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Merge pull request #156 from cmu-delphi/ds/merge-fetch
refactor: `fetch` by default
2 parents 3db0081 + a25e532 commit 7f2d73a

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‎.bumpversion.cfg

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[bumpversion]
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current_version = 0.8.0
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current_version = 0.9.0
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commit = False
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tag = False
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‎.github/CODEOWNERS

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* @dshemetov @brookslogan
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* @dshemetov @brookslogan @dsweber2

‎.github/workflows/ci.yml

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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::devtools, any::rcmdcheck, any::styler, any::lintr, local::.
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- name: Style / Format
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shell: Rscript {0}
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run: styler::style_pkg(dry="fail")
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- name: Lint
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shell: Rscript {0}
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run: |
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devtools::load_all()
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lintr::lint_package('.')
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extra-packages: any::devtools, any::rcmdcheck, local::.
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- uses: r-lib/actions/check-r-package@v2
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env:

‎.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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on:
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push:
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paths: ["R/**"]
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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: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- name: Checkout repo
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uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- name: Setup R
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uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- name: Install dependencies
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::roxygen2
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needs: roxygen2
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- name: Document
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run: roxygen2::roxygenise()
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shell: Rscript {0}
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- name: Commit and push changes
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run: |
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git config --local user.name "$GITHUB_ACTOR"
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git config --local user.email "[email protected]"
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git add man/\* NAMESPACE DESCRIPTION
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git commit -m "docs: update documentation (GHA)" || echo "No changes to commit"
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git pull --ff-only
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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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on:
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push:
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branches: [main, master, dev]
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pull_request:
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branches: [main, master, dev]
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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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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/style.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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paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown", "**.[rR]nw", "**.[rR]profile"]
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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: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- name: Checkout repo
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uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- name: Setup R
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uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- name: Install dependencies
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::styler, any::roxygen2
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needs: styler
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- name: Enable styler cache
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run: styler::cache_activate()
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shell: Rscript {0}
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- name: Determine cache location
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id: styler-location
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run: |
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cat(
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"location=",
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styler::cache_info(format = "tabular")$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 --ff-only
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git push origin
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else
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echo "No changes to commit."
73+
fi

‎.gitignore

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/doc/
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/Meta/
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.secrets
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epidatr.Rproj

‎.lintr

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linters: with_defaults(
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linters: linters_with_defaults(
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line_length_linter(120),
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cyclocomp_linter = NULL
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)

‎DESCRIPTION

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Package: epidatr
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Type: Package
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Title: Client for Delphi's Epidata API
4-
Version: 0.8.0
4+
Version: 0.9.0
55
Authors@R:
66
c(
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person("Logan", "Brooks", email = "[email protected]", role = c("aut", "cre")),
@@ -25,7 +25,6 @@ Imports:
2525
magrittr,
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MMWRweek,
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readr,
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rlang,
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tibble,
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xml2
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RoxygenNote: 7.2.3

‎NAMESPACE

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@@ -17,6 +17,7 @@ export(dengue_nowcast)
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export(ecdc_ili)
1818
export(epirange)
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export(fetch)
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export(fetch_args_list)
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export(flusurv)
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export(fluview)
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export(fluview_clinical)
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export(pvt_sensors)
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export(pvt_twitter)
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export(wiki)
41-
export(with_base_url)
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importFrom(MMWRweek,MMWRweek2Date)
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importFrom(checkmate,assert)
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importFrom(checkmate,assert_character)
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importFrom(checkmate,assert_integerish)
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importFrom(checkmate,assert_logical)
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importFrom(checkmate,assert_numeric)
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importFrom(checkmate,check_character)
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importFrom(checkmate,check_class)
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importFrom(checkmate,check_date)
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importFrom(jsonlite,fromJSON)
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importFrom(magrittr,"%>%")
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importFrom(readr,read_csv)
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importFrom(rlang,abort)
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importFrom(tibble,as_tibble)
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importFrom(tibble,tibble)
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importFrom(xml2,read_html)

‎NEWS.md

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# epidatr 0.9.0
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3+
- Major interface change: all endpoints now fetch by default.
4+
- Make all `fetch` function internal.
5+
- Change `fetch` and `fetch_*` function interfaces now rely on `fetch_args_list`.
6+
- Added `fetch_args_list` which returns a list of arguments to be passed to `fetch`.
7+
18
# epidatr 0.8.0
29

3-
- Fix source name duplication bug in `covidcast_epidata`
4-
- Mark `covidcast_epidata` as experimental and do not export it
5-
- Change `covidcast` arg `data_source` to `source`
6-
- Make `covidcast` args `issues`, `lag`, and `as_of` mutually exclusive
10+
- Fix source name duplication bug in `covidcast_epidata`.
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- Mark `covidcast_epidata` as experimental and do not export it.
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- Change `covidcast` arg `data_source` to `source`.
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- Make `covidcast` args `issues`, `lag`, and `as_of` mutually exclusive.
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- Make `covid_hosp_facility_lookup` args `state,` `ccn`, `city`, `zip`, and
8-
`fips_code` mutually exclusive
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`fips_code` mutually exclusive.
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- Update documentation to only refer to character or strings (not character
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vectors or character strings)
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vectors or character strings).
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# epidatr 0.7.1
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‎R/auth.R

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1717
return(key)
1818
}
1919

20-
rlang::warn(
20+
cli::cli_warn(
2121
c(
22-
"No API key found. You will be limited to non-complex queries and encounter rate limits if you proceed.",
23-
"To avoid this, you can get your key by registering at https://api.delphi.cmu.edu/epidata/admin/registration_form and then:",
22+
"No API key found. You will be limited to non-complex queries and encounter rate limits if you proceed.
23+
To avoid this, you can get your key by registering
24+
at https://api.delphi.cmu.edu/epidata/admin/registration_form and then:",
2425
"i" = "set the environment variable DELPHI_EPIDATA_KEY",
2526
"i" = "set the option 'delphi.epidata.key'",
2627
"",
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"To save your key for later sessions (and hide it from your code), you can edit your .Renviron file with:",
2829
"i" = "usethis::edit_r_environ()"
2930
),
30-
use_cli_format = TRUE,
3131
.frequency = "regularly",
3232
.frequency_id = "delphi.epidata.key"
3333
)

‎R/check.R

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#' @importFrom checkmate assert_character assert_integerish
33
#' @keywords internal
44
assert_character_param <- function(name, value, len = NULL, required = TRUE) {
5-
null.ok <- !required
5+
null_ok <- !required
66
assert_integerish(len, null.ok = TRUE, .var.name = "len")
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assert_character(value, null.ok = null.ok, len = len, any.missing = FALSE, .var.name = name)
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assert_character(value, null.ok = null_ok, len = len, any.missing = FALSE, .var.name = name)
88
}
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1010
#' Allows integer-like vectors
1111
#' @importFrom checkmate assert_integerish
1212
#' @keywords internal
1313
assert_integerish_param <- function(name, value, len = NULL, required = TRUE) {
14-
null.ok <- !required
14+
null_ok <- !required
1515
assert_integerish(len, null.ok = TRUE, .var.name = "len")
16-
assert_integerish(value, null.ok = null.ok, len = len, any.missing = FALSE, .var.name = name)
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assert_integerish(value, null.ok = null_ok, len = len, any.missing = FALSE, .var.name = name)
1717
}
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1919
#' Allows a vector of date_like params: date, character, or integer-like
2020
#' @importFrom checkmate check_date check_character check_integerish
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#' @keywords internal
2222
assert_date_param <- function(name, value, len = NULL, required = TRUE) {
23-
null.ok <- !required
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null_ok <- !required
2424
assert_integerish(len, null.ok = TRUE, .var.name = "len")
2525
assert(
26-
check_date(value, len = len, any.missing = FALSE, null.ok = null.ok),
27-
check_character(value, len = len, any.missing = FALSE, null.ok = null.ok),
28-
check_integerish(value, len = len, any.missing = FALSE, null.ok = null.ok),
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check_date(value, len = len, any.missing = FALSE, null.ok = null_ok),
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check_character(value, len = len, any.missing = FALSE, null.ok = null_ok),
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check_integerish(value, len = len, any.missing = FALSE, null.ok = null_ok),
2929
combine = "or",
3030
.var.name = name
3131
)
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3636
#' @importFrom checkmate assert check_character check_date check_integerish check_class check_list check_names
3737
#' @keywords internal
3838
assert_timeset_param <- function(name, value, len = NULL, required = TRUE) {
39-
null.ok <- !required
39+
null_ok <- !required
4040
assert_integerish(len, len = 1L, null.ok = TRUE, .var.name = "len")
4141
assert(
42-
check_class(value, "EpiRange", null.ok = null.ok),
42+
check_class(value, "EpiRange", null.ok = null_ok),
4343
check_names(names(value), type = "unnamed"),
4444
combine = "or",
4545
.var.name = name
4646
)
4747
assert(
48-
check_date(value, len = len, any.missing = FALSE, null.ok = null.ok),
49-
check_character(value, len = len, any.missing = FALSE, null.ok = null.ok),
50-
check_integerish(value, len = len, any.missing = FALSE, null.ok = null.ok),
51-
check_class(value, "EpiRange", null.ok = null.ok),
48+
check_date(value, len = len, any.missing = FALSE, null.ok = null_ok),
49+
check_character(value, len = len, any.missing = FALSE, null.ok = null_ok),
50+
check_integerish(value, len = len, any.missing = FALSE, null.ok = null_ok),
51+
check_class(value, "EpiRange", null.ok = null_ok),
5252
combine = "or",
5353
.var.name = name
5454
)

‎R/constants.R

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version <- "0.8.0"
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version <- "0.9.0"
22
http_headers <- httr::add_headers("User-Agent" = paste0("epidatr/", version), "Accept-Encoding" = "gzip")
33
global_base_url <- "https://api.delphi.cmu.edu/epidata/"

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