Dev

.github/workflows/R.yaml

@@ -68,7 +68,9 @@ jobs:
 
       - name: Upload test results
         if: failure()
+        continue-on-error: true
         uses: actions/upload-artifact@v5
         with:
           name: coverage-test-failures
           path: ${{ runner.temp }}/package
+          if-no-files-found: ignore

R/ebv_download.R

@@ -27,13 +27,13 @@
 #'
 #' @examples
 #'
-#' \donttest{
-#' #' #get all available datasets
+#' \dontrun{
+#' # get all available datasets
 #' datasets <- ebv_download()
 #'
 #' ebv_download(id = datasets$id[1], outputdir =
-#' tempdir(), overwrite=TRUE,
-#' verbose=FALSE)
+#'   tempdir(), overwrite = TRUE,
+#'   verbose = FALSE)
 #' }
 ebv_download <- function(id=NULL,
                          outputdir,
@@ -190,6 +190,6 @@
 
   }
 
   return(file.path(outputdir, name_nc))
 
 }

README.Rmd

@@ -67,6 +67,7 @@ install.packages("ebvcube", repos = c("https://b-cubed-eu.r-universe.dev", "http
 #troubleshooting in case the BioConductor packages are missing
 #if one of the following packages is not loaded: rhdf5, DelayedArray, HDF5Array
 install.packages("BiocManager")
+BiocManager::install(version = "3.22")
 BiocManager::install('rhdf5')
 BiocManager::install('DelayedArray')
 BiocManager::install('HDF5Array')

README.md

@@ -89,6 +89,7 @@ install.packages("ebvcube", repos = c("https://b-cubed-eu.r-universe.dev", "http
 #troubleshooting in case the BioConductor packages are missing
 #if one of the following packages is not loaded: rhdf5, DelayedArray, HDF5Array
 install.packages("BiocManager")
+BiocManager::install(version = "3.22")
 BiocManager::install('rhdf5')
 BiocManager::install('DelayedArray')
 BiocManager::install('HDF5Array')

tests/testthat/test-download.R

@@ -1,54 +1,57 @@
 # basic tests for ebv_download ----
-#check url
-portal_down <- ebv_i_check_url('https://portal.geobon.org/api/v1/datasets')
-
-if(portal_down){
-  #expect an error
-  expect_error(ebv_download(27, dir, verbose = FALSE))
-  }else{
-  #run 'normal' tests
-  test_that("test ebv_download ID=numeric", {
-    dir <- tempdir()
-    data <- ebv_download(27, dir, verbose = FALSE)
-    expect_true(basename(data) %in% list.files(dir))
-    #clean
-    unlink(dir, recursive=TRUE)
-  })
-
-  test_that("test ebv_download ID=doi", {
-    dir <- tempdir()
-    data <- ebv_download('10.25829/f2rdp4', dir, verbose = FALSE)
-    expect_true(basename(data) %in% list.files(dir))
-    #clean
-    unlink(dir, recursive=TRUE)
-  })
-
-  test_that("test ebv_download ID=title 1", {
-    dir <- tempdir()
-    data <- ebv_download('Local bird diversity (cSAR/BES-SIM)', dir, verbose = FALSE)
-    expect_true(basename(data) %in% list.files(dir))
-    #clean
-    unlink(dir, recursive=TRUE)
-  })
-
-  test_that("test ebv_download ID=title 2", {
-    dir <- tempdir()
-    data <- ebv_download("Global trends in biodiversity (BES-SIM PREDICTS)", dir, verbose = FALSE)
-    expect_true(basename(data) %in% list.files(dir))
-    #clean
-    unlink(dir, recursive=TRUE)
-  })
-
-  test_that("test ebv_download DOIs in download overview table", {
-    data <- ebv_download(verbose=FALSE)
-    #check col names
-    expect_equal(names(data), c("id","title","doi"))
-    #check a view DOIs
-    expect_equal(data[data$id==7, 'doi'], '10.25829/f2rdp4')
-    expect_equal(data[data$id==42, 'doi'], '10.25829/tder31')
-    expect_equal(data[data$id==28, 'doi'], '10.25829/bk5g87')
-  })
+skip_if_portal_tests_unavailable <- function() {
+  testthat::skip_on_ci()
+  testthat::skip_if_offline()
 
+  if (ebv_i_check_url("https://portal.geobon.org/api/v1/datasets")) {
+    testthat::skip("EBV Data Portal API is not reachable")
+  }
 }
 
+test_that("test ebv_download ID=numeric", {
+  skip_if_portal_tests_unavailable()
+
+  dir <- tempdir()
+  data <- ebv_download(27, dir, verbose = FALSE)
+  expect_true(basename(data) %in% list.files(dir))
+  unlink(dir, recursive = TRUE)
+})
+
+test_that("test ebv_download ID=doi", {
+  skip_if_portal_tests_unavailable()
+
+  dir <- tempdir()
+  data <- ebv_download("10.25829/f2rdp4", dir, verbose = FALSE)
+  expect_true(basename(data) %in% list.files(dir))
+  unlink(dir, recursive = TRUE)
+})
+
+test_that("test ebv_download ID=title 1", {
+  skip_if_portal_tests_unavailable()
+
+  dir <- tempdir()
+  data <- ebv_download("Local bird diversity (cSAR/BES-SIM)", dir, verbose = FALSE)
+  expect_true(basename(data) %in% list.files(dir))
+  unlink(dir, recursive = TRUE)
+})
+
+test_that("test ebv_download ID=title 2", {
+  skip_if_portal_tests_unavailable()
+
+  dir <- tempdir()
+  data <- ebv_download("Global trends in biodiversity (BES-SIM PREDICTS)", dir, verbose = FALSE)
+  expect_true(basename(data) %in% list.files(dir))
+  unlink(dir, recursive = TRUE)
+})
+
+test_that("test ebv_download DOIs in download overview table", {
+  skip_if_portal_tests_unavailable()
+
+  data <- ebv_download(verbose = FALSE)
+  expect_equal(names(data), c("id", "title", "doi"))
+  expect_equal(data[data$id == 7, "doi"], "10.25829/f2rdp4")
+  expect_equal(data[data$id == 42, "doi"], "10.25829/tder31")
+  expect_equal(data[data$id == 28, "doi"], "10.25829/bk5g87")
+})
+