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Fix #56: add Bioconductor version install step to README #59

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Merged
E-O-Conchas merged 3 commits into from
Mar 23, 2026
Merged

Fix #56: add Bioconductor version install step to README #59

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e532b43
make artificial upload non-blocking in CI
E-O-Conchas Mar 20, 2026
81bca4d
Stabilize portal download tests in CI
E-O-Conchas Mar 20, 2026
fd67666
Avoid live portal download in ebv_download example
E-O-Conchas Mar 20, 2026
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2 changes: 2 additions & 0 deletions .github/workflows/R.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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: ${{ runner.temp }}/package
if-no-files-found: ignore
8 changes: 4 additions & 4 deletions R/ebv_download.R
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Expand Up @@ -27,13 +27,13 @@
#'
#' @examples
#'
#' \donttest{
#' #' #get all available datasets
#' \dontrun{
#' # get all available datasets
#' datasets <- ebv_download()
#'
#' ebv_download(id = datasets$id[1], outputdir =
#' tempdir(), overwrite=TRUE,
#' verbose=FALSE)
#' tempdir(), overwrite = TRUE,
#' verbose = FALSE)
#' }
ebv_download <- function(id=NULL,
outputdir,
Expand Down Expand Up @@ -190,6 +190,6 @@

}

return(file.path(outputdir, name_nc))

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file=R/ebv_download.R,line=193,col=3,[return_linter] Use implicit return behavior; explicit return() is not needed.

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file=R/ebv_download.R,line=193,col=3,[return_linter] Use implicit return behavior; explicit return() is not needed.

}
8 changes: 4 additions & 4 deletions man/ebv_download.Rd
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101 changes: 52 additions & 49 deletions tests/testthat/test-download.R
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Original file line number Diff line number Diff line change
@@ -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()

@chatgpt-codex-connector chatgpt-codex-connector Bot Mar 23, 2026

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P2 Badge Avoid unconditionally skipping portal tests in CI

Because each test_that now calls skip_if_portal_tests_unavailable(), the first statement testthat::skip_on_ci() causes all download tests in this file to be skipped in GitHub Actions (the R.yaml workflow runs tests in a CI environment). This means ebv_download no longer gets any CI verification, so regressions in the package’s core download paths can merge undetected even when the portal is reachable.

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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")
})


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