Closes #136 set up styling links and spelling checks

.github/workflows/link_check.yml

@@ -0,0 +1,29 @@
+name: Links (Fail Fast)
+
+on:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  linkChecker:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up R  # Install R from CRAN
+        uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: '4.4.3' # You can specify a different R version if needed
+
+      - name: Install R packages
+        run: |
+          Rscript -e 'install.packages("fs")'
+        shell: bash
+
+      - name: Link Checker
+        uses: lycheeverse/[email protected]
+        with:
+          fail: true
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/spellcheck.yml

@@ -0,0 +1,42 @@
+name: Spellcheck
+on:
+  pull_request:
+    branches: ['main']
+jobs:
+  Spelling:
+    runs-on: ubuntu-latest
+    container:
+      image: "rocker/tidyverse:4.3.1"
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+
+      - name: Install packages
+        run: |
+          if (!require("roxygen2")) install.packages("roxygen2")
+          if (!require("spelling")) install.packages("spelling")
+          if (!require("testthat")) install.packages("testthat")
+        shell: Rscript {0}
+
+      - name: Check spelling
+        run: |
+          library(spelling)
+
+          # Check the entire package (R files, documentation, vignettes, etc.)
+          words <- spelling::spell_check_package()
+
+          print(words)
+
+          testthat::test_that(desc = "Check spelling", code = {
+            testthat::expect_equal(
+              object = nrow(words),
+              expected = 0,
+              info = if (nrow(words) > 0) {
+                paste("Spelling errors found:\n", 
+                      paste(capture.output(print(words)), collapse = "\n"))
+              } else {
+                "No spelling errors"
+              }
+            )
+          })
+        shell: Rscript {0}

.github/workflows/style_check.yml

@@ -0,0 +1,20 @@
+name: Style
+on:
+  pull_request: {branches: ['main']}
+
+jobs:
+  Style:
+    runs-on: ubuntu-latest
+    container: {image: "rocker/tidyverse:4.2.1"}
+    steps:
+      - name: Checkout repo
+        uses: actions/checkout@v4
+      - name: Install styler
+        run: install.packages("styler")
+        shell: Rscript {0}
+      - name: styler version
+        run: packageVersion("styler")
+        shell: Rscript {0}
+      - name: Run styler
+        run: styler::style_dir(dry = "fail")
+        shell: Rscript {0}

DESCRIPTION

@@ -46,4 +46,4 @@ VignetteBuilder:
     knitr
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE, r6 = FALSE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

R/DatasetMeta.R

@@ -10,64 +10,64 @@
 DatasetMeta <- R6::R6Class("DatasetMeta",
   inherit = MetaCore,
   private = list(
-     .name  = NA,
-     .label = NA,
-     .num_vars = NA,
-     .key_vars = NA,
-
-     .greet = function(quiet) {
-        cli_par()
-        cli_alert_success("{private$.name} dataset successfully selected")
-        if (quiet) {
-           cli_inform(c(
-              "i" = col_red("Dataset metadata specification subsetted with suppressed warnings")))
-        }
-        cli_end()
-     }
+    .name = NA,
+    .label = NA,
+    .num_vars = NA,
+    .key_vars = NA,
+    .greet = function(quiet) {
+      cli_par()
+      cli_alert_success("{private$.name} dataset successfully selected")
+      if (quiet) {
+        cli_inform(c(
+          "i" = col_red("Dataset metadata specification subsetted with suppressed warnings")
+        ))
+      }
+      cli_end()
+    }
   ),
-
   public = list(
-     initialize = function(metacore, quiet = FALSE) {
-        super$initialize(
-           ds_spec = metacore$ds_spec,
-           ds_vars = metacore$ds_vars,
-           var_spec = metacore$var_spec,
-           value_spec = metacore$value_spec,
-           derivations = metacore$derivations,
-           codelist = metacore$codelist,
-           supp = metacore$supp
-        )
-        private$.name  = metacore$ds_spec$dataset[1]
-        private$.label = metacore$ds_spec$label[1]
-        private$.num_vars = metacore$ds_vars |> nrow()
-        private$.key_vars = metacore$ds_vars |>
-           filter(!is.na(key_seq)) |>
-           pull(variable)
-
-        private$.greet(quiet)
-     },
+    initialize = function(metacore, quiet = FALSE) {
+      super$initialize(
+        ds_spec = metacore$ds_spec,
+        ds_vars = metacore$ds_vars,
+        var_spec = metacore$var_spec,
+        value_spec = metacore$value_spec,
+        derivations = metacore$derivations,
+        codelist = metacore$codelist,
+        supp = metacore$supp
+      )
+      private$.name <- metacore$ds_spec$dataset[1]
+      private$.label <- metacore$ds_spec$label[1]
+      private$.num_vars <- metacore$ds_vars |> nrow()
+      private$.key_vars <- metacore$ds_vars |>
+        filter(!is.na(key_seq)) |>
+        pull(variable)
 
-     print = function() {
-        tables <- ls(envir = self)
+      private$.greet(quiet)
+    },
+    print = function() {
+      tables <- ls(envir = self)
 
-        cli_par()
-        cli_rule(left = "Dataset specification object for {private$.name} ({private$.label})")
-        cli_text("The dataset contains {private$.num_vars} variable{?s}")
-        cli_text("Dataset key{?s}: {ansi_collapse(private$.key_vars, last = ', ')}")
-        cli_end()
+      cli_par()
+      cli_rule(left = "Dataset specification object for {private$.name} ({private$.label})")
+      cli_text("The dataset contains {private$.num_vars} variable{?s}")
+      cli_text("Dataset key{?s}: {ansi_collapse(private$.key_vars, last = ', ')}")
+      cli_end()
 
-        cli_par()
-        cli_text("The structure of the specification object is:")
-        for (table in tables) {
-           obj <- get(table, envir = self)
-           if (!is.list(obj)) { next }
-           cli_bullets(c(">" = "{table}: {typeof(table)} [{dim(obj)[1]} x {dim(obj)[2]}] {ansi_collapse(names(obj), last = ', ')}"))
+      cli_par()
+      cli_text("The structure of the specification object is:")
+      for (table in tables) {
+        obj <- get(table, envir = self)
+        if (!is.list(obj)) {
+          next
         }
-        cli_end()
+        cli_bullets(c(">" = "{table}: {typeof(table)} [{dim(obj)[1]} x {dim(obj)[2]}] {ansi_collapse(names(obj), last = ', ')}"))
+      }
+      cli_end()
 
-        cli_div()
-        cli_text("To inspect the specification object use {.fn View} in the console.")
-        cli_end()
-     }
+      cli_div()
+      cli_text("To inspect the specification object use {.fn View} in the console.")
+      cli_end()
+    }
   )
 )

R/checks.R

@@ -29,20 +29,20 @@
 #'
 #' check_inconsistent_types(metacore)
 #' @rdname checks
-check_inconsistent_labels <- function(metacore){
-   basic_check(label, metacore)
+check_inconsistent_labels <- function(metacore) {
+  basic_check(label, metacore)
 }
 
 #' @export
 #' @rdname checks
-check_inconsistent_types <- function(metacore){
-   basic_check(type, metacore)
+check_inconsistent_types <- function(metacore) {
+  basic_check(type, metacore)
 }
 
 #' @export
 #' @rdname checks
-check_inconsistent_formats <- function(metacore){
-   basic_check(format, metacore)
+check_inconsistent_formats <- function(metacore) {
+  basic_check(format, metacore)
 }
 
 #' Base code for running cross variable checks
@@ -55,32 +55,34 @@ check_inconsistent_formats <- function(metacore){
 #' @noRd
 #' @importFrom stringr str_glue
 #' @importFrom dplyr across
-basic_check <- function(col_to_check, metacore){
-   if(!is_metacore(metacore)){
-      cli_abort("Expects a metacore object", call. = FALSE)
-   }
+basic_check <- function(col_to_check, metacore) {
+  if (!is_metacore(metacore)) {
+    cli_abort("Expects a metacore object", call. = FALSE)
+  }
 
-   report_df <- metacore$var_spec %>%
-      mutate(var1 = str_remove(variable, "[[:alnum:]]+\\.")) %>%
-      group_by(var1) %>%
-      mutate(n_lab = n_distinct({{col_to_check}})) %>%
-      filter(n_lab > 1) %>%
-      mutate(across(everything(), remove_label)) %>%
-      group_by(var1, {{col_to_check}}) %>%
-      summarise(n_vars = n(),
-                ls_of_vars = list(variable),
-                .groups = "drop") %>%
-      select(variable = var1, everything())
+  report_df <- metacore$var_spec %>%
+    mutate(var1 = str_remove(variable, "[[:alnum:]]+\\.")) %>%
+    group_by(var1) %>%
+    mutate(n_lab = n_distinct({{ col_to_check }})) %>%
+    filter(n_lab > 1) %>%
+    mutate(across(everything(), remove_label)) %>%
+    group_by(var1, {{ col_to_check }}) %>%
+    summarise(
+      n_vars = n(),
+      ls_of_vars = list(variable),
+      .groups = "drop"
+    ) %>%
+    select(variable = var1, everything())
 
-   if(nrow(report_df) > 0){
-      cli_warn(str_glue("Mismatch {as_label(enexpr(col_to_check))}s detected"))
-      return(report_df)
-   } else {
-      cli_inform(str_glue("No mismatch {as_label(enexpr(col_to_check))}s detected"))
-   }
+  if (nrow(report_df) > 0) {
+    cli_warn(str_glue("Mismatch {as_label(enexpr(col_to_check))}s detected"))
+    return(report_df)
+  } else {
+    cli_inform(str_glue("No mismatch {as_label(enexpr(col_to_check))}s detected"))
+  }
 }
 
 remove_label <- function(x) {
-   attr(x, "label") <- NULL
-   x
+  attr(x, "label") <- NULL
+  x
 }