Merge branch 'main' of https://github.com/nhsbsa-data-analytics/nhsbs…

…aShinyR

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

@@ -18,7 +18,7 @@ jobs:
       RENV_PATHS_ROOT: ~/.local/share/renv
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -30,21 +30,12 @@ jobs:
         with:
           extra-packages: rcmdcheck
 
-      - uses: oleksiyrudenko/gha-git-credentials@v2-latest
-        with:
-          global: true
-          token: '${{ secrets.GITHUB_TOKEN }}'
-
       - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
 
       - name: Show testthat output
         if: always()
         run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
-
-      - name: Upload check results
-        if: failure()
-        uses: actions/upload-artifact@main
-        with:
-          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
-          path: check

.github/workflows/gitleaks.yaml

@@ -1,29 +1,16 @@
 name: gitleaks-action 
-
 on: [pull_request, push, workflow_dispatch] 
 
 jobs: 
-
   scan: 
-
     name: gitleaks-action 
-
     runs-on: ubuntu-latest 
-
     steps: 
-
-      - uses: actions/checkout@v3 
-
+      - uses: actions/checkout@v4 
         with: 
-
           fetch-depth: 0 
-
       - run: wget -O .gitleaks.toml https://raw.githubusercontent.com/nhsbsa-data-analytics/nhsbsaShinyR/main/gitleaks.toml 
-
       - uses: gitleaks/gitleaks-action@v2 
-
         env: 
-
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 
-
           GITLEAKS_LICENSE: ${{ secrets.GITLEAKS_LICENSE}} 

.github/workflows/lint.yaml

@@ -13,7 +13,7 @@ jobs:
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-r@v2
         with:

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: nhsbsaShinyR
-Title: Template for NHSBSA {shiny} apps
-Version: 0.0.0.9004
+Title: Template for NHSBSA \{shiny\} apps
+Version: 0.0.0.9005
 Authors@R: 
     c(person(given = "DALL",
              family = "",
@@ -23,7 +23,7 @@ Authors@R:
              role = "ctb",
              email = "[email protected]"))
 Description: Template used for NHSBSA Data Science and Advanced Analytics
-  {shiny} apps.
+  \{shiny\} apps.
 License: Apache License (>= 2)
 Depends: 
     R (>= 4.0)
@@ -61,6 +61,6 @@ Remotes:
     statistiekcbs/scrollytell
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr
 Config/testthat/edition: 3

R/mod_scrollytell_example.R

@@ -158,10 +158,10 @@ mod_scrollytell_example_server <- function(id) {
         highcharter::hchart(
           type = "scatter",
           highcharter::hcaes(
-            x = Sepal.Length,
-            y = Sepal.Width,
-            group = group_lvl,
-            color = point_col
+            x = .data$Sepal.Length,
+            y = .data$Sepal.Width,
+            group = .data$group_lvl,
+            color = .data$point_col
           )
         ) |>
         highcharter::hc_xAxis(

R/nhsbsaShinyR.R

@@ -1,22 +1,19 @@
-#' \code{nhsbsaShinyR} package
-#'
-#' Template app using `golem` for NHSBSA DALL `shiny` apps.
-#'
-#' @docType package
-#' @name nhsbsaShinyR
-#'
-#' @importFrom rlang := .data
-#'
+#' @keywords internal
+#' @importFrom rlang .data :=
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
 NULL
 
 if (getRversion() >= "2.15.1") {
   utils::globalVariables(
     c(
-      # data column names
-      "Sepal.Length",
-      "Sepal.Width",
-      "group_lvl",
-      "point_col"
+      # No unknown global variables
+      # Add any found during R CMD check, that cannot be handled with .data$
+      # e.g.
+
+      # "SOME_UNKNOWN_VARIABLE"
     )
   )
 }

R/utils_review.R

@@ -1,6 +1,6 @@
 #' Generate a initial Word doc to write draft text in
 #'
-#' The `{officer}` package works best with a Word document generated from
+#' The `\{officer\}` package works best with a Word document generated from
 #' Rmarkdown. This is just a wrapper around `rmarkdown::render` to do that, with
 #' default arguments matching our package conventions.
 #'
@@ -20,14 +20,14 @@
 #' # generate Word doc for adhoc purposes
 #' gen_template_doc(
 #'   "C:/Users/CYPHER/Downloads",
-#'   "adhoc.docx",
-#'   system.file(
-#'     "inst", "review", "styles", "draft-styles.rmd", package = "nhsbsaShinyR"
-#'   )
+#'   "adhoc.docx"
 #' )}
 gen_template_doc <- function(rv_dir = "inst/review",
                              docx_file = "review.docx",
-                             styles_rmd = "inst/review/styles/draft-styles.rmd") {
+                             styles_rmd = system.file(
+                               "review", "styles", "draft-styles.rmd",
+                               package = "nhsbsaShinyR"
+                             )) {
   rmarkdown::render(
     styles_rmd,
     output_dir = rv_dir,
@@ -61,15 +61,15 @@ gen_template_doc <- function(rv_dir = "inst/review",
 #' md_to_word(
 #'   "my/adhoc/markdown",
 #'   "C:/Users/CYPHER/Downloads",
-#'   "adhoc.docx",
-#'   system.file(
-#'     "inst", "review", "styles", "draft-styles.rmd", package = "nhsbsaShinyR"
-#'   )
+#'   "adhoc.docx"
 #' )}
 md_to_word <- function(md_dir = "inst/app/www/assets/markdown",
                        rv_dir = "inst/review",
                        docx_file = "review.docx",
-                       styles_rmd = "inst/review/styles/draft-styles.rmd") {
+                       styles_rmd = system.file(
+                         "review", "styles", "draft-styles.rmd",
+                         package = "nhsbsaShinyR"
+                       )) {
   styles_doc <- gen_template_doc(
     rv_dir = tempdir(),
     docx_file = tempfile(),
@@ -111,8 +111,8 @@ md_to_word <- function(md_dir = "inst/app/www/assets/markdown",
     quiet = TRUE
   )
 
-  # Return path of generated Word doc
-  docx_path
+  # Return path of generated Word doc invisibly
+  invisible(docx_path)
 }
 
 
@@ -627,6 +627,7 @@ word_to_md <- function(md_flag = "markdown/",
   # Unless disabled, create initial snapshot files if there is no or an empty
   # _snaps dir
   if (first_run_snaps) {
+    testthat::local_edition(3)
     if (file.exists(file.path(rv_dir, "_snaps"))) {
       if (!length(Sys.glob(file.path(rv_dir, "tests/_snaps/review_md", "*.md")))) {
         review_md_dir()
@@ -738,6 +739,8 @@ review_md <- function(path, snaps_dir = "inst/review/tests") {
 #' review_md_diff(snaps_dir = "C:/Users/CYPHER/Downloads")
 #' )}
 review_md_dir <- function(md_dir = "inst/review/temp", snaps_dir = "inst/review/tests") {
+  testthat::local_edition(3)
+
   md_files <- Sys.glob(file.path(md_dir, "*.md"))
 
   purrr::walk(

README.md

@@ -1,6 +1,13 @@
 # NHSBSA R Shiny template
 
-This R package has been developed by NHS Business Services Authority Data Analytics Learning Lab to use as a template for building NHSBSA branded R `{shiny}` dashboards. 
+This R package has been developed by NHS Business Services Authority Data Analytics Learning Lab to use as a template for building NHSBSA branded R `{shiny}` dashboards.
+
+## Installing from GitHub
+
+To install this package from GitHub, use the below code. Note that you must explicitly ask for vignettes to be built when installing from GitHub.
+
+`devtools::install_github("nhsbsa-data-analytics/nhsbsaShinyR", build_vignettes = TRUE)`
+
 
 ## Features
 
@@ -177,9 +184,3 @@ All code that is used internally and/or is to be exported from the package belon
 ### `README.md`
 
 Give an overview of your package including how to install and the simplest example of usage.
-
-## Installing from GitHub
-
-To install this package from GitHub, use the below code. Note that you must explicitly ask for vignettes to be built when installing from GitHub.
-
-`devtools::install_github("nhsbsa-data-analytics/nhsbsaShinyR", build_vignettes = TRUE)`

tests/testthat/test-utils_review.R

@@ -21,9 +21,9 @@ test_that("md_to_word generates expected Word doc", {
 
   # Due to how officer::read_docx works, we expect there to always be
   # differences in the package_dir and doc_properties$data.
-  # Also, when run on github CI, there are small differences in some of the
-  # colours used in the Word doc styles.
-  expected_differences <- ifelse(testthat:::on_ci(), 8, 2)
+  # Also, when run on github CI, there are small differences in the Word doc
+  # generated, due to the Windows OS being Windows Server.
+  expected_differences <- ifelse(testthat:::on_ci(), 56, 2)
 
   # If unexpected number of diffs, print out the comparison for ease of seeing
   # where the fail is.