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drought fix - live tests fix #240

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Merged
kyle-messier merged 5 commits into from
May 26, 2026
Merged

drought fix - live tests fix #240

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2459a4d
drought fix - live tests fix
kyle-messier May 26, 2026
21f330c
check_url update
kyle-messier May 26, 2026
f85dba0
live-edgar update
kyle-messier May 26, 2026
f9a6c90
proper patch increment
kyle-messier May 26, 2026
25ae200
Merge branch 'main' into live-fix
kyle-messier May 26, 2026
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4 changes: 2 additions & 2 deletions .github/workflows/check-standard.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,8 +27,8 @@ jobs:

env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
EARTHDATA_TOKEN: ${{ secrets.EARTHDATA_TOKEN }}
NASA_EARTHDATA_TOKEN: ${{ secrets.EARTHDATA_TOKEN }}
EARTHDATA_TOKEN: ${{ secrets.EARTHDATA_TOKEN || secrets.NASA_EARTHDATA_TOKEN }}
NASA_EARTHDATA_TOKEN: ${{ secrets.NASA_EARTHDATA_TOKEN || secrets.EARTHDATA_TOKEN }}
R_KEEP_PKG_SOURCE: yes

steps:
Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/test-coverage-local.yaml
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Expand Up @@ -18,8 +18,8 @@ jobs:
runs-on: ubuntu-latest
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
EARTHDATA_TOKEN: ${{ secrets.EARTHDATA_TOKEN }}
NASA_EARTHDATA_TOKEN: ${{ secrets.EARTHDATA_TOKEN }}
EARTHDATA_TOKEN: ${{ secrets.EARTHDATA_TOKEN || secrets.NASA_EARTHDATA_TOKEN }}
NASA_EARTHDATA_TOKEN: ${{ secrets.NASA_EARTHDATA_TOKEN || secrets.EARTHDATA_TOKEN }}

steps:
- uses: actions/checkout@v4
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8 changes: 4 additions & 4 deletions .github/workflows/test-live.yaml
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Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
# Scheduled live-API test workflow.
#
# Runs every Monday at 06:00 UTC, plus on-demand (with optional `filter`
# Runs nightly at 06:00 UTC, plus on-demand (with optional `filter`
# input). Sets AMADEUS_LIVE_TESTS=true so that `skip_if_no_live_tests()`
# does not skip the `test-*-live.R` files. On failure, an issue is
# auto-opened (label: live-test-failure) so repo watchers receive an
# email notification.
on:
schedule:
- cron: '0 6 * * 1'
- cron: '0 6 * * *'
workflow_dispatch:
Comment on lines 8 to 11
inputs:
filter:
Expand All @@ -25,8 +25,8 @@ jobs:
issues: write
env:
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
EARTHDATA_TOKEN: ${{ secrets.EARTHDATA_TOKEN }}
NASA_EARTHDATA_TOKEN: ${{ secrets.EARTHDATA_TOKEN }}
EARTHDATA_TOKEN: ${{ secrets.EARTHDATA_TOKEN || secrets.NASA_EARTHDATA_TOKEN }}
NASA_EARTHDATA_TOKEN: ${{ secrets.NASA_EARTHDATA_TOKEN || secrets.EARTHDATA_TOKEN }}
AMADEUS_LIVE_TESTS: "true"
NOT_CRAN: "true"

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
Package: amadeus
Title: Accessing and Analyzing Large-Scale Environmental Data
Version: 2.0.0
Version: 2.0.1
Comment on lines 1 to +3
Authors@R: c(
Comment on lines 1 to 4
person(given = "Mitchell", family = "Manware", role = c("aut", "ctb"), comment = c(ORCID = "0009-0003-6440-6106")),
person(given = "Insang", family = "Song", role = c("aut", "ctb"), comment = c(ORCID = "0000-0001-8732-3256")),
Expand Down
35 changes: 27 additions & 8 deletions R/download_auxiliary.R
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Original file line number Diff line number Diff line change
Expand Up @@ -842,9 +842,9 @@ check_url_status <- function(
) {
http_status_ok <- c(200, 206)

tryCatch(
status_head <- tryCatch(
{
status <- url |>
url |>
httr2::request() |>
httr2::req_method("HEAD") |>
httr2::req_error(is_error = \(resp) FALSE) |>
Expand All @@ -854,15 +854,34 @@ check_url_status <- function(
) |>
httr2::req_perform() |>
httr2::resp_status()
},
error = function(e) NA_integer_
)

if (!is.na(status_head) && status_head %in% http_status_ok) {
Sys.sleep(1)
return(TRUE)
}

Sys.sleep(1)
return(status %in% http_status_ok)
# Some hosts reject/flake on HEAD; probe with a tiny ranged GET.
status_get <- tryCatch(
{
url |>
httr2::request() |>
httr2::req_headers(Range = "bytes=0-0") |>
httr2::req_error(is_error = \(resp) FALSE) |>
httr2::req_retry(
max_tries = max_tries,
retry_on_failure = TRUE
) |>
httr2::req_perform() |>
httr2::resp_status()
},
error = function(e) {
# Return FALSE for any errors (network, DNS, SSL, etc.)
return(FALSE)
}
error = function(e) NA_integer_
)

Sys.sleep(1)
!is.na(status_get) && status_get %in% http_status_ok
}

#' Import download commands
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10 changes: 5 additions & 5 deletions tests/testthat/test-edgar-live.R
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ testthat::test_that(
{
skip_if_no_live_tests()
dir <- withr::local_tempdir()
amadeus::download_edgar(
amadeus::download_edgar(
species = "CO",
version = "8.1",
temp_res = "yearly",
Expand All @@ -35,7 +35,7 @@ testthat::test_that(
{
skip_if_no_live_tests()
dir <- withr::local_tempdir()
amadeus::download_edgar(
amadeus::download_edgar(
species = "SO2",
version = "8.1",
temp_res = "monthly",
Expand All @@ -53,15 +53,15 @@ amadeus::download_edgar(

testthat::test_that(
paste0(
"download_edgar(version='8.1_voc', voc='01'): ",
"download_edgar(version='8.1_voc', voc='1'): ",
"downloads VOC speciation file"
),
{
skip_if_no_live_tests()
dir <- withr::local_tempdir()
amadeus::download_edgar(
amadeus::download_edgar(
version = "8.1_voc",
voc = "01",
voc = "1",
format = "nc",
Comment on lines 63 to 65
Comment on lines +62 to 65
output = "emi",
directory_to_save = dir,
Expand Down
36 changes: 22 additions & 14 deletions tests/testthat/test-modis-live.R
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Expand Up @@ -9,13 +9,15 @@ testthat::test_that(
),
{
skip_if_no_live_tests()
testthat::skip_if(!nzchar(Sys.getenv("EARTHDATA_TOKEN")),
"no Earthdata token")
testthat::skip_if(
!nzchar(Sys.getenv("NASA_EARTHDATA_TOKEN")),
"no Earthdata token"
)
dir <- withr::local_tempdir()
amadeus::download_modis(
product = "MOD09GA",
version = "061",
nasa_earth_data_token = Sys.getenv("EARTHDATA_TOKEN"),
nasa_earth_data_token = Sys.getenv("NASA_EARTHDATA_TOKEN"),
date = c("2024-01-01", "2024-01-01"),
extent = c(-79, 35, -78, 36),
directory_to_save = dir,
Expand All @@ -34,13 +36,15 @@ testthat::test_that(
),
{
skip_if_no_live_tests()
testthat::skip_if(!nzchar(Sys.getenv("EARTHDATA_TOKEN")),
"no Earthdata token")
testthat::skip_if(
!nzchar(Sys.getenv("NASA_EARTHDATA_TOKEN")),
"no Earthdata token"
)
dir <- withr::local_tempdir()
amadeus::download_modis(
product = "MOD11A1",
version = "061",
nasa_earth_data_token = Sys.getenv("EARTHDATA_TOKEN"),
nasa_earth_data_token = Sys.getenv("NASA_EARTHDATA_TOKEN"),
date = c("2022-01-01", "2022-01-01"),
extent = c(-79, 35, -78, 36),
directory_to_save = dir,
Expand All @@ -59,13 +63,15 @@ testthat::test_that(
),
{
skip_if_no_live_tests()
testthat::skip_if(!nzchar(Sys.getenv("EARTHDATA_TOKEN")),
"no Earthdata token")
testthat::skip_if(
!nzchar(Sys.getenv("NASA_EARTHDATA_TOKEN")),
"no Earthdata token"
)
dir <- withr::local_tempdir()
amadeus::download_modis(
product = "MCD19A2",
version = "061",
nasa_earth_data_token = Sys.getenv("EARTHDATA_TOKEN"),
nasa_earth_data_token = Sys.getenv("NASA_EARTHDATA_TOKEN"),
date = c("2022-01-01", "2022-01-01"),
extent = c(-79, 35, -78, 36),
directory_to_save = dir,
Expand All @@ -79,18 +85,20 @@ testthat::test_that(

testthat::test_that(
paste0(
"download_modis(product='MOD06_L2', date=<single day>, extent=<NC>): ",
"download_modis(product='MOD06_L2', date=<month range>, extent=<NC>): ",
"downloads cloud product file"
),
{
skip_if_no_live_tests()
testthat::skip_if(!nzchar(Sys.getenv("EARTHDATA_TOKEN")),
"no Earthdata token")
testthat::skip_if(
!nzchar(Sys.getenv("NASA_EARTHDATA_TOKEN")),
"no Earthdata token"
)
dir <- withr::local_tempdir()
amadeus::download_modis(
product = "MOD06_L2",
nasa_earth_data_token = Sys.getenv("EARTHDATA_TOKEN"),
date = c("2022-01-01", "2022-01-01"),
nasa_earth_data_token = Sys.getenv("NASA_EARTHDATA_TOKEN"),
date = c("2022-01-01", "2022-01-31"),
extent = c(-79, 35, -78, 36),
Comment on lines 98 to 102
directory_to_save = dir,
acknowledgement = TRUE
Expand Down
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