Add linting to CI and style code

.Rbuildignore

@@ -9,3 +9,4 @@ $run_dev.*
 ^.here$
 ^LICENSE\.md$
 ^\.github$
+^\.lintr$

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

@@ -23,10 +23,11 @@ jobs:
         with:
           use-public-rspm: true
 
-      - uses: r-lib/actions/setup-r-dependencies@v2
-        with:
-          extra-packages: any::rcmdcheck
-          needs: check
+      - uses: r-lib/actions/setup-renv@v2
+
+      - name: Install rcmdcheck
+        run: install.packages("rcmdcheck")
+        shell: Rscript {0}
 
       - uses: r-lib/actions/check-r-package@v2
         with:

.github/workflows/lint.yaml

@@ -0,0 +1,35 @@
+# 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: lint.yaml
+
+permissions: read-all
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-renv@v2
+
+      - name: Install lintr
+        run: install.packages("lintr")
+        shell: Rscript {0}
+
+      - name: Lint
+        run: lintr::lint_package()
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/pr-commands.yaml

@@ -0,0 +1,86 @@
+# 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:
+  issue_comment:
+    types: [created]
+
+name: pr-commands.yaml
+
+permissions: read-all
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-renv@v2
+
+      - name: Install roxygen2
+        run: install.packages("roxygen2")
+        shell: Rscript {0}
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add \*.R
+          git commit -m 'Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.lintr

@@ -0,0 +1,5 @@
+linters: linters_with_defaults(
+    line_length_linter(120),
+    object_name_linter(styles = c("snake_case", "symbols", "camelCase"))
+  )
+encoding: "UTF-8"

DESCRIPTION

@@ -16,7 +16,8 @@ Suggests:
     usethis,
     styler,
     testthat (>= 3.0.0),
-    spelling
+    spelling,
+    lintr
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.2

R/app_config.R

@@ -23,18 +23,17 @@ app_sys <- function(...) {
 #'
 #' @noRd
 get_golem_config <- function(
-  value,
-  config = Sys.getenv(
-    "GOLEM_CONFIG_ACTIVE",
-    Sys.getenv(
-      "R_CONFIG_ACTIVE",
-      "default"
-    )
-  ),
-  use_parent = TRUE,
-  # Modify this if your config file is somewhere else
-  file = app_sys("golem-config.yml")
-) {
+    value,
+    config = Sys.getenv(
+      "GOLEM_CONFIG_ACTIVE",
+      Sys.getenv(
+        "R_CONFIG_ACTIVE",
+        "default"
+      )
+    ),
+    use_parent = TRUE,
+    # Modify this if your config file is somewhere else
+    file = app_sys("golem-config.yml")) {
   config::get(
     value = value,
     config = config,

R/app_server.R

@@ -5,25 +5,24 @@
 #' @import shiny
 #' @noRd
 app_server <- function(input, output, session) {
-
   # TODO: to be replaced by real data, which should be reactive so it responds to filtering options
   mock_data <- data.frame(
     concept_id = c(2212648, 2617206, 2212406),
     name = c(
-      "Blood count; complete (CBC), automated (Hgb, Hct, RBC, WBC and platelet count) and automated differential WBC count",
+      "Blood count; complete (CBC), automated (Hgb, Hct, RBC, WBC and platelet count) and automated differential WBC count", # nolint
       "Prostate specific antigen test (psa)",
       "Homocysteine"
     ),
     person_count = c(7080, 960, 10),
     records_per_person = c(4.37, 1.12, 1.06)
   )
   mock_data <- reactiveVal(mock_data)
 
   selected_data <- mod_select_concepts_server("select_concepts", mock_data)
 
   mod_date_range_server("date_range_1")
   mod_datatable_server("totals", selected_data)
   mod_monthly_count_server("monthly_count_1")
   mod_stat_numeric_server("stat_numeric_1")
   mod_export_tab_server("export_tab", selected_data)
 }

R/mod_daterange.R

@@ -19,10 +19,10 @@ mod_date_range_ui <- function(id) {
       format = "yyyy-mm",
     ),
     sliderInput(ns("slider"), "Date range:",
-                min = as.Date("2019-04-01", "%Y-%m-%d"),
-                max = as.Date("2024-08-01", "%Y-%m-%d"),
-                value = c(as.Date("2019-04-01"), as.Date("2024-08-01")),
-                timeFormat = "%Y-%m"
+      min = as.Date("2019-04-01", "%Y-%m-%d"),
+      max = as.Date("2024-08-01", "%Y-%m-%d"),
+      value = c(as.Date("2019-04-01"), as.Date("2024-08-01")),
+      timeFormat = "%Y-%m"
     )
   )
 }
@@ -32,7 +32,5 @@ mod_date_range_ui <- function(id) {
 #' @noRd
 mod_date_range_server <- function(id) {
   moduleServer(id, function(input, output, session) {
-    ns <- session$ns
   })
 }
-

R/mod_monthly_count.R

@@ -7,7 +7,7 @@
 #' @noRd
 #'
 #' @importFrom shiny NS tagList
-mod_monthly_count_ui <- function(id){
+mod_monthly_count_ui <- function(id) {
   ns <- NS(id)
   tagList(
     plotOutput(ns("monthly_count_plot"), height = 250)
@@ -23,7 +23,7 @@ mod_monthly_count_server <- function(id) {
     # Need to get the input data and filter it based on the selected timeframe and selected row
     # see https://stackoverflow.com/a/77039776/11801854
     monthly_count <- data.frame(
-      date = c("2020-01","2020-02", "2020-03", "2020-04"),
+      date = c("2020-01", "2020-02", "2020-03", "2020-04"),
       record_count = c(120, 250, 281, 220)
     )
     output$monthly_count_plot <- renderPlot({

R/run_app.R

@@ -8,12 +8,11 @@
 #' @importFrom shiny shinyApp
 #' @importFrom golem with_golem_options
 run_app <- function(
-  onStart = NULL,
-  options = list(),
-  enableBookmarking = NULL,
-  uiPattern = "/",
-  ...
-) {
+    onStart = NULL,
+    options = list(),
+    enableBookmarking = NULL,
+    uiPattern = "/",
+    ...) {
   with_golem_options(
     app = shinyApp(
       ui = app_ui,