Dev 202403

.github/workflows/check-standard.yaml

@@ -0,0 +1,50 @@
+# 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:
+    branches: [main, master]
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    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
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

.github/workflows/lint.yaml

@@ -14,7 +14,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:
@@ -28,3 +28,5 @@ jobs:
       - name: Lint
         run: lintr::lint_package()
         shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

DESCRIPTION

@@ -9,6 +9,7 @@ License: MIT + file LICENSE
 Depends: 
     R (>= 4.0.0)
 Imports:
+    bsicons,
     bslib,
     data.table,
     dplyr,
@@ -36,4 +37,4 @@ Suggests:
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1

R/app_server.R

@@ -83,30 +83,34 @@ app_server = function(input, output, session) {
     shiny::bindCache(input$widgetChoice)
 
 
-# Mutation colouring ------------------------------------------------------
+  # Mutation colouring ------------------------------------------------------
 
   # disable dropdown unless mutation treeview
   shiny::observe({
     choice = ifelse(input$widgetChoice != "", input$widgetChoice, "")
     # toggle mutation dropdown
-    shinyjs::toggleElement(id = "mutationChoice",
-                         condition = choice == "tree-mutations.rds")
+    shinyjs::toggleElement(
+      id = "mutationChoice",
+      condition = choice == "tree-mutations.rds"
+    )
     # toggle sequence dropdown
-    shinyjs::toggleElement(id = "sequenceChoice",
-                         condition = choice == "tree-sequences.rds")
+    shinyjs::toggleElement(
+      id = "sequenceChoice",
+      condition = choice == "tree-sequences.rds"
+    )
     # select input for sequences
     if (choice == "tree-sequences.rds") {
       avail_seqs = data.table::as.data.table(available_sequences(data_dir))
       names(avail_seqs) = "Sequences"
-      shiny::updateSelectInput(inputId = "sequenceChoice",
-                                  choices = avail_seqs
-                                  )
+      shiny::updateSelectInput(
+        inputId = "sequenceChoice",
+        choices = avail_seqs
+      )
     }
   })
 
   # get selected nodes from mutation choice
   shiny::observeEvent(input$mutationChoice, {
-
     nodeChoice = selected_mut_nodes(input$mutationChoice, data_dir)
 
     # the 'node' column contains integers that define the IDs for graph-nodes in the htmlwidget
@@ -124,11 +128,10 @@ app_server = function(input, output, session) {
     )
   })
 
-# Sequence colouring ------------------------------------------------------
+  # Sequence colouring ------------------------------------------------------
 
   # get selected nodes from sequence choice
   shiny::observeEvent(input$sequenceChoice, {
-
     nodeChoice = selected_seq_nodes(input$sequenceChoice, data_dir)
 
     # the 'node' column contains integers that define the IDs for graph-nodes in the htmlwidget
@@ -146,15 +149,17 @@ app_server = function(input, output, session) {
     )
   })
 
-# Get click ---------------------------------------------------------------
+  # Get click ---------------------------------------------------------------
 
   # get selected cluster id based on widget choice
   selected_cluster_id = shiny::reactive({
     shiny::req(input$widgetChoice)
     shiny::req(input$treeview_selected)
-    get_selected_cluster_id(widgetChoice = input$widgetChoice,
-                            treeviewSelected = utils::tail(input$treeview_selected, 1),
-                            data_dir = data_dir)
+    get_selected_cluster_id(
+      widgetChoice = input$widgetChoice,
+      treeviewSelected = utils::tail(input$treeview_selected, 1),
+      data_dir = data_dir
+    )
   }) %>%
     shiny::bindCache(input$widgetChoice, input$treeview_selected)
 
@@ -169,9 +174,10 @@ app_server = function(input, output, session) {
     shiny::req(input$widgetChoice)
     fname = stringr::str_replace(input$widgetChoice, ".rds", ".md")
     shiny::includeMarkdown(system.file("app", "www", "content", "treeview",
-                                       fname,
-                                       package = "tfpbrowser",
-                                       mustWork = TRUE))
+      fname,
+      package = "tfpbrowser",
+      mustWork = TRUE
+    ))
   })
 
   # Tables Tab --------------------------------------------------------------
@@ -194,5 +200,4 @@ app_server = function(input, output, session) {
     cluster_choice = selected_cluster_id,
     data_dir = data_dir
   )
-
 } # end server function

R/app_ui.R

@@ -3,103 +3,83 @@
 #' @param request Internal parameter for `{shiny}`.
 #' @noRd
 app_ui = function(request) {
-  data_dir <- get_data_dir()
+  data_dir = get_data_dir()
 
   shiny::tagList(
-
     shinyjs::useShinyjs(),
     shinybrowser::detect(),
-
     shiny::navbarPage(
       # title
       title = place_title_logo(),
-
       header = add_ext_resources(data_dir),
       # theme
-      theme = bslib::bs_theme(version = 4,
-                              bootswatch = "minty",
-                              bg = "#EBEEEE",
-                              fg = "#002147",
-                              primary = "#003E74",
-                              secondary = "#9D9D9D"),
+      theme = bslib::bs_theme(
+        version = 5,
+        bootswatch = "minty",
+        bg = "#EBEEEE",
+        fg = "#002147",
+        primary = "#003E74",
+        secondary = "#9D9D9D"
+      ),
 
       # Input widgets
       shiny::tabPanel(
         title = "Data",
-
         shiny::fluidRow(
-          shiny::column(12,
-                        # use details and summary to create expandable section
-                        htmltools::tags$details(
-                          # preview of expandable section
-                          htmltools::tags$summary("Cluster statistics (click to expand)"),
-
-                          shiny::br(),
-
-                          # text to print choice
-                          shiny::textOutput("select_text"),
-                          shiny::br(),
-
-                          # output options
-                          shiny::tabsetPanel(id = "plot_tabs",
-
-                                             # Tables tab
-                                             tablesUI("table1"),
-
-                                             # Plots tab
-                                             plotsUI("plot1"),
-
-                                             # RDS tab
-                                             rdsUI("rds1")
-
-                          )
-                        )
-          )
+          shiny::column(12, clusterStatsUI(id = NULL))
         ), # end fluid row
 
         # Bottom row - show tree (static html output from tfpscanner)
         shiny::fluidRow(
           shiny::column(12,
-            id="view-container",
-                        shiny::div(id="view-selection",
-                          htmltools::tags$details(
-                            id="sidebar-toggle",
-                            open="open",
-                            `aria-role`="button",
-                            `aria-label`="Toggle sidebar visibility",
-                            htmltools::tags$summary(
-                              shiny::span(">>"),
-                              shiny::span("<<")
-                            )
-                          ),
-                          # choose type of treeview
-                          shiny::selectInput(inputId = "widgetChoice",
-                                                label = "View",
-                                                choices = c("None" = ""),
-                                                selectize = FALSE),
-
-                          # choose type of mutation
-                          shiny::selectInput(inputId = "mutationChoice",
-                                                label = "Mutation",
-                                                choices = character(0),
-                                                selectize = FALSE),
-
-                          # choose type of sequence
-                          shiny::selectInput(inputId = "sequenceChoice",
-                                                label = "Sequence",
-                                                choices = NULL,
-                                                selectize = FALSE),
+            id = "view-container",
+            shiny::div(
+              id = "view-selection",
+              htmltools::tags$details(
+                id = "sidebar-toggle",
+                open = "open",
+                `aria-role` = "button",
+                `aria-label` = "Toggle sidebar visibility",
+                htmltools::tags$summary(
+                  shiny::span(">>"),
+                  shiny::span("<<")
+                )
+              ),
+              # choose type of treeview
+              shiny::selectInput(
+                inputId = "widgetChoice",
+                label = "View",
+                choices = c("None" = ""),
+                selectize = FALSE
+              ),
+
+              # choose type of mutation
+              shiny::selectInput(
+                inputId = "mutationChoice",
+                label = "Mutation",
+                choices = character(0),
+                selectize = FALSE
+              ),
+
+              # choose type of sequence
+              shiny::selectInput(
+                inputId = "sequenceChoice",
+                label = "Sequence",
+                choices = NULL,
+                selectize = FALSE
+              ),
             ),
-            shiny::div(id="view-graphic",
-                          # markdown files to add description
-                          shiny::uiOutput("tree_md_files"),
-
-                          # show treeview widget
-                          shiny::wellPanel(
-                            ggiraph::girafeOutput("treeview"),
-                            style = "background: white; height: 1800px;",
-                          ),
-                          shiny::br()
+            shiny::div(
+              id = "view-graphic",
+              # markdown files to add description
+              shiny::uiOutput("tree_md_files"),
+
+              # show treeview widget
+              shiny::wellPanel(
+                ggiraph::girafeOutput("treeview"),
+                style = "background: white; height: 1800px;",
+              ),
+              shiny::br()
             )
           )
         ) # end fluid row
@@ -108,12 +88,10 @@ app_ui = function(request) {
       # about page
       shiny::tabPanel(
         title = "About",
-        shiny::includeMarkdown(system.file("app", "www", "content", "about.md",
-                                           package = "tfpbrowser",
-                                           mustWork = TRUE))
+        shiny::includeMarkdown(
+          system.file("app", "www", "content", "about.md", package = "tfpbrowser", mustWork = TRUE)
+        )
       )
-
     ) # end navbar page
   ) # end tag list
-
 }

R/config.R

@@ -7,7 +7,7 @@
 #'
 #' @return   Scalar string. The data-directory for use in the app.
 
-get_data_dir <- function() {
+get_data_dir = function() {
   Sys.getenv(
     "APP_DATA_DIR",
     system.file("app", "www", "data", package = "tfpbrowser")