Merge branch 'devel'

ropensci · Aug 22, 2023 · 816dd70 · 816dd70
2 parents c23e96a + 9729c2e
commit 816dd70
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diff --git a/.github/workflows/tic.yml b/.github/workflows/tic.yml
@@ -30,7 +30,7 @@ jobs:
         config:
           # use a different tic template type if you do not want to build on all listed platforms
           - { os: windows-latest, r: "release" }
-          - { os: macOS-latest, r: "release", pkgdown: "true", latex: "true" }
+          - { os: macOS-latest, r: "release", pkgdown: "false", latex: "true" }
           - { os: ubuntu-latest, r: "devel" }
           - { os: ubuntu-latest, r: "release" }
 
@@ -39,9 +39,6 @@ jobs:
       TIC_DEPLOY_KEY: ${{ secrets.TIC_DEPLOY_KEY }}
       # prevent rgl issues because no X11 display is available
       RGL_USE_NULL: true
-      # if you use bookdown or blogdown, replace "PKGDOWN" by the respective
-      # capitalized term. This also might need to be done in tic.R
-      BUILD_PKGDOWN: ${{ matrix.config.pkgdown }}
       # use GITHUB_TOKEN from GitHub to workaround rate limits in {remotes}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,40 +1,41 @@
 Package: GSODR
 Type: Package
 Title: Global Surface Summary of the Day ('GSOD') Weather Data Client
-Version: 3.1.8.9000
-Authors@R: c(person("Adam H.", "Sparks", role = c("aut", "cre"),
-    email = "[email protected]",
-    comment = c(ORCID = "0000-0002-0061-8359")),
+Version: 3.1.9
+Authors@R: c(
+    person("Adam H.", "Sparks", role = c("aut", "cre"),
+        email = "[email protected]",
+        comment = c(ORCID = "0000-0002-0061-8359")),
     person("Tomislav", "Hengl", role = "aut",
-    email = "[email protected]",
-    comment = c(ORCID = "0000-0002-9921-5129")),
+        email = "[email protected]",
+        comment = c(ORCID = "0000-0002-9921-5129")),
     person("Andrew", "Nelson", role = "aut",
-    email = "[email protected]",
-    comment = c(ORCID = "0000-0002-7249-3778")),
+        email = "[email protected]",
+        comment = c(ORCID = "0000-0002-7249-3778")),
     person("Hugh", "Parsonage", role = c("cph", "ctb"),
-    email = "[email protected]",
-    comment = c(ORCID = "0000-0003-4055-0835")),
+        email = "[email protected]",
+        comment = c(ORCID = "0000-0003-4055-0835")),
     person("Taras", "Kaduk", role = "ctb",
-    email = "[email protected]",
-    comment = "Suggestion for handling bulk station downloads more
-    efficiently"),
+        email = "[email protected]",
+        comment = "Suggestion for handling bulk station downloads more
+        efficiently"),
     person("Gwenael", "Giboire", role = "ctb",
-    email = "[email protected]",
-    comment = "Several bug reports in early versions and testing feedback"),
+        email = "[email protected]",
+        comment = "Several bug reports in early versions and testing feedback"),
     person("Łukasz", "Pawlik", role = "ctb", email = "[email protected]", 
-    comment = "Reported bug in windspeed conversion calculation"),
+        comment = "Reported bug in windspeed conversion calculation"),
     person("Ross","Darnell", role = "ctb",
-    email = "[email protected]", comment = c(
-    "Reported bug in 'Windows OS' versions causing 'GSOD' data untarring to
-    fail",
-    ORCID = "0000-0002-7973-6322")),
+        email = "[email protected]", comment = c(
+        "Reported bug in 'Windows OS' versions causing 'GSOD' data untarring to
+        fail",
+        ORCID = "0000-0002-7973-6322")),
     person("Tyler", "Widdison", role = "ctb",
-    email = "[email protected]", comment = "Reported bug where
-    `nearest_stations()` did not return stations in order of nearest to
-    farthest"),
+        email = "[email protected]", comment = "Reported bug where
+        `nearest_stations()` did not return stations in order of nearest to
+        farthest"),
     person(given = "Western Australia Agriculture Authority (WAAA)",
-    role = "cph", comment = c("Supported the development of 'GSODR' through
-    Adam H. Sparks's time.")))
+        role = "cph", comment = c("Supported the development of 'GSODR' through
+        Adam H. Sparks's time.")))
 URL: https://docs.ropensci.org/GSODR/
 BugReports: https://github.com/ropensci/GSODR/issues
 Description: Provides automated downloading, parsing, cleaning, unit conversion
@@ -61,7 +62,6 @@ Imports:
     countrycode,
     curl,
     data.table,
-    httr,
     R.utils,
     stats,
     utils
@@ -73,9 +73,7 @@ Suggests:
     knitr,
     mapproj,
     maps,
-    remotes,
     rmarkdown,
-    roxygen2,
     testthat,
     tidyr
 RoxygenNote: 7.2.3

diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,19 @@
-# GSODR (development version)
+# GSODR 3.1.9
+
+## Bug fixes
 
 - Fix duplicated elevation columns.
 
+## Minor changes
+
+- Remove {httr} as an Import. Use base functionality to check existence first and then {curl} will properly error if a download fails, we will use that functionality.
+
+- Fix codecov badge to point at proper branch.
+
+- Ensure function titles are all proper title case.
+
+- Enhanced handling of data requests for incompatible station-year combinations. A `warning()` is issued for each bad combo, but if a `vector()` of stations is requested, any valid stations will still be downloaded with the bad combos omitted after the warning is emitted.
+
 # GSODR 3.1.8
 
 - Update CITATION file to follow CRAN's ~ever-changing whims~ guidelines.

diff --git a/R/get_GSOD.R b/R/get_GSOD.R
@@ -1,5 +1,4 @@
-
-#' Download and return a data.table object of GSOD weather data
+#' Download and Return a data.table Object of GSOD Weather Data
 #'
 #' @description
 #' This function automates downloading, cleaning, reformatting of data from
@@ -99,46 +98,59 @@ get_GSOD <- function(years,
                      country = NULL,
                      max_missing = NULL,
                      agroclimatology = FALSE) {
-
   # Validate user inputs -------------------------------------------------------
   .validate_years(years)
   # Validate stations for missing days -----------------------------------------
   if (!is.null(max_missing)) {
     if (is.na(max_missing) | max_missing < 1) {
-      stop(call. = FALSE,
-           "\nThe `max_missing` parameter must be a positive",
-           "value larger than 1\n")
+      stop(
+        call. = FALSE,
+        "\nThe `max_missing` parameter must be a positive",
+        "value larger than 1\n"
+      )
     }
   }
 
   if (!is.null(max_missing)) {
     if (format(Sys.Date(), "%Y") %in% years) {
-      stop(call. = FALSE,
-           "You cannot use `max_missing` with the current, incomplete year.")
+      stop(
+        call. = FALSE,
+        "You cannot use `max_missing` with the current, incomplete year."
+      )
     }
   }
 
   if (isTRUE(agroclimatology) & !is.null(station)) {
-    stop(call. = FALSE,
-         "You cannot specify a single station along with agroclimatology.")
+    stop(
+      call. = FALSE,
+      "You cannot specify a single station along with agroclimatology."
+    )
   }
 
-# CRAN NOTE avoidance
-  isd_history <- NULL # nocov
-
   # Load station list
   load(system.file("extdata", "isd_history.rda", package = "GSODR")) # nocov
 
-  # Validate user entered stations for existence in stations list from NCEI
-  invisible(lapply(
-    X = station,
-    FUN = .validate_station,
-    isd_history = isd_history,
-    years = years
-  ))
+  if (!is.null(station)) {
+    # Validate user entered stations for existence in stations list from NCEI
+    invisible(lapply(
+      X = station,
+      FUN = .validate_station_id,
+      isd_history = isd_history
+    ))
+
+    # Validate station data against years available. If years are requested w/ no
+    # data, an Warning and an `NA` is returned and removed here before passing the
+    # modified vector to `.download_files()`
+    station <- lapply(
+      X = station,
+      FUN = .validate_station_data_years,
+      isd_history = isd_history,
+      years = years
+    )
+    station <- station[!is.na(station)]
+  }
 
   # Download files from server -------------------------------------------------
-  # remove "-" from station to construct proper URL
   file_list <- .download_files(station, years)
 
   # Subset file_list for agroclimatology only stations -----------------------
@@ -155,19 +167,23 @@ get_GSOD <- function(years,
     country <- .validate_country(country, isd_history)
 
     file_list <-
-      .subset_country_list(country = country,
-                           isd_history = isd_history,
-                           file_list = file_list,
-                           years = years)
+      .subset_country_list(
+        country = country,
+        isd_history = isd_history,
+        file_list = file_list,
+        years = years
+      )
   }
 
   # Validate stations for missing days -----------------------------------------
   if (!is.null(max_missing)) {
     file_list <-
       .validate_missing_days(max_missing, file_list)
     if (length(file_list) == 0) {
-      stop(call. = FALSE,
-           "There were no stations that had a max of ", max_missing, " days.")
+      stop(
+        call. = FALSE,
+        "There were no stations that had a max of ", max_missing, " days."
+      )
     }
   }
 

diff --git a/R/get_inventory.R b/R/get_inventory.R
@@ -1,5 +1,4 @@
-
-#' Download and return a data.table object GSOD weather station data inventories
+#' Download and Return a data.table Object of GSOD Weather Station Data Inventories
 #'
 #' The \acronym{NCEI} maintains a document,
 #' \url{https://www1.ncdc.noaa.gov/pub/data/noaa/isd-inventory.txt}, which lists
@@ -28,78 +27,81 @@
 #' @export get_inventory
 
 get_inventory <- function() {
-  "STNID" <- isd_history <- NULL #nocov
-  load(system.file("extdata", "isd_history.rda", package = "GSODR")) #nocov
+  load(system.file("extdata", "isd_history.rda", package = "GSODR")) # nocov
   setkeyv(isd_history, "STNID")
 
-  tryCatch({
-    curl::curl_download(
-      "https://www1.ncdc.noaa.gov/pub/data/noaa/isd-inventory.txt",
-      destfile = file.path(tempdir(), "inventory.txt"),
-      quiet = TRUE
-    )
+  tryCatch(
+    {
+      curl::curl_download(
+        "https://www1.ncdc.noaa.gov/pub/data/noaa/isd-inventory.txt",
+        destfile = file.path(tempdir(), "inventory.txt"),
+        quiet = TRUE
+      )
 
-    main_body <-
-      fread(
-        file.path(tempdir(), "inventory.txt"),
-        skip = 8,
-        col.names = c(
-          "USAF",
-          "WBAN",
-          "YEAR",
-          "JAN",
-          "FEB",
-          "MAR",
-          "APR",
-          "MAY",
-          "JUN",
-          "JUL",
-          "AUG",
-          "SEP",
-          "OCT",
-          "NOV",
-          "DEC"
+      main_body <-
+        fread(
+          file.path(tempdir(), "inventory.txt"),
+          skip = 8,
+          col.names = c(
+            "USAF",
+            "WBAN",
+            "YEAR",
+            "JAN",
+            "FEB",
+            "MAR",
+            "APR",
+            "MAY",
+            "JUN",
+            "JUL",
+            "AUG",
+            "SEP",
+            "OCT",
+            "NOV",
+            "DEC"
+          )
         )
-      )
 
-    main_body[, STNID := paste(main_body$USAF, main_body$WBAN, sep = "-")]
-    setkeyv(main_body, "STNID")
+      main_body[, STNID := paste(main_body$USAF, main_body$WBAN, sep = "-")]
+      setkeyv(main_body, "STNID")
 
-    main_body[, c("USAF", "WBAN") := NULL]
+      main_body[, c("USAF", "WBAN") := NULL]
 
-    setcolorder(main_body, "STNID")
+      setcolorder(main_body, "STNID")
 
-    header <-
-      readLines(file.path(tempdir(), "inventory.txt"), n = 6)
+      header <-
+        readLines(file.path(tempdir(), "inventory.txt"), n = 6)
 
-    # sift out the year and month
-    year_month <- grep("[0-9]{4}", header)
+      # sift out the year and month
+      year_month <- grep("[0-9]{4}", header)
 
-    year_month <-
-      tools::toTitleCase(tolower(gsub("^([^\\D]*\\d+).*", "\\1",
-                                      header[[year_month]])))
-    year_month <- gsub("Through ", "", year_month)
-    year_month <- gsub("\\..*", "", year_month)
+      year_month <-
+        tools::toTitleCase(tolower(gsub(
+          "^([^\\D]*\\d+).*", "\\1",
+          header[[year_month]]
+        )))
+      year_month <- gsub("Through ", "", year_month)
+      year_month <- gsub("\\..*", "", year_month)
 
-    main_body <- isd_history[main_body, on = "STNID"]
+      main_body <- isd_history[main_body, on = "STNID"]
 
-    class(main_body) <- c("GSODR.Info", class(main_body))
+      class(main_body) <- c("GSODR.Info", class(main_body))
 
-    # add attributes for printing df
-    attr(main_body, "GSODR.Inventory") <- c(
-      "  *** FEDERAL CLIMATE COMPLEX INTEGRATED SURFACE DATA INVENTORY ***  \n",
-      "  This inventory provides the number of weather observations by  \n",
-      "  STATION-YEAR-MONTH for beginning of record through", year_month, "  \n"
-    )
-  },
-  error = function(cond) {
-    stop(
-      "There was a problem retrieving the inventory file. Perhaps \n",
-      "the server is not responding currently or there is no \n",
-      "Internet connection. Please try again later.",
-      call. = FALSE
-    )
-  })
+      # add attributes for printing df
+      attr(main_body, "GSODR.Inventory") <- c(
+        "  *** FEDERAL CLIMATE COMPLEX INTEGRATED SURFACE DATA INVENTORY ***  \n",
+        "  This inventory provides the number of weather observations by  \n",
+        "  STATION-YEAR-MONTH for beginning of record through", year_month, "  \n"
+      )
+    },
+    error = function(cond) {
+      stop(
+        "There was a problem retrieving the inventory file. Perhaps \n",
+        "the server is not responding currently or there is no \n",
+        "Internet connection. Please try again later.",
+        call. = FALSE
+      )
+    }
+  )
 
   unlink(file.path(tempdir(), "inventory.txt"))
   return(main_body)