Merge pull request #156 from cmu-delphi/ds/merge-fetch

refactor: `fetch` by default

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.8.0
+current_version = 0.9.0
 commit = False
 tag = False
 

.github/CODEOWNERS

@@ -1 +1 @@
-* @dshemetov @brookslogan
+* @dshemetov @brookslogan @dsweber2

.github/workflows/ci.yml

@@ -19,17 +19,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::devtools, any::rcmdcheck, any::styler, any::lintr, local::.
-
-      - name: Style / Format
-        shell: Rscript {0}
-        run: styler::style_pkg(dry="fail")
-
-      - name: Lint
-        shell: Rscript {0}
-        run: |
-          devtools::load_all()
-          lintr::lint_package('.')
+          extra-packages: any::devtools, any::rcmdcheck, local::.
 
       - uses: r-lib/actions/check-r-package@v2
         env:

.github/workflows/document.yaml

@@ -0,0 +1,42 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    paths: ["R/**"]
+
+name: Document
+
+jobs:
+  document:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: roxygen2
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add man/\* NAMESPACE DESCRIPTION
+          git commit -m "docs: update documentation (GHA)" || echo "No changes to commit"
+          git pull --ff-only
+          git push origin

.github/workflows/lint.yaml

@@ -0,0 +1,32 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master, dev]
+  pull_request:
+    branches: [main, master, dev]
+
+name: lint
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::lintr, local::.
+          needs: lint
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/style.yaml

@@ -0,0 +1,73 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    paths: ["**.[rR]", "**.[qrR]md", "**.[rR]markdown", "**.[rR]nw", "**.[rR]profile"]
+
+name: Style
+
+jobs:
+  style:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - name: Install dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::styler, any::roxygen2
+          needs: styler
+
+      - name: Enable styler cache
+        run: styler::cache_activate()
+        shell: Rscript {0}
+
+      - name: Determine cache location
+        id: styler-location
+        run: |
+          cat(
+            "location=",
+            styler::cache_info(format = "tabular")$location,
+            "\n",
+            file = Sys.getenv("GITHUB_OUTPUT"),
+            append = TRUE,
+            sep = ""
+          )
+        shell: Rscript {0}
+
+      - name: Cache styler
+        uses: actions/cache@v3
+        with:
+          path: ${{ steps.styler-location.outputs.location }}
+          key: ${{ runner.os }}-styler-${{ github.sha }}
+          restore-keys: |
+            ${{ runner.os }}-styler-
+            ${{ runner.os }}-
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: Commit and push changes
+        run: |
+          if FILES_TO_COMMIT=($(git diff-index --name-only ${{ github.sha }} \
+              | egrep --ignore-case '\.(R|[qR]md|Rmarkdown|Rnw|Rprofile)$'))
+          then
+            git config --local user.name "$GITHUB_ACTOR"
+            git config --local user.email "[email protected]"
+            git commit ${FILES_TO_COMMIT[*]} -m "style: styler (GHA)"
+            git pull --ff-only
+            git push origin
+          else
+            echo "No changes to commit."
+          fi

.gitignore

@@ -16,3 +16,4 @@ env
 /doc/
 /Meta/
 .secrets
+epidatr.Rproj

.lintr

@@ -1,4 +1,4 @@
-linters: with_defaults(
+linters: linters_with_defaults(
   line_length_linter(120),
   cyclocomp_linter = NULL
   )

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: epidatr
 Type: Package
 Title: Client for Delphi's Epidata API
-Version: 0.8.0
+Version: 0.9.0
 Authors@R: 
   c(
     person("Logan", "Brooks", email = "[email protected]", role = c("aut", "cre")),
@@ -25,7 +25,6 @@ Imports:
     magrittr,
     MMWRweek,
     readr,
-    rlang,
     tibble,
     xml2
 RoxygenNote: 7.2.3

NAMESPACE

@@ -17,6 +17,7 @@ export(dengue_nowcast)
 export(ecdc_ili)
 export(epirange)
 export(fetch)
+export(fetch_args_list)
 export(flusurv)
 export(fluview)
 export(fluview_clinical)
@@ -38,11 +39,12 @@ export(pvt_quidel)
 export(pvt_sensors)
 export(pvt_twitter)
 export(wiki)
-export(with_base_url)
 importFrom(MMWRweek,MMWRweek2Date)
 importFrom(checkmate,assert)
 importFrom(checkmate,assert_character)
 importFrom(checkmate,assert_integerish)
+importFrom(checkmate,assert_logical)
+importFrom(checkmate,assert_numeric)
 importFrom(checkmate,check_character)
 importFrom(checkmate,check_class)
 importFrom(checkmate,check_date)
@@ -63,7 +65,6 @@ importFrom(httr,stop_for_status)
 importFrom(jsonlite,fromJSON)
 importFrom(magrittr,"%>%")
 importFrom(readr,read_csv)
-importFrom(rlang,abort)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
 importFrom(xml2,read_html)

NEWS.md

@@ -1,13 +1,20 @@
+# epidatr 0.9.0
+
+- Major interface change: all endpoints now fetch by default.
+- Make all `fetch` function internal.
+- Change `fetch` and `fetch_*` function interfaces now rely on `fetch_args_list`.
+- Added `fetch_args_list` which returns a list of arguments to be passed to `fetch`.
+
 # epidatr 0.8.0
 
-- Fix source name duplication bug in `covidcast_epidata`
-- Mark `covidcast_epidata` as experimental and do not export it
-- Change `covidcast` arg `data_source` to `source`
-- Make `covidcast` args `issues`, `lag`, and `as_of` mutually exclusive
+- Fix source name duplication bug in `covidcast_epidata`.
+- Mark `covidcast_epidata` as experimental and do not export it.
+- Change `covidcast` arg `data_source` to `source`.
+- Make `covidcast` args `issues`, `lag`, and `as_of` mutually exclusive.
 - Make `covid_hosp_facility_lookup` args `state,` `ccn`, `city`, `zip`, and
-  `fips_code` mutually exclusive
+  `fips_code` mutually exclusive.
 - Update documentation to only refer to character or strings (not character
-  vectors or character strings)
+  vectors or character strings).
 
 # epidatr 0.7.1
 

R/auth.R

@@ -17,17 +17,17 @@ get_auth_key <- function() {
     return(key)
   }
 
-  rlang::warn(
+  cli::cli_warn(
     c(
-      "No API key found. You will be limited to non-complex queries and encounter rate limits if you proceed.",
-      "To avoid this, you can get your key by registering at https://api.delphi.cmu.edu/epidata/admin/registration_form and then:",
+      "No API key found. You will be limited to non-complex queries and encounter rate limits if you proceed.
+      To avoid this, you can get your key by registering
+      at https://api.delphi.cmu.edu/epidata/admin/registration_form and then:",
       "i" = "set the environment variable DELPHI_EPIDATA_KEY",
       "i" = "set the option 'delphi.epidata.key'",
       "",
       "To save your key for later sessions (and hide it from your code), you can edit your .Renviron file with:",
       "i" = "usethis::edit_r_environ()"
     ),
-    use_cli_format = TRUE,
     .frequency = "regularly",
     .frequency_id = "delphi.epidata.key"
   )

R/check.R

@@ -2,30 +2,30 @@
 #' @importFrom checkmate assert_character assert_integerish
 #' @keywords internal
 assert_character_param <- function(name, value, len = NULL, required = TRUE) {
-  null.ok <- !required
+  null_ok <- !required
   assert_integerish(len, null.ok = TRUE, .var.name = "len")
-  assert_character(value, null.ok = null.ok, len = len, any.missing = FALSE, .var.name = name)
+  assert_character(value, null.ok = null_ok, len = len, any.missing = FALSE, .var.name = name)
 }
 
 #' Allows integer-like vectors
 #' @importFrom checkmate assert_integerish
 #' @keywords internal
 assert_integerish_param <- function(name, value, len = NULL, required = TRUE) {
-  null.ok <- !required
+  null_ok <- !required
   assert_integerish(len, null.ok = TRUE, .var.name = "len")
-  assert_integerish(value, null.ok = null.ok, len = len, any.missing = FALSE, .var.name = name)
+  assert_integerish(value, null.ok = null_ok, len = len, any.missing = FALSE, .var.name = name)
 }
 
 #' Allows a vector of date_like params: date, character, or integer-like
 #' @importFrom checkmate check_date check_character check_integerish
 #' @keywords internal
 assert_date_param <- function(name, value, len = NULL, required = TRUE) {
-  null.ok <- !required
+  null_ok <- !required
   assert_integerish(len, null.ok = TRUE, .var.name = "len")
   assert(
-    check_date(value, len = len, any.missing = FALSE, null.ok = null.ok),
-    check_character(value, len = len, any.missing = FALSE, null.ok = null.ok),
-    check_integerish(value, len = len, any.missing = FALSE, null.ok = null.ok),
+    check_date(value, len = len, any.missing = FALSE, null.ok = null_ok),
+    check_character(value, len = len, any.missing = FALSE, null.ok = null_ok),
+    check_integerish(value, len = len, any.missing = FALSE, null.ok = null_ok),
     combine = "or",
     .var.name = name
   )
@@ -36,19 +36,19 @@ assert_date_param <- function(name, value, len = NULL, required = TRUE) {
 #' @importFrom checkmate assert check_character check_date check_integerish check_class check_list check_names
 #' @keywords internal
 assert_timeset_param <- function(name, value, len = NULL, required = TRUE) {
-  null.ok <- !required
+  null_ok <- !required
   assert_integerish(len, len = 1L, null.ok = TRUE, .var.name = "len")
   assert(
-    check_class(value, "EpiRange", null.ok = null.ok),
+    check_class(value, "EpiRange", null.ok = null_ok),
     check_names(names(value), type = "unnamed"),
     combine = "or",
     .var.name = name
   )
   assert(
-    check_date(value, len = len, any.missing = FALSE, null.ok = null.ok),
-    check_character(value, len = len, any.missing = FALSE, null.ok = null.ok),
-    check_integerish(value, len = len, any.missing = FALSE, null.ok = null.ok),
-    check_class(value, "EpiRange", null.ok = null.ok),
+    check_date(value, len = len, any.missing = FALSE, null.ok = null_ok),
+    check_character(value, len = len, any.missing = FALSE, null.ok = null_ok),
+    check_integerish(value, len = len, any.missing = FALSE, null.ok = null_ok),
+    check_class(value, "EpiRange", null.ok = null_ok),
     combine = "or",
     .var.name = name
   )

R/constants.R

@@ -1,3 +1,3 @@
-version <- "0.8.0"
+version <- "0.9.0"
 http_headers <- httr::add_headers("User-Agent" = paste0("epidatr/", version), "Accept-Encoding" = "gzip")
 global_base_url <- "https://api.delphi.cmu.edu/epidata/"