From d55867c2274eb95e6fac6bc51f43051043011737 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ma=C3=ABlle=20Salmon?= Date: Wed, 28 Feb 2024 15:35:07 +0100 Subject: [PATCH] docs: fix examples, set up pkgdown workflow to run the rundontrun ones --- .github/workflows/pkgdown.yaml | 2 +- DESCRIPTION | 2 +- R/info.R | 11 ++++------- R/layer_attributes.R | 20 ++++++++++---------- R/layers.R | 24 ++++++++---------------- man/EMODnetWFS-package.Rd | 2 +- man/emodnet_get_layers.Rd | 24 ++++++++---------------- man/emodnet_get_wfs_info.Rd | 11 ++++------- man/layer_attribute_descriptions.Rd | 4 ++-- man/layer_attribute_inspect.Rd | 6 +++--- man/layer_attributes_get_names.Rd | 4 ++-- man/layer_attributes_summarise.Rd | 4 ++-- man/layer_attributes_tbl.Rd | 2 +- 13 files changed, 47 insertions(+), 69 deletions(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index dafd10d0..ef7cc67e 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.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 🚀 diff --git a/DESCRIPTION b/DESCRIPTION index 018a44a7..a3eead3f 100644 --- a/DESCRIPTION +++ b/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) diff --git a/R/info.R b/R/info.R index 1055e56f..96780fb7 100644 --- a/R/info.R +++ b/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) diff --git a/R/layer_attributes.R b/R/layer_attributes.R index f36744ea..3a17b1d8 100644 --- a/R/layer_attributes.R +++ b/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, diff --git a/R/layers.R b/R/layers.R index 5a16c142..618da2f5 100644 --- a/R/layers.R +++ b/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, diff --git a/man/EMODnetWFS-package.Rd b/man/EMODnetWFS-package.Rd index 4027ce9c..85bc0021 100644 --- a/man/EMODnetWFS-package.Rd +++ b/man/EMODnetWFS-package.Rd @@ -18,7 +18,7 @@ Useful links: } \author{ -\strong{Maintainer}: Salvador Fernández-Bejarano \email{salvador.fernandez@vliz.be} (\href{https://orcid.org/0000-0003-0535-7677}{ORCID}) [contributor] +\strong{Maintainer}: Salvador Fernández-Bejarano \email{salvador.fernandez@vliz.be} (\href{https://orcid.org/0000-0003-0535-7677}{ORCID}) Authors: \itemize{ diff --git a/man/emodnet_get_layers.Rd b/man/emodnet_get_layers.Rd index 1d5bbd80..787876a3 100644 --- a/man/emodnet_get_layers.Rd +++ b/man/emodnet_get_layers.Rd @@ -71,30 +71,22 @@ of layer features can also be handled via ECQL language filters. \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 ) } } diff --git a/man/emodnet_get_wfs_info.Rd b/man/emodnet_get_wfs_info.Rd index 3d3b74b8..2efdd75d 100644 --- a/man/emodnet_get_wfs_info.Rd +++ b/man/emodnet_get_wfs_info.Rd @@ -56,13 +56,10 @@ services from server. \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) } } diff --git a/man/layer_attribute_descriptions.Rd b/man/layer_attribute_descriptions.Rd index 866586fd..4634c685 100644 --- a/man/layer_attribute_descriptions.Rd +++ b/man/layer_attribute_descriptions.Rd @@ -33,8 +33,8 @@ Get layer attribute description \examples{ \dontrun{ layer_attribute_descriptions( - service = "human_activities", - layer = "maritimebnds" + service = "biology", + layer = "mediseh_zostera_m_pnt" ) } } diff --git a/man/layer_attribute_inspect.Rd b/man/layer_attribute_inspect.Rd index b53b1834..217d3a89 100644 --- a/man/layer_attribute_inspect.Rd +++ b/man/layer_attribute_inspect.Rd @@ -38,8 +38,8 @@ Inspect layer attributes } \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") } } diff --git a/man/layer_attributes_get_names.Rd b/man/layer_attributes_get_names.Rd index 199c8258..84819c55 100644 --- a/man/layer_attributes_get_names.Rd +++ b/man/layer_attributes_get_names.Rd @@ -33,8 +33,8 @@ Get names of layer attributes \examples{ \dontrun{ layer_attributes_get_names( - service = "human_activities", - layer = "maritimebnds" + service = "biology", + layer = "mediseh_zostera_m_pnt" ) } } diff --git a/man/layer_attributes_summarise.Rd b/man/layer_attributes_summarise.Rd index 714a52e7..e05085a9 100644 --- a/man/layer_attributes_summarise.Rd +++ b/man/layer_attributes_summarise.Rd @@ -34,8 +34,8 @@ Get summaries of layer attributes (variables) \examples{ \dontrun{ layer_attributes_summarise( - service = "human_activities", - layer = "maritimebnds" + service = "biology", + layer = "mediseh_zostera_m_pnt" ) } } diff --git a/man/layer_attributes_tbl.Rd b/man/layer_attributes_tbl.Rd index 51d40de8..b456d0b6 100644 --- a/man/layer_attributes_tbl.Rd +++ b/man/layer_attributes_tbl.Rd @@ -35,6 +35,6 @@ targeted and faster layer download. } \examples{ \dontrun{ -layer_attributes_tbl(service = "human_activities", layer = "maritimebnds") +layer_attributes_tbl(service = "biology", layer = "mediseh_zostera_m_pnt") } }