Up minimum required R version, switch to native pipes.

.github/workflows/R-CMD-check-lite.yaml

@@ -27,7 +27,7 @@ jobs:
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: '3.6.3'}
+          - {os: windows-latest,   r: '4.1.0'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

DESCRIPTION

@@ -16,6 +16,8 @@ Description: Provides API endpoints to the European Tracking Network.
 License: MIT + file LICENSE
 URL: https://github.com/inbo/etnservice
 BugReports: https://github.com/inbo/etnservice/issues
+Depends:
+    R (>= 4.1.0)
 Imports: 
     arrow,
     assertthat,

NAMESPACE

@@ -23,7 +23,6 @@ export(list_scientific_names)
 export(list_station_names)
 export(list_tag_serial_numbers)
 export(validate_login)
-importFrom(dplyr,"%>%")
 importFrom(dplyr,.data)
 importFrom(dplyr,distinct)
 importFrom(dplyr,filter)

NEWS.md

@@ -1,6 +1,7 @@
 # etnservice (development version)
 - The function `write_dwc()` has been updated in the `etn` package and is no longer needed in `etnservice`. (#141)
 - The `jsonlite` package is no longer a direct dependency, it is only used by a maintenance script. (#144)
+- etnservice now relies on R >= 4.1.0 and uses base pipes (`|>` rather than `%>%`) (#151).
 # etnservice 0.6.0
 - Added `get_receiver_logs()` to fetch receiver logs from the database. The data is returned as a tibble with a column with logs in JSON format. (#117)
 

R/etnservice-package.R

@@ -2,7 +2,6 @@
 "_PACKAGE"
 
 ## usethis namespace: start
-#' @importFrom dplyr %>%
 #' @importFrom dplyr .data
 #' @importFrom dplyr distinct
 #' @importFrom dplyr filter

R/get_acoustic_deployments.R

@@ -205,7 +205,7 @@ get_acoustic_deployments <- function(
 
   # Sort data
   deployments <-
-    deployments %>%
+    deployments |>
     dplyr::arrange(
       .data$acoustic_project_code,
       factor(.data$station_name, levels = list_station_names(credentials)),

R/get_acoustic_detections.R

@@ -270,7 +270,7 @@ get_acoustic_detections <- function(credentials = list(
 
   # Sort data (faster than in SQL)
   detections <-
-    detections %>%
+    detections |>
     dplyr::arrange(
       factor(.data$acoustic_tag_id, levels = list_acoustic_tag_ids(credentials)),
       .data$date_time

R/get_acoustic_detections_page.R

@@ -264,7 +264,8 @@ get_acoustic_detections_page <- function(credentials = list(
   # Apply mapping -----
   if (!count) {
     # No need to apply mapping if we're only returning the number of records
-    returned_page <- returned_page %>%
+    returned_page <-
+      returned_page |>
       dplyr::transmute(
         detection_id = .data$detection_id_pk,
         date_time = .data$datetime,

R/get_acoustic_projects.R

@@ -78,7 +78,7 @@ get_acoustic_projects <- function(credentials = list(
 
   # Sort data
   projects <-
-    projects %>%
+    projects |>
     dplyr::arrange(.data$project_code)
 
   dplyr::as_tibble(projects)

R/get_acoustic_receivers.R

@@ -124,7 +124,7 @@ get_acoustic_receivers <- function(credentials = list(
 
   # Sort data
   receivers <-
-    receivers %>%
+    receivers |>
     dplyr::arrange(.data$receiver_id)
 
   # Close connection

R/get_animal_projects.R

@@ -77,7 +77,7 @@ get_animal_projects <- function(credentials = list(
 
   # Sort data
   projects <-
-    projects %>%
+    projects |>
     dplyr::arrange(.data$project_code)
 
   dplyr::as_tibble(projects)

R/get_animals.R

@@ -223,24 +223,24 @@ get_animals <- function(credentials = list(
 
   # Collapse tag information, to obtain one row = one animal
   tag_cols <-
-    animals %>%
-    dplyr::select(dplyr::starts_with("tag"), dplyr::starts_with("acoustic_tag_id")) %>%
+    animals |>
+    dplyr::select(dplyr::starts_with("tag"), dplyr::starts_with("acoustic_tag_id")) |>
     names()
   other_cols <-
-    animals %>%
-    dplyr::select(-dplyr::starts_with("tag"), -dplyr::starts_with("acoustic_tag_id")) %>%
+    animals |>
+    dplyr::select(-dplyr::starts_with("tag"), -dplyr::starts_with("acoustic_tag_id")) |>
     names()
   animals <-
-    animals %>%
-    dplyr::group_by_at(other_cols) %>%
-    dplyr::summarize_at(tag_cols, paste, collapse = ",") %>% # Collapse multiple tags by comma
-    dplyr::ungroup() %>%
-    dplyr::mutate_at(tag_cols, gsub, pattern = "NA", replacement = "") %>% # Use "" instead of "NA"
+    animals |>
+    dplyr::group_by_at(other_cols) |>
+    dplyr::summarize_at(tag_cols, paste, collapse = ",") |> # Collapse multiple tags by comma
+    dplyr::ungroup() |>
+    dplyr::mutate_at(tag_cols, gsub, pattern = "NA", replacement = "") |> # Use "" instead of "NA"
     dplyr::select(names(animals)) # Use the original column order
 
   # Sort data
   animals <-
-    animals %>%
+    animals |>
     dplyr::arrange(
       .data$animal_project_code,
       .data$release_date_time,

R/get_cpod_projects.R

@@ -74,7 +74,7 @@ get_cpod_projects <- function(credentials = list(
 
   # Sort data
   projects <-
-    projects %>%
+    projects |>
     dplyr::arrange(.data$project_code)
   # Close connection
   DBI::dbDisconnect(connection)

R/get_receiver_logs.R

@@ -138,7 +138,7 @@ get_receiver_logs <- function(credentials = list(
 
   # Sort data
   receiver_logs <-
-    receiver_logs %>%
+    receiver_logs |>
     dplyr::arrange(factor(
       .data$deployment_id, levels = list_deployment_ids(credentials)
     ))

R/get_tags.R

@@ -213,7 +213,7 @@ get_tags <- function(credentials = list(
 
   # Sort data
   tags <-
-    tags %>%
+    tags |>
     dplyr::arrange(factor(.data$tag_serial_number, levels = list_tag_serial_numbers(credentials)))
 
   dplyr::as_tibble(tags)

R/get_version.R

@@ -22,8 +22,8 @@ get_version <- function() {
   # Get all functions from etnservice and their code
   fn_names <- ls(envir = getNamespace("etnservice"))
   fn_code <- purrr::map(fn_names,
-                            ~ get(.x, envir = getNamespace("etnservice"))) %>%
-    purrr::map(deparse) %>%
+                            ~ get(.x, envir = getNamespace("etnservice"))) |>
+    purrr::map(deparse) |>
     purrr::set_names(fn_names)
   # Calculate hashes for the functions, report on the installed version of
   # etnservice

R/utils.R

@@ -169,8 +169,8 @@ check_credentials <- function(credentials) {
 #' @family helper functions
 #' @noRd
 extract_temp_key <- function(response) {
-  response %>%
-    httr::content(as = "text") %>%
+  response |>
+    httr::content(as = "text") |>
     stringr::str_extract("(?<=tmp\\/).{15}(?=\\/)")
 }
 
@@ -188,13 +188,13 @@ extract_temp_key <- function(response) {
 #' @noRd
 #' @examples
 #' \dontrun{
-#' etn:::extract_temp_key(response) %>% get_val()
+#' etn:::extract_temp_key(response) |> get_val()
 #' }
 #'
 #' # using the opencpu test instance
 #' api_url <- "https://cloud.opencpu.org/ocpu/library/stats/R/rnorm"
-#' httr::POST(api_url, body = list(n = 10, mean = 5)) %>%
-#'   extract_temp_key() %>%
+#' httr::POST(api_url, body = list(n = 10, mean = 5)) |>
+#'   extract_temp_key() |>
 #'   get_val(api_domain = "https://cloud.opencpu.org/ocpu")
 get_val <- function(temp_key, api_domain = "https://opencpu.lifewatch.be") {
   httr::GET(
@@ -203,9 +203,9 @@ get_val <- function(temp_key, api_domain = "https://opencpu.lifewatch.be") {
       "tmp/{temp_key}/R/.val/rds",
       .sep = "/"
     )
-  ) %>%
-    httr::content(as = "raw") %>%
-    rawConnection() %>%
-    gzcon() %>%
+  ) |>
+    httr::content(as = "raw") |>
+    rawConnection() |>
+    gzcon() |>
     readRDS()
 }

README.Rmd

@@ -59,7 +59,6 @@ This is a basic example which shows you how adress the API directly:
 
 ```{r example, eval = FALSE}
 library(httr2) # to talk to the internet
-library(magrittr) # to use pipes
 library(askpass) # to safly enter a password in R
 
 # To access the ETN database, we need a login (username + password). We'll ask
@@ -69,16 +68,16 @@ username <- "<your-username-here>"
 endpoint <- "https://opencpu.lifewatch.be/library/etnservice/R/list_scientific_names"
 # Request the result of the function to be a json, and put in a request
 response <-
-    httr2::request(endpoint) %>% 
+    httr2::request(endpoint) |> 
     ## In this case we'll request the data in JSON format and parse it
-    httr2::req_url_path_append("json") %>%
+    httr2::req_url_path_append("json") |>
     httr2::req_body_json(
       list(credentials = list(username = username,
                               password = askpass::askpass()))
-    ) %>% 
+    ) |> 
     httr2::req_perform()
 # Take the response of the server, and convert it into an R object we can use
-response %>%
+response |>
     httr2::resp_body_json(simplifyVector = TRUE)
 
 ```

README.md

@@ -55,7 +55,6 @@ This is a basic example which shows you how adress the API directly:
 
 ``` r
 library(httr2) # to talk to the internet
-library(magrittr) # to use pipes
 library(askpass) # to safly enter a password in R
 
 # To access the ETN database, we need a login (username + password). We'll ask
@@ -65,16 +64,16 @@ username <- "<your-username-here>"
 endpoint <- "https://opencpu.lifewatch.be/library/etnservice/R/list_scientific_names"
 # Request the result of the function to be a json, and put in a request
 response <-
-    httr2::request(endpoint) %>% 
+    httr2::request(endpoint) |> 
     ## In this case we'll request the data in JSON format and parse it
-    httr2::req_url_path_append("json") %>%
+    httr2::req_url_path_append("json") |>
     httr2::req_body_json(
       list(credentials = list(username = username,
                               password = askpass::askpass()))
-    ) %>% 
+    ) |> 
     httr2::req_perform()
 # Take the response of the server, and convert it into an R object we can use
-response %>%
+response |>
     httr2::resp_body_json(simplifyVector = TRUE)
 ```
 

inst/postman-helpers/find-postman-test-mismatch.R

@@ -40,9 +40,9 @@ assertthat::assert_that(!httr2::resp_is_error(response))
 ## extract current expectation --------------------------------------------
 expectation <- readr::read_lines(
   glue::glue("tests/postman/test-{fn_to_test}.js")
-) %>%
+) |>
   grep("pm.expect(jsonData).to.include.members(",
-       .,
+       x = _,
        fixed = TRUE,
        value = TRUE) |>
   stringr::str_extract_all('(?<=")[^,]*?(?=\\")') |>

inst/postman-helpers/postman-export-to-js.R

@@ -12,24 +12,24 @@ export <- jsonlite::read_json("tests/postman/etnservice.postman_collection.json"
 # helper to get test script out -------------------------------------------
 
 get_script <- function(event) {
-  event[[1]] %>%
-    pluck("script") %>%
-    pluck("exec") %>%
+  event[[1]] |>
+    pluck("script") |>
+    pluck("exec") |>
     paste(collapse = "\n")
 }
 
 # get names and scripts and write out -------------------------------------
 
 request_names <-
-  export %>%
-  pluck("item") %>%
+  export |>
+  pluck("item") |>
   map_chr(~ pluck(.x, "name"))
 
-export %>%
-  pluck("item") %>%
-  map(~ pluck(.x, "event")) %>%
-  map(get_script) %>%
-  set_names(request_names) %>%
+export |>
+  pluck("item") |>
+  map(~ pluck(.x, "event")) |>
+  map(get_script) |>
+  set_names(request_names) |>
   walk2(request_names, ~ readr::write_lines(.x, file.path(
     "tests", "postman", paste0("test-", .y, ".js")
   )))

tests/testthat/test-get_acoustic_deployments.R

@@ -24,7 +24,7 @@ test_that("get_acoustic_deployments() returns a tibble", {
 
 test_that("get_acoustic_deployments() returns unique deployment_id", {
   df <- get_acoustic_deployments(credentials)
-  expect_equal(nrow(df), nrow(df %>% distinct(deployment_id)))
+  expect_equal(nrow(df), nrow(df |> distinct(deployment_id)))
 })
 
 test_that("get_acoustic_deployments() returns the expected columns", {
@@ -81,7 +81,7 @@ test_that("get_acoustic_deployments() allows selecting on deployment_id", {
   single_select <- 1437 # From demer
   single_select_df <- get_acoustic_deployments(credentials, deployment_id = single_select)
   expect_equal(
-    single_select_df %>% distinct(deployment_id) %>% pull(),
+    single_select_df |> distinct(deployment_id) |> pull(),
     c(single_select)
   )
   expect_gt(nrow(single_select_df), 0)
@@ -90,7 +90,7 @@ test_that("get_acoustic_deployments() allows selecting on deployment_id", {
   multi_select <- c("1437", 1588) # Characters are allowed
   multi_select_df <- get_acoustic_deployments(credentials, deployment_id = multi_select)
   expect_equal(
-    multi_select_df %>% distinct(deployment_id) %>% pull() %>% sort(),
+    multi_select_df |> distinct(deployment_id) |> pull() |> sort(),
     c(as.integer(multi_select)) # Output will be all integer
   )
   expect_gt(nrow(multi_select_df), nrow(single_select_df))
@@ -105,7 +105,7 @@ test_that("get_acoustic_deployments() allows selecting on receiver_id", {
   single_select <- "VR2W-124070" # From demer
   single_select_df <- get_acoustic_deployments(credentials, receiver_id = single_select)
   expect_equal(
-    single_select_df %>% distinct(receiver_id) %>% pull(),
+    single_select_df |> distinct(receiver_id) |> pull(),
     c(single_select)
   )
   expect_gt(nrow(single_select_df), 0)
@@ -114,7 +114,7 @@ test_that("get_acoustic_deployments() allows selecting on receiver_id", {
   multi_select <- c("VR2W-124070", "VR2W-124078")
   multi_select_df <- get_acoustic_deployments(credentials, receiver_id = multi_select)
   expect_equal(
-    multi_select_df %>% distinct(receiver_id) %>% pull() %>% sort(),
+    multi_select_df |> distinct(receiver_id) |> pull() |> sort(),
     c(multi_select)
   )
   expect_gt(nrow(multi_select_df), nrow(single_select_df))
@@ -129,7 +129,7 @@ test_that("get_acoustic_deployments() allows selecting on acoustic_project_code"
   single_select <- "demer"
   single_select_df <- get_acoustic_deployments(credentials, acoustic_project_code = single_select)
   expect_equal(
-    single_select_df %>% distinct(acoustic_project_code) %>% pull(),
+    single_select_df |> distinct(acoustic_project_code) |> pull(),
     c(single_select)
   )
   expect_gt(nrow(single_select_df), 0)
@@ -144,7 +144,7 @@ test_that("get_acoustic_deployments() allows selecting on acoustic_project_code"
   multi_select <- c("demer", "dijle")
   multi_select_df <- get_acoustic_deployments(credentials, acoustic_project_code = multi_select)
   expect_equal(
-    multi_select_df %>% distinct(acoustic_project_code) %>% pull() %>% sort(),
+    multi_select_df |> distinct(acoustic_project_code) |> pull() |> sort(),
     c(multi_select)
   )
   expect_gt(nrow(multi_select_df), nrow(single_select_df))
@@ -159,7 +159,7 @@ test_that("get_acoustic_deployments() allows selecting on station_name", {
   single_select <- "de-9" # From demer
   single_select_df <- get_acoustic_deployments(credentials, station_name = single_select)
   expect_equal(
-    single_select_df %>% distinct(station_name) %>% pull(),
+    single_select_df |> distinct(station_name) |> pull(),
     c(single_select)
   )
   expect_gt(nrow(single_select_df), 0)
@@ -168,7 +168,7 @@ test_that("get_acoustic_deployments() allows selecting on station_name", {
   multi_select <- c("de-10", "de-9") # Note that sort() will put de-10 before de-9
   multi_select_df <- get_acoustic_deployments(credentials, station_name = multi_select)
   expect_equal(
-    multi_select_df %>% distinct(station_name) %>% pull() %>% sort(),
+    multi_select_df |> distinct(station_name) |> pull() |> sort(),
     c(multi_select)
   )
   expect_gt(nrow(multi_select_df), nrow(single_select_df))