Merge pull request #133 from SpatLyu/master

explicitly namespace function calls using pkg::fun() to improve clarity and avoid ambiguity

Author: tim-salabim

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

@@ -5,21 +5,39 @@ on:
     branches: [main, master]
   pull_request:
 
-name: R-CMD-check.yaml
+name: R-CMD-check
 
 permissions: read-all
 
 jobs:
   R-CMD-check:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
+          - {os: ubuntu-latest,   r: 'release'}
+          - {os: ubuntu-latest,   r: 'oldrel-1'}
+
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_KEEP_PKG_SOURCE: yes
+
     steps:
       - uses: actions/checkout@v4
 
+      - uses: r-lib/actions/setup-pandoc@v2
+
       - uses: r-lib/actions/setup-r@v2
         with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2

DESCRIPTION

@@ -38,7 +38,8 @@ Imports:
     sf (>= 0.5-2),
     shiny,
     tmaptools,
-    shinyWidgets (>= 0.4.3)
+    shinyWidgets (>= 0.4.3),
+    magrittr
 Suggests:
     crayon,
     sp

NAMESPACE

@@ -8,6 +8,7 @@ S3method(editMap,mapview)
 S3method(selectFeatures,Spatial)
 S3method(selectFeatures,sf)
 S3method(selectMap,leaflet)
+export("%>%")
 export(createFeatures)
 export(drawFeatures)
 export(editAttributes)
@@ -19,26 +20,4 @@ export(selectFeatures)
 export(selectMap)
 export(selectMod)
 export(selectModUI)
-import(dplyr)
-import(htmltools)
-import(leafem)
-import(leaflet)
-import(leafpop)
-import(mapview)
-import(sf)
-import(shiny)
-importFrom(dplyr,bind_rows)
-importFrom(leaflet,setView)
-importFrom(mapview,mapview)
-importFrom(miniUI,gadgetTitleBar)
-importFrom(miniUI,miniButtonBlock)
-importFrom(miniUI,miniContentPanel)
-importFrom(miniUI,miniPage)
-importFrom(rstudioapi,getActiveDocumentContext)
-importFrom(sf,write_sf)
-importFrom(shinyWidgets,actionBttn)
-importFrom(shinyWidgets,show_alert)
-importFrom(shinyWidgets,switchInput)
-importFrom(shinyWidgets,updateSwitchInput)
-importFrom(shinyWidgets,useSweetAlert)
-importFrom(tmaptools,geocode_OSM)
+importFrom(magrittr,"%>%")

R/addin.R

@@ -1,6 +1,3 @@
-
-
-
 #' @title mapedit create features Addin
 #' @description Create and save spatial objects within the Rstudio IDE. Objects
 #' can then be saved to file types such as \code{.geojson} or \code{.shp}.
@@ -17,30 +14,22 @@
 #' @param SF_OBJECT sf Simple feature collection
 #'
 #' @return sf object and/or saved to file
-#' @importFrom miniUI miniPage miniContentPanel gadgetTitleBar miniButtonBlock
-#' @import shiny
-#' @importFrom shinyWidgets switchInput updateSwitchInput
-#' @importFrom mapview mapview
-#' @importFrom sf write_sf
-#' @importFrom dplyr bind_rows
-#' @importFrom leaflet setView
-#' @importFrom rstudioapi getActiveDocumentContext
 #' @export
 #'
 createFeatures <- function(SF_OBJECT = NULL) {
 
-  ui <- miniPage(
-    gadgetTitleBar("Edit Map"),
-    miniContentPanel(
-      editModUI("editor"),
-      miniButtonBlock(
-        div(style="display: inline-block;padding-top:22px;padding-left:30px;width:200px;",
-            switchInput('savefile', 'Save', value = FALSE, onStatus = "success", offStatus = "danger")),
-        div(style="display: inline-block; width: 400px;",
-            textInput('filename', '', value = 'saved_geometry.geojson')),
-        div(style="display: inline-block;padding-top:18px;width: 400px;font-size: 10pt;color: #313844;",
-            'The filename can include a path relative to working directory. ',
-            'A different file type can be selected by changing the file extension.')
+  ui <- miniUI::miniPage(
+    miniUI::gadgetTitleBar("Edit Map"),
+    miniUI::miniContentPanel(
+      mapedit::editModUI("editor"),
+      miniUI::miniButtonBlock(
+        htmltools::div(style="display: inline-block;padding-top:22px;padding-left:30px;width:200px;",
+                       shinyWidgets::switchInput('savefile', 'Save', value = FALSE, onStatus = "success", offStatus = "danger")),
+        htmltools::div(style="display: inline-block; width: 400px;",
+                       shiny::textInput('filename', '', value = 'saved_geometry.geojson')),
+        htmltools::div(style="display: inline-block;padding-top:18px;width: 400px;font-size: 10pt;color: #313844;",
+                       'The filename can include a path relative to working directory. ',
+                       'A different file type can be selected by changing the file extension.')
       )
     )
   )
@@ -63,36 +52,38 @@ createFeatures <- function(SF_OBJECT = NULL) {
     }, silent = TRUE)
 
     # update UI based on inputs
-    updateTextInput(session, 'filename', value = FILENAME)
+    shiny::updateTextInput(session, 'filename', value = FILENAME)
     if (FILENAME != 'saved_geometry.geojson') {
-      updateSwitchInput(session, 'savefile', value = TRUE)
+      shinyWidgets::updateSwitchInput(session, 'savefile', value = TRUE)
     }
 
     # load mapedit
     if ('sf' %in% class(SF_OBJECT)) {
-      geo <- callModule(editMod, "editor", mapview(SF_OBJECT)@map)
+      geo <- shiny::callModule(mapedit::editMod, "editor", mapview::mapview(SF_OBJECT)@map)
     } else {
-      geo <- callModule(editMod, "editor", setView(mapview()@map, 80, 0, 3))
+      geo <- shiny::callModule(mapedit::editMod, "editor", leaflet::setView(mapview::mapview()@map, 80, 0, 3))
     }
 
-    observe({
+    shiny::observe({
       input$filename
       OBJECTNAME <- tools::file_path_sans_ext(basename(input$filename))
     })
 
     # return geometry to file and object in console
-    observeEvent(input$done, {
+    shiny::observeEvent(input$done, {
       geom <- geo()$finished
 
-      if (!is.null(geom) & !is.null(SF_OBJECT)) geom <- dplyr::bind_rows(SF_OBJECT, geom)
+      if (!is.null(geom) & !is.null(SF_OBJECT)) {
+        geom <- dplyr::bind_rows(SF_OBJECT, geom)
+      }
 
       if (!is.null(geom)) {
         if (input$savefile) {
           sf::write_sf(geom, input$filename, delete_layer = TRUE, delete_dsn = TRUE)
         }
       }
 
-      stopApp({
+      shiny::stopApp({
         if (!is.null(geom)) {
           geom
         }
@@ -101,7 +92,7 @@ createFeatures <- function(SF_OBJECT = NULL) {
 
   }
 
-  viewer <- paneViewer(600)
-  runGadget(ui, server, viewer = viewer)
+  viewer <- shiny::paneViewer(600)
+  shiny::runGadget(ui, server, viewer = viewer)
 
 }

R/edit.R

@@ -77,7 +77,7 @@ editMap.leaflet <- function(
       title = title,
       right = miniUI::miniTitleBarButton("done", "Done", primary = TRUE)
     ),
-    tags$script(HTML(
+    htmltools::tags$script(htmltools::HTML(
       "
 // close browser window on session end
 $(document).on('shiny:disconnected', function() {
@@ -95,7 +95,7 @@ $(document).on('shiny:disconnected', function() {
   )
 
   server <- function(input, output, session) {
-    crud <- callModule(
+    crud <- shiny::callModule(
       editMod,
       ns,
       x,
@@ -107,7 +107,7 @@ $(document).on('shiny:disconnected', function() {
       editorOptions = editorOptions
     )
 
-    observe({crud()})
+    shiny::observe({crud()})
 
     # if browser viewer and user closes tab/window
     #  then Shiny does not stop so we will stopApp
@@ -117,7 +117,7 @@ $(document).on('shiny:disconnected', function() {
     sessionEnded <- session$onSessionEnded(function() {
       # should this be a cancel where we send NULL
       #  or a done where we send crud()
-      shiny::stopApp(isolate(crud()))
+      shiny::stopApp(shiny::isolate(crud()))
     })
 
     shiny::observeEvent(input$done, {

R/editAttributes.R

@@ -34,17 +34,6 @@
 #' @note Editing of feature geometries does not work for multi-geometry inputs. For this use case it is advisable to
 #' split the data set by geometry type and edit separately
 #'
-#' @import sf
-#' @import leaflet
-#' @import mapview
-#' @import leafem
-#' @import leafpop
-#' @import dplyr
-#' @import shiny
-#' @import htmltools
-#' @importFrom shinyWidgets actionBttn show_alert useSweetAlert
-#' @importFrom tmaptools geocode_OSM
-#'
 #' @return sf data.frame
 #' @export
 #'
@@ -81,7 +70,8 @@ editAttributes <- function(dat, zoomto = NULL, col_add = TRUE, reset = TRUE, pro
 
   #create base df if dat missing
   if (missing(dat)) {
-    dat <- data.frame(id = 'CHANGE ME', comments = 'ADD COMMENTS...') %>% mutate(leaf_id = 1)
+    dat <- data.frame(id = 'CHANGE ME', comments = 'ADD COMMENTS...') %>%
+      dplyr::mutate(leaf_id = 1)
     if (is.null(zoomto)) {
       message(MSG)
       zoomto <- DEFAULT_ZOOM
@@ -97,13 +87,13 @@ editAttributes <- function(dat, zoomto = NULL, col_add = TRUE, reset = TRUE, pro
   original_sf <- NULL
   if (all(class(dat) == 'list')) {
     original_sf <- lapply(dat, function(df){
-      df %>% mutate(leaf_id = 1:nrow(df))
+      df %>% dplyr::mutate(leaf_id = 1:nrow(df))
     })
-    dat <- bind_rows(dat) %>% mutate(leaf_id = 1:nrow(dat))
+    dat <- dplyr::bind_rows(dat) %>% dplyr::mutate(leaf_id = 1:nrow(dat))
   }
 
   if (all(class(dat) == 'data.frame')) {
-    dat <- dat %>% mutate(leaf_id = 1:nrow(dat))
+    dat <- dat %>% dplyr::mutate(leaf_id = 1:nrow(dat))
     data_copy <- sf::st_as_sf(
       dat,
       geometry = sf::st_sfc(lapply(seq_len(nrow(dat)),function(i){sf::st_point()}))
@@ -119,7 +109,7 @@ editAttributes <- function(dat, zoomto = NULL, col_add = TRUE, reset = TRUE, pro
 
    } else if (any(type %in% class(dat))) {
 
-    dat <- dat %>% mutate(leaf_id = 1:nrow(dat)) %>% sf::st_transform(APP_CRS)
+    dat <- dat %>% dplyr::mutate(leaf_id = 1:nrow(dat)) %>% sf::st_transform(APP_CRS)
     data_copy <- dat # TODO check orig crs and transform to 4326
 
     if(is.na(sf::st_crs(dat))){dat <- dat %>% sf::st_set_crs(APP_CRS)}
@@ -144,13 +134,13 @@ editAttributes <- function(dat, zoomto = NULL, col_add = TRUE, reset = TRUE, pro
   }
 
 
-  ui <- tagList(
+  ui <- htmltools::tagList(
     shinyWidgets::useSweetAlert(),
     shiny::fluidPage(
       shiny::fluidRow(
         shiny::column(12, editModUI("map"))
       ),
-      tags$hr(),
+      htmltools::tags$hr(),
       shiny::fluidRow(
         shiny::column(ifelse(col_add, 6, 9),
                DT::dataTableOutput("tbl",width="100%", height=200)),
@@ -182,7 +172,7 @@ editAttributes <- function(dat, zoomto = NULL, col_add = TRUE, reset = TRUE, pro
           }
         }
       ),
-      shiny::fluidRow(tags$hr(),
+      shiny::fluidRow(htmltools::tags$hr(),
                       shiny::div(style = 'padding: 20px',
                                  shinyWidgets::actionBttn("donebtn", "Done",
                                                           icon = shiny::icon('check-circle'),
@@ -269,7 +259,7 @@ editAttributes <- function(dat, zoomto = NULL, col_add = TRUE, reset = TRUE, pro
 
       output$dyn_form <- shiny::renderUI({
 
-        shiny::tagList(
+        htmltools::tagList(
           lapply(1:length(df$types), function(n){
             name <- names(df$types[n])
             label <- paste0(names(df$types[n]), ' (', df$types[n], ')')
@@ -502,7 +492,7 @@ editAttributes <- function(dat, zoomto = NULL, col_add = TRUE, reset = TRUE, pro
               proxy_map %>%
                 leaflet::flyTo(lng = pnt$X, lat = pnt$Y, zoom = input[[nsm('map_zoom')]])
             } else {
-              bb <- st_bbox(sf::st_geometry(rowsel))
+              bb <- sf::st_bbox(sf::st_geometry(rowsel))
               proxy_map %>%
                 leaflet::flyToBounds(bb[['xmin']], bb[['ymin']], bb[['xmax']], bb[['ymax']])
             }

R/helpers.R

@@ -8,3 +8,16 @@ insane_longitude_warning = function() {
             call. = FALSE)
   }
 }
+
+#' @title Pipe operator
+#' @description
+#' See \code{magrittr::\link[magrittr:pipe]{\%>\%}} for details.
+#'
+#' @name %>%
+#' @usage lhs \%>\% rhs
+#' @rdname pipe
+#' @keywords internal
+#' @importFrom magrittr %>%
+#' @return `NULL` (this is the magrittr pipe operator)
+#' @export
+NULL