Merge 154cbd2 into cdcf933

NEWS.md

@@ -14,19 +14,19 @@ bioRad 0.7 includes a major backend overhaul that deprecates the use of Docker.
 
 * Faster implementations of functions previously dependent on Docker, such as `calculate_vp()`, `apply_mistnet()` and `read_pvolfile()`.
 
-* Support for reading [VPTS CSV](https://aloftdata.eu/vpts-csv/) format through updated function `read_vpts()`. VPTS CSV table schema included to allow offline parsing of VPTS CSV files as a [frictionless](https://CRAN.R-project.org/package=frictionless) data package (#551, #590)
+* Support for reading [VPTS CSV](https://aloftdata.eu/vpts-csv/) format through updated function `read_vpts()`. VPTS CSV table schema included to allow offline parsing of VPTS CSV files as a [frictionless](https://CRAN.R-project.org/package=frictionless) data package (#551, #590).
 
-* Updated function `read_vpts()` supports reading `vp`/`vpts` data in ODIM HDF, [VPTS CSV](https://aloftdata.eu/vpts-csv/) format (#551, #590)
+* Updated function `read_vpts()` supports reading `vp`/`vpts` data in ODIM HDF and [VPTS CSV](https://aloftdata.eu/vpts-csv/) format (#551, #590).
 
 * New function `list_vpts_aloft()` produces a list of [aloft](https://aloftdata.eu/browse/) archive URLs for time series of vertical profiles (`vpts`). This list of URLs can then be used to bulk download data using any number of external tools (#553).
 
 * New function `read_stdout()` replaces previous functionality of `read_vpts()` to read vol2bird stdout format. It also has a new `sep` argument (#536) to support both fixed-delimited and comma-separated stdout data.
 
-* New function `as.vpts` converts a data.frame originating from a VPTS CSV file into a vpts object (#555). Inverse operation of as.data.frame.vpts
+* New function `as.vpts` converts a data.frame originating from a VPTS CSV file into a vpts object (#555). Inverse operation of `as.data.frame.vpts()`.
 
 * `read_pvolfiles()` now allows ODIM H5 files with missing `source` attribute. The functionality is similar to `read_vpfiles()`, i.e. extracting the NOD, RAD or WMO identifier, otherwise using `unknown` (2f6935c).
 
-* `bind_into_vpts()` now works for vp and vpts objects with different heights (#343)
+* `bind_into_vpts()` now works for vp and vpts objects with different heights (#343).
 
 * Faster parallel mistnet runs (https://github.com/adokter/vol2birdR/issues/16).
 
@@ -42,9 +42,9 @@ bioRad 0.7 includes a major backend overhaul that deprecates the use of Docker.
 
 * Function `vol2bird_version()` has been migrated to package vol2birdR and can be accessed by `vol2birdR::vol2bird_version()`.
 
-* Dependency `maptools` has been replaced with [suntools](https://github.com/adokter/suntools), `rgdal` has been removed in accordance with the evolution of `sp` and the [imminent archiving](https://r-spatial.org/r/2023/05/15/evolution4.html) of `rgdal` 
+* Dependency `maptools` has been replaced with [suntools](https://github.com/adokter/suntools), `rgdal` has been removed in accordance with the evolution of `sp` and the [imminent archiving](https://r-spatial.org/r/2023/05/15/evolution4.html) of `rgdal`.
 
-* Function `as.data.frame.vpts()` has output column names `lat`, `lon`, `antenna_height` renamed to `radar_latitude`, `radar_longitude`, `radar_height` for compatibility with the [VPTS CSV](https://aloftdata.eu/vpts-csv/) data format. The function also outputs an additional column `radar_wavelength` (#609)
+* Function `as.data.frame.vpts()` has output column names `lat`, `lon`, `antenna_height` renamed to `radar_latitude`, `radar_longitude`, `radar_height` for compatibility with the [VPTS CSV](https://aloftdata.eu/vpts-csv/) data format. The function also outputs an additional column `radar_wavelength` (#609).
 
 # bioRad 0.6.1
 

R/list_vpts_aloft.R

@@ -94,7 +94,7 @@ list_vpts_aloft <- function(date_min = NULL,
 
   ## set static urls --------------------------------------------------------
   # Set base URL
-  base_url <- "https://aloft.s3-eu-west-1.amazonaws.com"
+  base_url <- "https://aloftdata.s3-eu-west-1.amazonaws.com"
 
   # format csv --------------------------------------------------------------
   if (format == "csv") {
@@ -104,7 +104,7 @@ list_vpts_aloft <- function(date_min = NULL,
 
     found_vpts_aloft <-
       aws.s3::get_bucket_df(
-        bucket = "s3://aloft",
+        bucket = "s3://aloftdata",
         prefix = glue::glue("{source}/monthly"),
         region = "eu-west-1",
         max = Inf
@@ -124,7 +124,7 @@ list_vpts_aloft <- function(date_min = NULL,
   } else {
     # hdf5 files
     # TODO: create file paths of form
-    # https://aloft.s3-eu-west-1.amazonaws.com/baltrad/hdf5/bejab/2023/05/02/bejab_vp_20230502T000000Z_0x9.h5
+    # https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/hdf5/bejab/2023/05/02/bejab_vp_20230502T000000Z_0x9.h5
   }
 
   # format found data -------------------------------------------------------

tests/testthat/test-read_vpts.R

@@ -1,14 +1,13 @@
 # Define the URLs of test files
 urls <- c(
-  "https://aloft.s3-eu-west-1.amazonaws.com/baltrad/hdf5/czbrd/2023/06/01/czbrd_vp_20230601T000000Z_0xb.h5",
-  "https://aloft.s3-eu-west-1.amazonaws.com/baltrad/hdf5/czbrd/2023/06/01/czbrd_vp_20230601T000500Z_0xb.h5",
-  "https://aloft.s3-eu-west-1.amazonaws.com/baltrad/hdf5/czbrd/2023/06/01/czbrd_vp_20230601T001000Z_0xb.h5",
-  "https://aloft.s3-eu-west-1.amazonaws.com/baltrad/monthly/bejab/2023/bejab_vpts_202303.csv.gz",
-  "https://aloft.s3-eu-west-1.amazonaws.com/baltrad/monthly/bejab/2023/bejab_vpts_202304.csv.gz",
-  "https://aloft.s3-eu-west-1.amazonaws.com/baltrad/monthly/bewid/2023/bewid_vpts_202303.csv.gz"
+  "https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/hdf5/czbrd/2023/06/01/czbrd_vp_20230601T000000Z_0xb.h5",
+  "https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/hdf5/czbrd/2023/06/01/czbrd_vp_20230601T000500Z_0xb.h5",
+  "https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/hdf5/czbrd/2023/06/01/czbrd_vp_20230601T001000Z_0xb.h5",
+  "https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/monthly/bejab/2023/bejab_vpts_202303.csv.gz",
+  "https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/monthly/bejab/2023/bejab_vpts_202304.csv.gz",
+  "https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/monthly/bewid/2023/bewid_vpts_202303.csv.gz"
 )
 
-
 # Define the path to the new temporary directory
 temp_dir <- tempdir()
 
@@ -111,7 +110,7 @@ test_that("read_vpts() can read local vp hdf5 files", {
 
 test_that("read_vpts() returns error on multiple radars in vp hdf5 files", {
   # add eehar h5
-  eehar <- "https://aloft.s3-eu-west-1.amazonaws.com/baltrad/hdf5/eehar/2023/06/01/eehar_vp_20230601T001000Z_0xb.h5"
+  eehar <- "https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/hdf5/eehar/2023/06/01/eehar_vp_20230601T001000Z_0xb.h5"
   download_test_file(eehar, temp_dir, h5_dir, csv_dir)
 
   h5_files <- list.files(temp_h5_dir, pattern = "*.h5", full.names = TRUE)
@@ -194,7 +193,7 @@ test_that("read_vpts() returns equal summaries from h5 and csv files from 1 day
 
     # Get the files for the current prefix
     h5_files <- aws.s3::get_bucket_df(
-      bucket = "s3://aloft/",
+      bucket = "s3://aloftdata/",
       prefix = prefix,
       region = "eu-west-1"
     )
@@ -204,7 +203,7 @@ test_that("read_vpts() returns equal summaries from h5 and csv files from 1 day
       aws.s3::save_object(
         file = paste0(h5_dir, "/", basename(file_name)),
         object = file_name,
-        bucket = "s3://aloft/",
+        bucket = "s3://aloftdata/",
         region = "eu-west-1"
       )
     })
@@ -216,7 +215,7 @@ test_that("read_vpts() returns equal summaries from h5 and csv files from 1 day
 
   # VPTS CSV
 
-  urls <- c("https://aloft.s3-eu-west-1.amazonaws.com/baltrad/daily/bewid/2023/bewid_vpts_20230414.csv")
+  urls <- c("https://aloftdata.s3-eu-west-1.amazonaws.com/baltrad/daily/bewid/2023/bewid_vpts_20230414.csv")
 
   # Use lapply to download each file to a temporary location
   csv_files <- lapply(urls, function(url) {