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lint:
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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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DELPHI_EPIDATA_KEY: ${{ secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY }}
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steps:
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- uses: actions/checkout@v3
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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::lintr, local::.
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needs: lint
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- name: Lint
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run: lintr::lint_package()
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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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# Edits from above workflow: also check pkgdown for PRs to `dev` branch, and
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# update the documentation web site on pushes to `dev` branch.
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# Modifications:
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# * workflow_dispatch added to allow manual triggering of the workflow
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# * trigger branches changed
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# * API key secrets.SECRET_EPIPROCESS_GHACTIONS_DELPHI_EPIDATA_KEY
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on:
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push:
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branches: [main, dev]
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needs: website
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- name: Build site
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# - target_ref gets the ref from a different variable, depending on the event
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# - override allows us to set the pkgdown mode and version_label
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# - mode: release is the standard build mode, devel places the site in /dev
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# - version_label: 'light' and 'success' are CSS labels for Bootswatch: Cosmo
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# https://bootswatch.com/cosmo/
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# - we use pkgdown:::build_github_pages to build the site because of an issue in pkgdown
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# https://github.com/r-lib/pkgdown/issues/2257
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run: |
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override <- if (startsWith("${{ github.event_name }}", "pull_request")) {
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if ("${{ github.base_ref }}" == "main") {
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list(development = list(mode = "release", version_label = "light"))
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} else {
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list(development = list(mode = "devel", version_label = "success"))
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}
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target_ref <- ${{ github.event_name == 'pull_request' && github.base_ref || github.ref }}
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override <- if (target_ref == "main") {
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list(development = list(mode = "release", version_label = "light"))
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} else if (target_ref == "dev") {
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list(development = list(mode = "devel", version_label = "success"))
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} else {
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if ("${{ github.ref_name }}" == "main") {
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list(development = list(mode = "release", version_label = "light"))
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} else {
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list(development = list(mode = "devel", version_label = "success"))
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}
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stop("Unexpected target_ref: ", target_ref)
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}
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pkg <- pkgdown::as_pkgdown(".", override = override)
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cli::cli_rule("Cleaning files from old site...")

‎.github/workflows/style.yml

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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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# Modifications:
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# * workflow_dispatch added to allow manual triggering of the workflow
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# * trigger branches changed
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# * API key secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY
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on:
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push:
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paths:
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[
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"**.[rR]",
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"**.[qrR]md",
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"**.[rR]markdown",
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"**.[rR]nw",
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"**.[rR]profile",
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]
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workflow_dispatch:
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name: Style
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jobs:
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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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DELPHI_EPIDATA_KEY: ${{ secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY }}
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steps:
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- name: Checkout repo
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uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- name: Setup R
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uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- name: Install dependencies
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::styler, any::roxygen2
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needs: styler
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- name: Enable styler cache
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run: styler::cache_activate()
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shell: Rscript {0}
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- name: Determine cache location
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id: styler-location
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run: |
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cat(
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"location=",
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styler::cache_info(format = "tabular")$location,
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"\n",
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file = Sys.getenv("GITHUB_OUTPUT"),
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append = TRUE,
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sep = ""
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)
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shell: Rscript {0}
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- name: Cache styler
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uses: actions/cache@v3
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with:
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path: ${{ steps.styler-location.outputs.location }}
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key: ${{ runner.os }}-styler-${{ github.sha }}
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restore-keys: |
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${{ runner.os }}-styler-
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${{ runner.os }}-
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- name: Style
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run: styler::style_pkg()
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shell: Rscript {0}
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- name: Commit and push changes
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run: |
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if FILES_TO_COMMIT=($(git diff-index --name-only ${{ github.sha }} \
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| egrep --ignore-case '\.(R|[qR]md|Rmarkdown|Rnw|Rprofile)$'))
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then
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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 commit ${FILES_TO_COMMIT[*]} -m "style: styler (GHA)"
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git pull --rebase
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git push origin
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else
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echo "No changes to commit."
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fi

‎DESCRIPTION

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Version: 0.7.5
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Authors@R: c(
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person("Jacob", "Bien", role = "ctb"),
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person("Logan", "Brooks", role = "aut"),
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person("Logan", "Brooks", email = "[email protected]", role = c("aut", "cre")),
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person("Rafael", "Catoia", role = "ctb"),
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person("Nat", "DeFries", role = "ctb"),
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person("Daniel", "McDonald", role = "aut"),
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person("Quang", "Nguyen", role = "ctb"),
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person("Evan", "Ray", role = "aut"),
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person("Dmitry", "Shemetov", role = "ctb"),
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person("Ryan", "Tibshirani", , "[email protected]", role = c("aut", "cre")),
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person("Ryan", "Tibshirani", role = "aut"),
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person("Lionel", "Henry", role = "ctb", comment = "Author of included rlang fragments"),
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person("Hadley", "Wickham", role = "ctb", comment = "Author of included rlang fragments"),
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person("Posit", role = "cph", comment = "Copyright holder of included rlang fragments")

‎DEVELOPMENT.md

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Please follow the guidelines in the [PR template document](.github/pull_request_template.md).
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## Release process
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## Planned CRAN release process
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Open a release issue and then copy and follow this checklist in the issue (modified from the checklist generated by `usethis::use_release_issue(version = "1.0.2")`):
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- [ ] `git pull`
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- [ ] Check [current CRAN check results](https://cran.rstudio.org/web/checks/check_results_epiprocess.html)
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- [ ] `devtools::check(".", manual = TRUE, env_vars = c(NOT_CRAN = "FALSE"))`.
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- [ ] `git pull` on `dev` branch.
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- [ ] Make sure all changes are committed and pushed.
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- [ ] Check [current CRAN check results](https://cran.rstudio.org/web/checks/check_results_epiprocess.html).
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- [ ] `devtools::check(".", manual = TRUE, env_vars = c(NOT_CRAN = "false"))`.
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- Aim for 10/10, no notes.
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- [ ] If check works well enough, merge to main. Otherwise open a PR to fix up.
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- [ ] [Polish NEWS](https://github.com/cmu-delphi/epiprocess/blob/dev/NEWS.md).
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- This may choke on the MIT license url, and that's ok.
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- [ ] `devtools::build_readme()`
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- [ ] `devtools::check_win_devel()`
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- [ ] Check email for problems
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- [ ] Have maintainer ("cre" in description) check email for problems.
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- [ ] `revdepcheck::revdep_check(num_workers = 4)`.
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- This may choke, it is very sensitive to the binary versions of packages on a given system. Either bypass or ask someone else to run it if you're concerned.
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- [ ] Update `cran-comments.md`
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- [ ] PR with any changes
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- [ ] PR with any changes (and go through the list again) into `dev` and run through the list again.
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Submit to CRAN:
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- [ ] `devtools::submit_cran()`
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- [ ] Approve email
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- [ ] `devtools::submit_cran()`.
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- [ ] Maintainer approves email.
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Wait for CRAN...
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- [ ] Accepted :tada:
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- [ ] `dev`
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- [ ] `usethis::use_github_release(publish = FALSE)` (publish off, otherwise it won't push).
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- [ ] check the release notes and publish the branch on github
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- [ ] If accepted :tada:, move to next steps. If rejected, fix and resubmit.
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- [ ] Open and merge a PR containing any updates made to `main` back to `dev`.
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- [ ] `usethis::use_github_release(publish = FALSE)` (publish off, otherwise it won't push) will create a draft release based on the commit hash in CRAN-SUBMISSION and push a tag to the GitHub repo.
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- [ ] Go to the repo, verify the release notes, and publish when ready.

‎man/autoplot.epi_df.Rd

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‎man/epiprocess.Rd

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