use rhino

.Rprofile

@@ -1 +1,9 @@
-source("renv/activate.R")
+if (file.exists("renv")) {
+  source("renv/activate.R")
+} else {
+  # The `renv` directory is automatically skipped when deploying with rsconnect.
+  message("No 'renv' directory found; renv won't be activated.")
+}
+
+# Allow absolute module imports (relative to the app root).
+options(box.path = getwd())

.github/workflows/rhino-test.yml

@@ -0,0 +1,72 @@
+name: Rhino Test
+on: push
+permissions:
+  contents: read
+jobs:
+  main:
+    name: Run linters and tests
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Setup system dependencies
+        run: |
+          packages=(
+            # List each package on a separate line.
+          )
+          sudo apt-get update
+          sudo apt-get install --yes "${packages[@]}"
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: renv
+
+      - name: Setup R dependencies
+        uses: r-lib/actions/setup-renv@v2
+
+      - name: Setup Node
+        uses: actions/setup-node@v3
+        with:
+          node-version: 20
+
+      - name: Lint R
+        if: always()
+        shell: Rscript {0}
+        run: rhino::lint_r()
+
+      - name: Lint JavaScript
+        if: always()
+        shell: Rscript {0}
+        run: rhino::lint_js()
+
+      - name: Lint Sass
+        if: always()
+        shell: Rscript {0}
+        run: rhino::lint_sass()
+
+      - name: Build JavaScript
+        if: always()
+        shell: Rscript {0}
+        run: rhino::build_js()
+
+      - name: Build Sass
+        if: always()
+        shell: Rscript {0}
+        run: rhino::build_sass()
+
+      - name: Run R unit tests
+        if: always()
+        shell: Rscript {0}
+        run: rhino::test_r()
+
+      - name: Run Cypress end-to-end tests
+        if: always()
+        uses: cypress-io/github-action@v6
+        with:
+          working-directory: .rhino # Created by earlier commands which use Node.js
+          start: npm run run-app
+          project: ../tests
+          wait-on: 'http://localhost:3333/'
+          wait-on-timeout: 60

.lintr

@@ -0,0 +1,9 @@
+linters:
+  linters_with_defaults(
+    line_length_linter = line_length_linter(100),
+    box_func_import_count_linter = rhino::box_func_import_count_linter(),
+    box_separate_calls_linter = rhino::box_separate_calls_linter(),
+    box_trailing_commas_linter = rhino::box_trailing_commas_linter(),
+    box_universal_import_linter = rhino::box_universal_import_linter(),
+    object_usage_linter = NULL  # Does not work with `box::use()`.
+  )

.renvignore

@@ -0,0 +1,3 @@
+# Only use `dependencies.R` to infer project dependencies.
+*
+!dependencies.R

.rscignore

@@ -0,0 +1,7 @@
+.github
+.lintr
+.renvignore
+.Renviron
+.rhino
+.rscignore
+tests

app.R

@@ -0,0 +1,2 @@
+# Rhino / shinyApp entrypoint. Do not edit.
+rhino::app()

app/app.R

@@ -25,6 +25,7 @@ facilities <<- process_facilities(facilities)
 polyline_paths <<- process_polyline_paths(iTRAQI_paths, facilities)
 observed_paths <<- process_observed_paths(observed_paths, iTRAQI_paths, polyline_paths)
 observed_polyline_paths <<- process_observed_polyline_paths(observed_paths)
+age_cats <<- get_age_cats(observed_paths = observed_paths)
 
 source(file.path(app_dir, "mod-filters.R"))
 source(file.path(app_dir, "mod-map-tab.R"))
@@ -35,27 +36,42 @@ moduleServer <- function(id, module) {
   callModule(module, id)
 }
 
+library(shiny)
+library(bs4Dash)
 bodyTag <- dashboardBody(
-  tags$head(
-    includeCSS(file.path(app_dir, "styles.css"))
-  ),
-  tagList(
-    ui_map("main")
-  )
+  # tags$head(
+  #   includeCSS(file.path(app_dir, "styles.css"))
+  # ),
+  # tagList(
+  #   ui_map("main")
+  # )
 )
 
 bodyTag$children[[1]]$attribs$style <- "padding: 0px 0px !important"
 
 
 ui <- dashboardPage(
-  dark = TRUE,
+  # dark = TRUE,
   header = dashboardHeader(),
   sidebar = dashboardSidebar(width = "0px"),
   body = bodyTag
 )
 
 server <- function(input, output, session) {
-  server_map("main")
-  server_mapclick("main")
+  # server_map("main")
+  # server_mapclick("main")
 }
 shinyApp(ui, server)
+
+
+library(shiny)
+
+ui <- fluidPage(
+
+)
+
+server <- function(input, output, session) {
+
+}
+
+shinyApp(ui, server)

app/base-map.R

@@ -1,9 +1,9 @@
 # base-map.R
 
 base_map <- function(map_bounds, facilities, iTRAQI_paths, polyline_paths, observed_paths, observed_polyline_paths) {
-  if ("base-map.rds" %in% list.files(fixtures_path)) {
-    return(readRDS(file.path(fixtures_path, "base-map.rds")))
-  }
+  # if ("base-map.rds" %in% list.files(fixtures_path)) {
+  #   return(readRDS(file.path(fixtures_path, "base-map.rds")))
+  # }
 
   # load palettes and acute raster from iTRAQI GitHub repo
   source(file.path(here::here(), "app", "palettes.R"))

app/logic/__init__.R

@@ -0,0 +1,2 @@
+# Logic: application code independent from Shiny.
+# https://go.appsilon.com/rhino-project-structure

app/main.R

@@ -0,0 +1,25 @@
+box::use(
+  shiny[bootstrapPage, div, moduleServer, NS, renderUI, tags, uiOutput],
+)
+
+#' @export
+ui <- function(id) {
+  ns <- NS(id)
+  bootstrapPage(
+    uiOutput(ns("message"))
+  )
+}
+
+#' @export
+server <- function(id) {
+  moduleServer(id, function(input, output, session) {
+    output$message <- renderUI({
+      div(
+        style = "display: flex; justify-content: center; align-items: center; height: 100vh;",
+        tags$h1(
+          tags$a("Check out Rhino docs!", href = "https://appsilon.github.io/rhino/")
+        )
+      )
+    })
+  })
+}

app/path-category-controls.R

@@ -4,7 +4,11 @@ path_cats <- c("NO HLC", "FOLLOWED ITRAQI", "DID NOT FOLLOW ITRAQI")
 death_flags <- c("Survived", "QAS", "Hospital", "ED")
 
 age_cat_breaks <- c(0, 16, 24, 65, 99)
-age_cats <- c(levels(cut(observed_paths$PAT_AGE, breaks = age_cat_breaks)), NA)
+
+get_age_cats <- function(observed_paths){
+  c(levels(cut(observed_paths$PAT_AGE, breaks = age_cat_breaks)), NA)
+}
+
 
 final_facility_cats <- c("Brisbane (RBWH/PA/QCH)", "GOLD COAST", "OTHER", "TOWNSVILLE")
 

app/view/__init__.R

@@ -0,0 +1,2 @@
+# View: Shiny modules and related code.
+# https://go.appsilon.com/rhino-project-structure

config.yml

@@ -0,0 +1,3 @@
+default:
+  rhino_log_level: !expr Sys.getenv("RHINO_LOG_LEVEL", "INFO")
+  rhino_log_file: !expr Sys.getenv("RHINO_LOG_FILE", NA)

dependencies.R

@@ -0,0 +1,19 @@
+# This file allows packrat (used by rsconnect during deployment) to pick up dependencies.
+library(bs4Dash)
+library(dplyr)
+library(glue)
+library(haven)
+library(here)
+library(janitor)
+library(leaflet)
+library(parallel)
+library(pbapply)
+library(progress)
+library(raster)
+library(rhino)
+library(sf)
+library(shiny)
+library(shinyjs)
+library(shinyWidgets)
+library(sp)
+library(tidyverse)

old.Rprofile

@@ -0,0 +1,9 @@
+if (file.exists("renv")) {
+  source("renv/activate.R")
+} else {
+  # The `renv` directory is automatically skipped when deploying with rsconnect.
+  message("No 'renv' directory found; renv won't be activated.")
+}
+
+# Allow absolute module imports (relative to the app root).
+options(box.path = getwd())