Merge pull request #12 from jrdnbradford/tax-update-action

Tax update action

.github/workflows/taxonomy-check.yaml → .github/workflows/taxonomy-version-check.yaml

@@ -1,29 +1,24 @@
-name: taxonomy-check
+name: taxonomy-version-check
 
 on:
   schedule:
-    - cron: '0 13 * * 1' # Weekly on Mondays at 9AM EST
+    - cron: '0 0 * 8-11 1' # Midnight on Mondays from August through November
 
 env:
-  ISSUE_TITLE: 'eBird taxonomy different than expected'
+  ISSUE_TITLE: 'eBird taxonomy has updated'
   ISSUE_BODY: |
-    This issue has been opened by the GitHub Action workflow `taxonomy-check`.
+    This issue has been opened by the GitHub Action workflow `taxonomy-version-check`.
 
-    The `tax` dataset is different than data retrieved using `rebird::ebirdtaxonomy()`. Potential causes of this could include:
-      * an update to the eBird taxonomy
-      * issues with eBird's API
-      * different versions of R/packages resulting in data being loaded, retrieved, compared, and/or saved differently
-
-    Check if there has been an update to eBird's taxonomy data. If not, investigate the other potential causes.
+    There is an update to the eBird taxonomy. The `rebird::tax` dataset and documentation needs to be updated.    
 
 jobs:
-  taxonomy-check-job:
+  taxonomy-version-check-job:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
     outputs:
-      result: ${{ steps.check-taxonomy.outputs.result }}
+      check-failed: ${{ steps.check-taxonomy-version.outputs.failed }}
     steps:
       - name: checkout-step
         uses: actions/checkout@v4
@@ -39,13 +34,14 @@ jobs:
         with:
           extra-packages: local::.
 
-      - name: check-taxonomy-step
-        id: check-taxonomy
-        run: Rscript data-raw/tax_check.R
+      - name: check-taxonomy-version-step
+        id: check-taxonomy-version
+        run: |
+          Rscript -e "testthat::test_file('tests/testthat/test-data.R', load_package = 'source', stop_on_failure = TRUE)" && echo "failed=false" >> "$GITHUB_OUTPUT" || echo "failed=true" >> "$GITHUB_OUTPUT" 
 
   check-and-create-issue-job:
-    needs: taxonomy-check-job
-    if: needs.taxonomy-check-job.outputs.result == 'TRUE'
+    needs: taxonomy-version-check-job
+    if: needs.taxonomy-version-check-job.outputs.check-failed == 'true'
     runs-on: ubuntu-latest
     steps:
       - name: check-issue-step

DESCRIPTION

@@ -36,7 +36,7 @@ Suggests:
     covr,
     vcr (>= 0.6.0),
     withr
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 X-schema.org-applicationCategory: Data Access
 X-schema.org-keywords: birds, birding, ebird, database, data, biology, observations, sightings, ornithology
 X-schema.org-isPartOf: https://ropensci.org

NAMESPACE

@@ -15,6 +15,7 @@ export(ebirdregioninfo)
 export(ebirdregionspecies)
 export(ebirdsubregionlist)
 export(ebirdtaxonomy)
+export(ebirdtaxonomyversion)
 export(getlatlng)
 export(nearestobs)
 export(species_code)

R/ebirdtaxonomy.R

@@ -61,14 +61,12 @@ ebirdtaxonomy <- function(cat=NULL, locale=NULL, species = NULL, key = NULL, ...
   species <- if(!is.null(species)) species <- paste0(species, collapse = ",")
   args <- list(fmt='json', cat=cat, locale=locale, species=species)
 
-  # Allow not using a key for just this function, it's the only endpoint 
-  # that allows it
+  # Allow not using a key for this function
   if (is.null(key) && !nzchar(Sys.getenv("EBIRD_KEY"))) {
     key <- ""
   }
-  
+
   tax <- ebird_GET(paste0(ebase(), 'ref/taxonomy/ebird'), args, key = key, ...)
-  tax$comNameCodes <- sort_comma_separated(tax$comNameCodes)
-  tax$sciNameCodes <- sort_comma_separated(tax$sciNameCodes)
+  attr(tax, "version") <- ebirdtaxonomyversion(latest_only = TRUE)
   tax
 }

R/ebirdtaxonomyversion.R

@@ -0,0 +1,42 @@
+#' eBird Taxonomy Version
+#'
+#' Returns a data.frame of available version numbers of
+#' the eBird taxonomy or the latest version number of the
+#' taxonomy.
+#'
+#' @param key eBird API key. You can obtain one from https://ebird.org/api/keygen.
+#'    We strongly recommend storing it in your \code{.Renviron} file as an
+#'    environment variable called \code{EBIRD_KEY} to avoid having to constantly 
+#'    supply the key, and to avoid accidentally sharing it publicly.
+#' @param latest_only Whether to return only the latest version number
+#' @param ... Curl options passed on to \code{\link[httr]{GET}}
+#' 
+#' @return If `latest_only = FALSE`, a data.frame containing the collected information:
+#' @return "authorityVer": Character of version.
+#' @return "latest": Boolean indicating whether `authorityVer`` is the latest taxonomy version
+#' @return If `latest_only = TRUE`, a character of the latest `authorityVer`
+#' 
+#' @export
+#' 
+#' @examples \dontrun{
+#' ebirdtaxonomyversion()
+#' ebirdtaxonomyversion(latest_only = TRUE)
+#' }
+#' @author Jordan Bradford \email{jrdnbradford@gmail.com}
+#' @references \url{http://ebird.org/}
+ebirdtaxonomyversion <- function(key = NULL, latest_only = FALSE, ...) {
+  args <- list(fmt = 'json')
+
+  # Allow not using a key for this function
+  if (is.null(key) && !nzchar(Sys.getenv("EBIRD_KEY"))) {
+    key <- ""
+  }
+
+  versions <- ebird_GET(paste0(ebase(), 'ref/taxonomy/versions'), args, key = key, ...)
+  versions$authorityVer <- sub("0+$", "", as.character(versions$authorityVer))
+
+  if (latest_only) {
+    return(subset(versions, latest == TRUE)$authorityVer)
+  }
+  versions
+}

R/zzz.R

@@ -87,16 +87,3 @@ ebird_GET <- function(url, args, key = NULL, ...){
     }
   }
 }
-
-sort_comma_separated <- function(x) {
-  sapply(strsplit(as.character(x), ","), function(x) {
-    x <- x[x != ""]
-    if (length(x) == 0) {
-      return(NA_character_)
-    } else if (length(x) == 1) {
-      return(x)
-    } else {
-      return(paste(sort(x), collapse = ","))
-    }
-  })
-}

README.Rmd

@@ -20,7 +20,6 @@ knitr::opts_chunk$set(
 [![Codecov test coverage](https://codecov.io/gh/ropensci/rebird/branch/master/graph/badge.svg)](https://app.codecov.io/gh/ropensci/rebird?branch=master)
 [![rstudio mirror downloads](https://cranlogs.r-pkg.org/badges/rebird)](https://github.com/r-hub/cranlogs.app)
 [![cran version](https://www.r-pkg.org/badges/version/rebird)](https://cran.r-project.org/package=rebird/)
-[![taxonomy-check](https://github.com/ropensci/rebird/actions/workflows/taxonomy-check.yaml/badge.svg)](https://github.com/ropensci/rebird/actions/workflows/taxonomy-check.yaml)
 <!-- badges: end -->
 
 `rebird` is a package to interface with the eBird webservices.

README.md

@@ -15,8 +15,6 @@ coverage](https://codecov.io/gh/ropensci/rebird/branch/master/graph/badge.svg)](
 downloads](https://cranlogs.r-pkg.org/badges/rebird)](https://github.com/r-hub/cranlogs.app)
 [![cran
 version](https://www.r-pkg.org/badges/version/rebird)](https://cran.r-project.org/package=rebird/)
-[![taxonomy-check](https://github.com/ropensci/rebird/actions/workflows/taxonomy-check.yaml/badge.svg)](https://github.com/ropensci/rebird/actions/workflows/taxonomy-check.yaml)
-
 <!-- badges: end -->
 
 `rebird` is a package to interface with the eBird webservices.