fix: styler, build, test, check all happy

DESCRIPTION

@@ -28,6 +28,7 @@ Imports:
     checkmate,
     cli,
     httr,
+    glue,
     jsonlite,
     magrittr,
     MMWRweek,

NAMESPACE

@@ -45,6 +45,7 @@ export(pvt_twitter)
 export(set_cache)
 export(wiki)
 import(cachem)
+import(glue)
 import(openssl)
 importFrom(MMWRweek, MMWRweek2Date)
 importFrom(checkmate, assert)

R/cache.R

@@ -1,21 +1,32 @@
 # IMPORTANT DEV NOTE:
-# make sure to @include cache.R in the Roxygen docs of any function referencing this environment, so this file is loaded first
+# make sure to @include cache.R in the Roxygen docs of any function referencing this environment, so this file is loaded
+# first
 cache_environ <- new.env(parent = emptyenv())
 cache_environ$use_cache <- NULL
 cache_environ$epidatr_cache <- NULL
 #' create or renew a cache for this session
-#'
+#' @aliases set_cache
 #' @description
-#' By default, epidatr re-requests data from the API on every call of `fetch`. In case you find yourself repeatedly calling the same data, you can enable the cache using either this function for a given session, or environmental variables for a persistent cache.
-#' The typical recommended workflow for using the cache is to set the environmental variables `EPIDATR_USE_CACHE=TRUE` and `EPIDATR_CACHE_DIRECTORY="/your/directory/here"`in your `.Renviron`, for example by calling `usethis::edit_r_environ()`.
+#' By default, epidatr re-requests data from the API on every call of `fetch`. In case you find yourself repeatedly
+#'   calling the same data, you can enable the cache using either this function for a given session, or environmental
+#'   variables for a persistent cache.
+#' The typical recommended workflow for using the cache is to set the environmental variables `EPIDATR_USE_CACHE=TRUE`
+#'   and `EPIDATR_CACHE_DIRECTORY="/your/directory/here"`in your `.Renviron`, for example by calling
+#'   `usethis::edit_r_environ()`.
 #' See the parameters below for some more configurables if you're so inclined.
 #'
-#' `set_cache` (re)defines the cache to use in a particular R session. This does not clear existing data at any previous location, but instead creates a handle to the new cache using [cachem](https://cachem.r-lib.org/index.html) that seamlessly handles caching for you.
-#' Say your cache is normally stored in some default directory, but for the current session you want to save your results in `~/my/temporary/savedirectory`, then you would call `set_cache(dir = "~/my/temporary/savedirectory")`.
-#' Or if you know the data from 2 days ago is wrong, you could call `set_cache(days = 1)` to clear older data whenever the cache is referenced.
-#' In both cases, these changes would only last for a single session (though the deleted data would be gone permanently!).
+#' `set_cache` (re)defines the cache to use in a particular R session. This does not clear existing data at any previous
+#'   location, but instead creates a handle to the new cache using [cachem](https://cachem.r-lib.org/index.html) that
+#'   seamlessly handles caching for you.
+#' Say your cache is normally stored in some default directory, but for the current session you want to save your
+#'   results in `~/my/temporary/savedirectory`, then you would call `set_cache(dir = "~/my/temporary/savedirectory")`.
+#' Or if you know the data from 2 days ago is wrong, you could call `set_cache(days = 1)` to clear older data whenever
+#'   the cache is referenced.
+#' In both cases, these changes would only last for a single session (though the deleted data would be gone
+#'   permanently!).
 #'
-#' An important feature of the caching in this package is that only calls which specify either `issues` before a certain date, or `as_of` before a certain date will actually cache. For example the call
+#' An important feature of the caching in this package is that only calls which specify either `issues` before a certain
+#'   date, or `as_of` before a certain date will actually cache. For example the call
 #' ```
 #' covidcast(
 #'   source = "jhu-csse",
@@ -26,7 +37,8 @@ cache_environ$epidatr_cache <- NULL
 #'   time_values = epirange(20200601, 20230801)
 #' )
 #' ```
-#' *won't* cache, since it is possible for the cache to be invalidated by new releases with no warning. On the other hand, the call
+#' *won't* cache, since it is possible for the cache to be invalidated by new releases with no warning. On the other
+#'   hand, the call
 #' ```
 #' covidcast(
 #'   source = "jhu-csse",
@@ -38,9 +50,13 @@ cache_environ$epidatr_cache <- NULL
 #'   as_of = "2023-08-01"
 #' )
 #' ```
-#' *will* cache, since normal new versions of data can't invalidate it (since they would be `as_of` a later date). It is still possible that Delphi may patch such data, but the frequency is on the order of months rather than days. We are working on creating a public channel to communicate such updates. While specifying `issues` will usually cache, a call with `issues="*"` won't cache, since its subject to cache invalidation by normal versioning.
+#' *will* cache, since normal new versions of data can't invalidate it (since they would be `as_of` a later date). It is
+#'   still possible that Delphi may patch such data, but the frequency is on the order of months rather than days. We
+#'   are working on creating a public channel to communicate such updates. While specifying `issues` will usually cache,
+#'   a call with `issues="*"` won't cache, since its subject to cache invalidation by normal versioning.
 #'
-#' On the backend, the cache uses cachem, with filenames generated using an md5 encoding of the call url. Each file corresponds to a unique epidata-API call.
+#' On the backend, the cache uses cachem, with filenames generated using an md5 encoding of the call url. Each file
+#'   corresponds to a unique epidata-API call.
 #' @examples
 #' \dontrun{
 #' set_cache(
@@ -52,15 +68,26 @@ cache_environ$epidatr_cache <- NULL
 #' )
 #' }
 #'
-#' @param cache_dir the directory in which the cache is stored. By default, this is `tools::R_user_dir()` if on R 4.0+, but must be specified for earlier versions of R. The path can be either relative or absolute. The environmental variable is `EPIDATR_CACHE_DIR`.
-#' @param days the maximum length of time in days to keep any particular cached call. By default this is `1`. The environmental variable is `EPIDATR_CACHE_MAX_AGE_DAYS`.
-#' @param max_size the size of the entire cache, in MB, at which to start pruning entries. By default this is `1024`, or 1GB. The environmental variable is `EPIDATR_CACHE_MAX_SIZE_MB`.
-#' @param logfile where cachem's log of transactions is stored, relative to the cache directory. By default, it is `"logfile.txt"`. The environmental variable is `EPIDATR_CACHE_LOGFILE`.
-#' @param prune_rate how many calls to go between checking if any cache elements are too old or if the cache overall is too large. Defaults to `2000L`. Since cachem fixes the max time between prune checks to 5 seconds, there's little reason to actually change this parameter. Doesn't have a corresponding environmental variable.
-#' @param confirm whether to confirm directory creation. default is `TRUE`; should only be set in non-interactive scripts
-#' @seealso [clear_cache] to delete the old cache while making a new one, [disable_cache] to disable without deleting, and [cache_info]
+#' @param cache_dir the directory in which the cache is stored. By default, this is `tools::R_user_dir()` if on R 4.0+,
+#'   but must be specified for earlier versions of R. The path can be either relative or absolute. The environmental
+#'   variable is `EPIDATR_CACHE_DIR`.
+#' @param days the maximum length of time in days to keep any particular cached call. By default this is `1`. The
+#'   environmental variable is `EPIDATR_CACHE_MAX_AGE_DAYS`.
+#' @param max_size the size of the entire cache, in MB, at which to start pruning entries. By default this is `1024`, or
+#'   1GB. The environmental variable is `EPIDATR_CACHE_MAX_SIZE_MB`.
+#' @param logfile where cachem's log of transactions is stored, relative to the cache directory. By default, it is
+#'   `"logfile.txt"`. The environmental variable is `EPIDATR_CACHE_LOGFILE`.
+#' @param prune_rate how many calls to go between checking if any cache elements are too old or if the cache overall is
+#'   too large. Defaults to `2000L`. Since cachem fixes the max time between prune checks to 5 seconds, there's little
+#'   reason to actually change this parameter. Doesn't have a corresponding environmental variable.
+#' @param confirm whether to confirm directory creation. default is `TRUE`; should only be set in non-interactive
+#'   scripts
+#' @seealso [clear_cache] to delete the old cache while making a new one, [disable_cache] to disable without deleting,
+#'   and [cache_info]
 #' @export
 #' @import cachem
+#' @import glue
+#' @importFrom utils sessionInfo
 set_cache <- function(cache_dir = NULL,
                       days = NULL,
                       max_size = NULL,
@@ -72,7 +99,7 @@ set_cache <- function(cache_dir = NULL,
   } else if (is.null(cache_dir)) {
     # earlier version, so no tools
     cache_dir <- Sys.getenv("EPIDATR_CACHE_DIR")
-    if (cach_dir == "") {
+    if (cache_dir == "") {
       cli::cli_abort("no valid EPIDATR_CACHE_DIR", class = "epidatr_cache_error")
     }
   }
@@ -94,9 +121,13 @@ set_cache <- function(cache_dir = NULL,
   cache_usable <- file.access(cache_dir, mode = 6) == 0
   if (!(cache_exists)) {
     if (confirm) {
-      user_input <- readline(glue::glue("there is no directory at {cache_dir}; the cache will be turned off until a viable directory has been set. Create one? (yes|no) "))
+      user_input <- readline(glue::glue(
+        "there is no directory at {cache_dir}; the cache will be turned off until a ",
+        "viable directory has been set. Create one? (yes|no(default)) "
+      ))
       repeat {
         valid_user_input <- ifelse(grepl("yes|no", user_input), sub(".*(yes|no).*", "\\1", user_input), NA)
+        valid_user_input <- ifelse(grepl("", user_input), "", NA)
         if (!is.na(valid_user_input)) {
           break
         }
@@ -114,7 +145,10 @@ set_cache <- function(cache_dir = NULL,
 
 
   if (!cache_usable) {
-    print(glue::glue("The directory at {cache_dir} is not accessible; check permissions and/or use a different directory for the cache (see the `set_cache` documentation)."))
+    print(glue::glue(
+      "The directory at {cache_dir} is not accessible; check permissions and/or use a different ",
+      "directory for the cache (see the `set_cache` documentation)."
+    ))
   } else if (cache_exists) {
     cache_environ$epidatr_cache <- cachem::cache_disk(
       dir = cache_dir,
@@ -128,7 +162,9 @@ set_cache <- function(cache_dir = NULL,
 
 #' manually reset the cache, deleting all currently saved data and starting afresh
 #' @description
-#' deletes the current cache and resets a new cache. Deletes local data! If you are using a session unique cache, you will have to pass the arguments you used for `set_cache` earlier, otherwise the system-wide `.Renviron`-based defaults will be used.
+#' deletes the current cache and resets a new cache. Deletes local data! If you are using a session unique cache, you
+#'   will have to pass the arguments you used for `set_cache` earlier, otherwise the system-wide `.Renviron`-based
+#'   defaults will be used.
 #' @examples
 #' \dontrun{
 #' clear_cache(
@@ -140,22 +176,29 @@ set_cache <- function(cache_dir = NULL,
 #' )
 #' }
 #' @param disable instead of setting a new cache, disable caching entirely; defaults to `FALSE`
+#' @param ... see the `set_cache` arguments below
 #' @inheritParams set_cache
-#' @seealso [set_cache] to start a new cache (and general caching info), [disable_cache] to only disable without deleting, and [cache_info]
+#' @seealso [set_cache] to start a new cache (and general caching info), [disable_cache] to only disable without
+#'   deleting, and [cache_info]
 #' @export
 #' @import cachem
 clear_cache <- function(disable = FALSE, ...) {
   cache_environ$epidatr_cache$destroy()
   if (!disable) {
     set_cache(...)
+  } else {
+    cache_environ$epidatr_cache <- NULL
   }
 }
 
 #' turn off the caching for this session
 #' @description
-#' Disable caching until you call `set_cache` or restart R. The files defining the cache are untouched. If you are looking to disable the caching more permanently, set `EPIDATR_USE_CACHE=FALSE` as environmental variable in your `.Renviron`.
+#' Disable caching until you call `set_cache` or restart R. The files defining the cache are untouched. If you are
+#'   looking to disable the caching more permanently, set `EPIDATR_USE_CACHE=FALSE` as environmental variable in your
+#'   `.Renviron`.
 #' @export
-#' @seealso [set_cache] to start a new cache (and general caching info), [clear_cache] to delete the cache and set a new one, and [cache_info]
+#' @seealso [set_cache] to start a new cache (and general caching info), [clear_cache] to delete the cache and set a new
+#'   one, and [cache_info]
 #' @import cachem
 disable_cache <- function() {
   cache_environ$epidatr_cache <- NULL
@@ -164,12 +207,16 @@ disable_cache <- function() {
 #' describe current cache
 #' @description
 #' Print out the information about the cache (as would be returned by cachem's `info()` method)
-#' @examples
-#' cache_info()
-#' @seealso [set_cache] to start a new cache (and general caching info), [clear_cache] to delete the cache and set a new one, and [disable_cache] to disable without deleting
+#' @seealso [set_cache] to start a new cache (and general caching info),
+#'   [clear_cache] to delete the cache and set a new one, and [disable_cache] to
+#'   disable without deleting
 #' @export
 cache_info <- function() {
-  cache_environ$epidatr_cache$info()
+  if (is.null(cache_environ$epidatr_cache)) {
+    return("there is no cache")
+  } else {
+    return(cache_environ$epidatr_cache$info())
+  }
 }
 
 #' dispatch caching
@@ -190,9 +237,12 @@ 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
-1. disabling the cache for this session with `disable_cache` or permanently with environmental variable `EPIDATR_USE_CACHE=FALSE`
-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("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/epidatr-package.R

@@ -4,7 +4,7 @@
 
 .onLoad <- function(libname, pkgname) {
   cache_environ$use_cache <- Sys.getenv("EPIDATR_USE_CACHE", unset = FALSE)
-  cache_environ$use_cache <- cache_environ$use_cache == "TRUE"
+  cache_environ$use_cache <- (cache_environ$use_cache == "TRUE")
   if (cache_environ$use_cache) {
     set_cache()
   }