Merge pull request #170 from cmu-delphi/cleanup

Cleanup

Author: dsweber2

.github/workflows/R-CMD-check-full.yaml

@@ -0,0 +1,61 @@
+# 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
+#
+# NOTE: This workflow is overkill for most R packages and
+# check-standard.yaml is likely a better choice.
+# usethis::use_github_action("check-standard") will install it.
+on:
+  workflow_dispatch:
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: macos-latest, r: "release" }
+
+          - { os: windows-latest, r: "release" }
+          # Use 3.6 to trigger usage of RTools35
+          - { os: windows-latest, r: "3.6" }
+          # use 4.1 to check with rtools40's older compiler
+          - { os: windows-latest, r: "4.1" }
+
+          - { os: ubuntu-latest, r: "devel", http-user-agent: "release" }
+          - { os: ubuntu-latest, r: "release" }
+          - { os: ubuntu-latest, r: "oldrel-1" }
+          - { os: ubuntu-latest, r: "oldrel-2" }
+          - { os: ubuntu-latest, r: "oldrel-3" }
+          - { os: ubuntu-latest, r: "oldrel-4" }
+          # The oldest version of R we claim to support
+          - { os: ubuntu-latest, r: "3.5" }
+
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+      R_KEEP_PKG_SOURCE: yes
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

.github/workflows/R-CMD-check.yaml

@@ -10,15 +10,33 @@ name: R-CMD-check
 
 jobs:
   R-CMD-check:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: macos-latest, r: "release" }
+          - { os: windows-latest, r: "release" }
+          - { os: ubuntu-latest, r: "devel", http-user-agent: "release" }
+          - { os: ubuntu-latest, r: "release" }
+          - { os: ubuntu-latest, r: "oldrel-1" }
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+
     steps:
       - uses: actions/checkout@v3
 
+      - uses: r-lib/actions/setup-pandoc@v2
+
       - uses: r-lib/actions/setup-r@v2
         with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
@@ -27,3 +45,5 @@ jobs:
           needs: check
 
       - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true

DEVELOPMENT.md

@@ -27,6 +27,6 @@ The release consists of multiple steps which can be all done via the GitHub webs
 5. Release to CRAN
 
 [mit-image]: https://img.shields.io/badge/License-MIT-yellow.svg
-[mit-url]: https://opensource.org/licenses/MIT
+[mit-url]: https://opensource.org/license/MIT
 [github-actions-image]: https://github.com/cmu-delphi/epidatr/workflows/ci/badge.svg
 [github-actions-url]: https://github.com/cmu-delphi/epidatr/actions

R/cache.R

@@ -250,12 +250,15 @@ cache_epidata_call <- function(epidata_call, fetch_args = fetch_args_list()) {
     as_of_recent <- check_is_recent(epidata_call$params$as_of, 7)
     issues_recent <- check_is_recent(epidata_call$params$issues, 7)
     if (as_of_recent || issues_recent) {
-      cli::cli_warn("using cached results with `as_of` within the past week (or the future!). This will likely result ",
-        "in an invalid cache. Consider\n",
-        "1. disabling the cache for this session with `disable_cache` or permanently with environmental ",
-        "variable `EPIDATR_USE_CACHE=FALSE`\n",
-        "2. setting `EPIDATR_CACHE_MAX_AGE_DAYS={Sys.getenv('EPIDATR_CACHE_MAX_AGE_DAYS', unset = 1)}` to e.g. `3/24` ",
-        "(3 hours).",
+      cli::cli_warn(
+        c(
+          "using cached results with `as_of` within the past week (or the future!).",
+          "This will likely result in an invalid cache. Consider\n",
+          "1. disabling the cache for this session with `disable_cache` or permanently with environmental ",
+          "variable `EPIDATR_USE_CACHE=FALSE`\n",
+          "2. setting `EPIDATR_CACHE_MAX_AGE_DAYS={Sys.getenv('EPIDATR_CACHE_MAX_AGE_DAYS', unset = 1)}`",
+          " to e.g. `3/24` (3 hours)."
+        ),
         .frequency = "regularly",
         .frequency_id = "cache timing issues",
         class = "cache_recent_data"

R/endpoints.R

@@ -1715,13 +1715,6 @@ pvt_twitter <- function(auth, locations, ..., dates = NULL, epiweeks = NULL, fet
 #' @description
 #' API docs: <https://cmu-delphi.github.io/delphi-epidata/api/wiki.html>
 #'
-#' ```{r results="asis", echo = FALSE}
-#' url <- "https://github.com/raw/cmu-delphi/delphi-epidata/dev/docs/api/covidcast_signals.md"
-#' txt <- readLines(url)
-#' txt <- txt[7:length(txt)]
-#' cat(txt, sep = "\n")
-#' ```
-#'
 #' @examples
 #' \dontrun{
 #' pub_wiki(articles = "avian_influenza", epiweeks = epirange(201501, 201601))

README.md

@@ -1,7 +1,7 @@
 # Delphi Epidata R client
 
 [![License: MIT][mit-image]][mit-url] [![Github Actions][github-actions-image]][github-actions-url]
-[![codecov](https://codecov.io/gh/dsweber2/epidatr/branch/dev/graph/badge.svg?token=jVHL9eHZNZ)](https://codecov.io/gh/dsweber2/epidatr)
+[![codecov](https://codecov.io/gh/dsweber2/epidatr/branch/dev/graph/badge.svg?token=jVHL9eHZNZ)](https://app.codecov.io/gh/dsweber2/epidatr)
 
 The [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/) provides real-time access to epidemiological surveillance data for influenza, COVID-19, and other diseases from both official government sources such as the [Center for Disease Control (CDC)](https://www.cdc.gov/datastatistics/index.html) and [Google Trends](https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/google-symptoms.html) and private partners such as [Facebook](https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/) and [Change Healthcare](https://www.changehealthcare.com/). It is built and maintained by the Carnegie Mellon University [Delphi research group](https://delphi.cmu.edu/).
 
@@ -82,7 +82,7 @@ Note that for the time being, the private endpoints (i.e. those prefixed with
 `pvt`) will require a separate key that needs to be passed as an argument.
 
 [mit-image]: https://img.shields.io/badge/License-MIT-yellow.svg
-[mit-url]: https://opensource.org/licenses/MIT
+[mit-url]: https://opensource.org/license/mit
 [github-actions-image]: https://github.com/cmu-delphi/epidatr/workflows/ci/badge.svg
 [github-actions-url]: https://github.com/cmu-delphi/epidatr/actions
 

man/pub_wiki.Rd

@@ -2,17 +2,7 @@ test_that("basic cache setup", {
   expect_true(is.null(cache_environ$epidatr_cache))
 })
 
-tmp_base_dir <- Sys.getenv("TMPDIR")
-new_temp_dir <- NULL
-if (tmp_base_dir == "") {
-  new_temp_dir <- md5(paste(Sys.time(), "I am the very model of a modern major general"))
-} else {
-  new_temp_dir <- file.path(
-    Sys.getenv("TMPDIR"),
-    md5(paste(Sys.time(), "I am the very model of a modern major general"))
-  )
-}
-
+new_temp_dir <- tempdir()
 test_set_cache <- function(cache_dir = new_temp_dir,
                            days = 1,
                            max_size = 1,
@@ -31,11 +21,11 @@ test_that("cache set as expected", {
   test_set_cache()
   if (grepl("/", as.character(new_temp_dir))) {
     # this is what check produces
-    expect_equal(cache_info()$dir, as.character(new_temp_dir))
+    expect_equal(cache_info()$dir, normalizePath(new_temp_dir))
   } else {
     # this is what test produces directly
     tmp <- strsplit(cache_info()$dir, "/")[[1]]
-    expect_equal(tmp[length(tmp)], as.character(new_temp_dir))
+    expect_equal(tmp[length(tmp)], normalizePath(new_temp_dir))
   }
   expect_equal(cache_info()$max_size, 1024^2)
   expect_equal(cache_info()$max_age, 24 * 60 * 60)