Add pkgdown website

.Rbuildignore

@@ -5,5 +5,6 @@
 [.]js$
 ^\.github$
 ^CITATION\.cff$
-^\.positai$
-^\.claude$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.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: windows-latest,   r: '4.1.0'}
+          - {os: ubuntu-latest,   r: '3.6.3'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/github-pages-deploy-action@v4.5.0
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

.gitignore

@@ -51,6 +51,4 @@ rsconnect/
 
 # Postman collection exports
 tests/postman/*.json
-
-# PositAI (default RStudio)
-.positai
+docs

DESCRIPTION

@@ -16,15 +16,14 @@ 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,
     DBI,
     dplyr,
     glue,
     httr,
+    jsonlite,
     lubridate,
     methods,
     odbc,
@@ -33,7 +32,6 @@ Imports:
     stringr,
     utils
 Suggests: 
-    jsonlite,
     purrr,
     testthat (>= 3.0.0)
 Config/testthat/edition: 3

NAMESPACE

@@ -23,6 +23,8 @@ export(list_scientific_names)
 export(list_station_names)
 export(list_tag_serial_numbers)
 export(validate_login)
+export(write_dwc)
+importFrom(dplyr,"%>%")
 importFrom(dplyr,.data)
 importFrom(dplyr,distinct)
 importFrom(dplyr,filter)

NEWS.md

@@ -1,7 +1,6 @@
 # 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 now has a pkgdown website: [inbo.github.io/etnservice/](https://inbo.github.io/etnservice/).
+
 # 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

@@ -2,6 +2,7 @@
 "_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

@@ -264,8 +264,7 @@ 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()
 }