rgbif v3.8.0 (#738)

Author: jhnwllr

.github/workflows/rhub.yaml

@@ -24,7 +24,6 @@ on:
         type: string
 
 jobs:
-
   setup:
     runs-on: ubuntu-latest
     outputs:

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 3.7.9
-Date: 2024-01-10 13:29:08 UTC
-SHA: e472449532c920d1eb370230cba7ce11e024ff58
+Version: 3.8.0
+Date: 2024-05-23 07:22:30 UTC
+SHA: 891268cb6c9c91878188b673db49f737d83e7920

DESCRIPTION

@@ -8,7 +8,7 @@ Description: A programmatic interface to the Web Service methods
     retrieving information on data providers, getting species occurrence
     records, getting counts of occurrence records, and using the GBIF
     tile map service to make rasters summarizing huge amounts of data.
-Version: 3.7.9.3
+Version: 3.8.0
 License: MIT + file LICENSE
 Authors@R: c(
     person("Scott", "Chamberlain", role = "aut", comment = c(ORCID="0000-0003-1444-9135")),

NAMESPACE

@@ -20,7 +20,6 @@ S3method(print,occ_download_meta)
 S3method(print,occ_download_prep)
 S3method(print,occ_predicate)
 S3method(print,occ_predicate_list)
-S3method(print,verbatim_extensions)
 export("%>%")
 export(DownReq)
 export(GbifQueue)
@@ -130,7 +129,6 @@ export(pred_within)
 export(rgb_country_codes)
 export(suggestfields)
 export(taxrank)
-export(verbatim_extensions)
 export(wkt_parse)
 importFrom(R6,R6Class)
 importFrom(data.table,fread)

NEWS.md

@@ -1,3 +1,30 @@
+rgbif 3.8.0
+===========
+
+### NEW FEATURES
+
+* Added many missing `occ_search()` terms. (#698)
+* New function `occ_download_describe()` for getting information about download formats. (#721)
+
+### MINOR IMPROVEMENTS
+
+* Added `constituentKey` to `name_lookup()`. (#729)
+* Added support for `gbifId` downloads (#711)
+
+## BUG FIXES
+* `check_inputs()`bug fixed. (#706)
+
+### DOCUMENTATION
+
+* New article [Effectively using occ_search](https://docs.ropensci.org/rgbif/articles/effectively_using_occ_search.html)
+* Guidance for reversing WKT winding order. (#724)
+
+### DEPRECATED
+
+* `gbif_citation()` datasetKey methods no longer supported (#716)
+* "axe" feature in `occ_data()` is no longer supported. (#718)
+* `occ_data()` is soft deprecated and supported for legacy reasons only, and will no longer add new features. 
+
 rgbif 3.7.9
 ===========
 

R/download_predicate_dsl.R

@@ -278,13 +278,6 @@ pred_default <- function() {
   pred_not(pred_in("BASIS_OF_RECORD",c("FOSSIL_SPECIMEN","LIVING_SPECIMEN")))
   )
 }
-#' @rdname download_predicate_dsl
-#' @export
-verbatim_extensions <- function(...) {
-  x <- unlist(list(...))
-  assert(x,"character")
-  structure(x, class = "verbatim_extensions")
-}
 
 #' @export
 print.occ_predicate <- function(x, ...) {
@@ -305,14 +298,6 @@ print.occ_predicate_list <- function(x, ...) {
   }
 }
 
-#' @export
-print.verbatim_extensions <- function(...) {
-  x <- unlist(list(...))
-  cat("<<gbif download - verbatim_extensions>>", sep = "\n")
-  for(i in seq_along(x)) {
-  cat("  ", x[i], "\n", sep = "")
-  }
-}
 
 # helpers
 pred_factory <- function(type) {
@@ -599,7 +584,7 @@ parse_predicates <- function(user, email, type, format, ...) {
     stop("You are requesting a full download. Please use a predicate to filter the data. For example, pred_default().")
   }  
 clzzs <- vapply(tmp,
-    function(z) inherits(z, c("verbatim_extensions","occ_predicate", "occ_predicate_list")),
+    function(z) inherits(z, c("occ_predicate", "occ_predicate_list")),
     logical(1)
   )
   if (!all(clzzs))
@@ -611,20 +596,6 @@ clzzs <- vapply(tmp,
     format = unbox(format),
     predicate = list()
   )
-  # handle verbatim_extensions 
-  if(any(sapply(tmp,class) %in% "verbatim_extensions")) {
-    if(!format == "DWCA") stop("verbatim_extensions only work with format='DWCA'")
-    ve_idx <- which(sapply(tmp,class) == "verbatim_extensions")
-    if(!length(ve_idx) == 1) stop("Please supply only one verbatim_extensions() expression.")
-    payload <- list(
-      creator = unbox(user),
-      notification_address = email,
-      format = unbox(format),
-      predicate = list(),
-      verbatimExtensions = unclass(tmp[[ve_idx]])
-    )
-    tmp[ve_idx] <- NULL
-  }
   if (any(vapply(tmp, function(w) "predicates" %in% names(w), logical(1)))) {
     payload$predicate <- list(unclass(tmp[[1]]))
   } else {

codemeta.json

@@ -8,7 +8,7 @@
   "codeRepository": "https://github.com/ropensci/rgbif",
   "issueTracker": "https://github.com/ropensci/rgbif/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "3.7.9",
+  "version": "3.8.0",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -358,7 +358,7 @@
   "applicationCategory": "Biodiversity",
   "isPartOf": "https://ropensci.org",
   "keywords": ["GBIF", "specimens", "API", "web-services", "occurrences", "species", "taxonomy", "gbif", "api", "data", "biodiversity", "rstats", "r", "spocc", "r-package", "lifewatch", "oscibio"],
-  "fileSize": "11587.689KB",
+  "fileSize": "6425.728KB",
   "citation": [
     {
       "@type": "SoftwareSourceCode",
@@ -402,7 +402,7 @@
       ],
       "name": "rgbif: Interface to the Global Biodiversity Information Facility API",
       "url": "https://CRAN.R-project.org/package=rgbif",
-      "description": "R package version 3.7.9"
+      "description": "R package version 3.8.0"
     },
     {
       "@type": "ScholarlyArticle",

cran-comments.md

@@ -1,17 +1,17 @@
 ## Test environments
 
 * local windows, R 4.2.3
-* windows latest R 4.3.2 (GitHub Actions)
-* ubuntu 20.04, R 4.3.2 (GitHub Actions)
-* macOS latest, R 4.3.2 (GitHub Actions)
+* windows latest R "release" version (GitHub Actions)
+* ubuntu 20.04, R "release" version (GitHub Actions)
+* macOS latest, R "release" version (GitHub Actions)
 
 ## R CMD check results
 
 0 errors | 0 warnings | 0 notes
 
 ## Reverse dependencies
 
-* I have run R CMD check on the 16 reverse dependencies. Reverse dependency checks at <https://github.com/ropensci/rgbif/actions?query=workflow%3Arevdep>. No problems were found related to this package.
+* I have run R CMD check on the 13 reverse dependencies. Reverse dependency checks at <https://github.com/ropensci/rgbif/actions?query=workflow%3Arevdep>. No problems were found related to this package.
 
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