docs: fix examples, set up pkgdown workflow to run the rundontrun ones

.github/workflows/pkgdown.yaml

@@ -35,7 +35,7 @@ jobs:
           needs: website
 
       - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE, run_dont_run = TRUE)
         shell: Rscript {0}
 
       - name: Deploy to GitHub pages 🚀

DESCRIPTION

@@ -55,6 +55,6 @@ Config/testthat/edition: 3
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 SystemRequirements: C++11, GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>=
     4.8.0)

R/info.R

@@ -90,14 +90,11 @@ emodnet_get_layer_info <- memoise::memoise(.emodnet_get_layer_info)
 #' \dontrun{
 #' emodnet_get_wfs_info(service = "bathymetry")
 #' # Query a wfs object
-#' wfs_cml <- emodnet_init_wfs_client("chemistry_marine_litter")
-#' emodnet_get_wfs_info(wfs_cml)
+#' wfs_bio <- emodnet_init_wfs_client("biology")
+#' emodnet_get_wfs_info(wfs_bio)
 #' # Get info for specific layers from wfs object
-#' layers <- c(
-#'   "bl_fishing_monitoring",
-#'   "bl_beacheslocations_monitoring"
-#' )
-#' emodnet_get_layer_info(wfs = wfs_cml, layers = layers)
+#' layers <- c("mediseh_zostera_m_pnt", "mediseh_posidonia_nodata")
+#' emodnet_get_layer_info(wfs = wfs_bio, layers = layers)
 #' }
 emodnet_get_wfs_info <- memoise::memoise(.emodnet_get_wfs_info)
 

R/layer_attributes.R

@@ -12,8 +12,8 @@
 #' @examples
 #' \dontrun{
 #' layer_attributes_summarise(
-#'   service = "human_activities",
-#'   layer = "maritimebnds"
+#'   service = "biology",
+#'   layer = "mediseh_zostera_m_pnt"
 #' )
 #' }
 layer_attributes_summarise <- function(wfs = NULL,
@@ -45,8 +45,8 @@ layer_attributes_summarise <- function(wfs = NULL,
 #' @examples
 #' \dontrun{
 #' layer_attribute_descriptions(
-#'   service = "human_activities",
-#'   layer = "maritimebnds"
+#'   service = "biology",
+#'   layer = "mediseh_zostera_m_pnt"
 #' )
 #' }
 layer_attribute_descriptions <- function(wfs = NULL,
@@ -76,8 +76,8 @@ layer_attribute_descriptions <- function(wfs = NULL,
 #' @examples
 #' \dontrun{
 #' layer_attributes_get_names(
-#'   service = "human_activities",
-#'   layer = "maritimebnds"
+#'   service = "biology",
+#'   layer = "mediseh_zostera_m_pnt"
 #' )
 #' }
 layer_attributes_get_names <- function(wfs = NULL,
@@ -111,9 +111,9 @@ layer_attributes_get_names <- function(wfs = NULL,
 #'
 #' @examples
 #' \dontrun{
-#' wfs <- emodnet_init_wfs_client(service = "human_activities")
-#' layer_attributes_get_names(wfs, layer = "maritimebnds")
-#' layer_attribute_inspect(wfs, layer = "maritimebnds", attribute = "sitename")
+#' wfs <- emodnet_init_wfs_client(service = "biology")
+#' layer_attributes_get_names(wfs, layer = "mediseh_zostera_m_pnt")
+#' layer_attribute_inspect(wfs, layer = "mediseh_zostera_m_pnt", attribute = "country")
 #' }
 layer_attribute_inspect <- function(wfs = NULL,
                                     service = NULL,
@@ -175,7 +175,7 @@ layer_attribute_inspect <- function(wfs = NULL,
 #'
 #' @examples
 #' \dontrun{
-#' layer_attributes_tbl(service = "human_activities", layer = "maritimebnds")
+#' layer_attributes_tbl(service = "biology", layer = "mediseh_zostera_m_pnt")
 #' }
 layer_attributes_tbl <- function(wfs = NULL,
                                  service = NULL,

R/layers.R

@@ -41,30 +41,22 @@
 #' \dontrun{
 #' # Layers as character vector
 #' emodnet_get_layers(
-#'   service = "seabed_habitats_individual_habitat_map_and_model_datasets",
-#'   layers = c("dk003069", "dk003070")
+#'   service = "biology",
+#'   layers = c("mediseh_zostera_m_pnt", "mediseh_posidonia_nodata")
 #' )
 #'
-#' # Layers as character vector, layers to be reduced
-#' emodnet_get_layers(
-#'   service = "seabed_habitats_individual_habitat_map_and_model_datasets",
-#'   layers = c("dk003069", "dk003070"),
-#'   reduce_layers = TRUE
-#' )
 #'
 #' # Usage of cql_filter
 #' emodnet_get_layers(
-#'   service = "human_activities",
-#'   layers = "maritimebnds",
-#'   cql_filter = "sitename='Territory sea (12 nm)'",
-#'   reduce_layers = TRUE
+#'   service = "biology",
+#'   layers = "mediseh_zostera_m_pnt",
+#'   cql_filter = "country = 'Francia'"
 #' )
 #' # Usage of vendor parameter
 #' emodnet_get_layers(
-#'   service = "human_activities",
-#'   layers = "maritimebnds",
-#'   count = 1,
-#'   reduce_layers = TRUE
+#'   service = "biology",
+#'   layers = "mediseh_zostera_m_pnt",
+#'   count = 1
 #' )
 #' }
 emodnet_get_layers <- function(wfs = NULL,