169 wrapping up the long code in the Report (#218)

this Fixes
#169

I've implemented a solution that relies on the formatR package. I've
ensured that this solution checks for the package in the namespace; if
it's not accessible, the user will be notified. To maintain flexibility,
I've included the formatR package in the suggested dependencies, as
there are no strict dependencies on it.

In response to the feedback provided by @m7pr in [this
comment](#169 (comment)),
I've updated the default value of global_knitr to list(echo = TRUE,
tidy.opts = list(width.cutoff = 60), tidy = FALSE).

Please note that there was an alternative option to set tidy = "styler",
but I opted against it due to the additional dependency it would
introduce (the styler package). Feel free to review the changes and let
me know if any further adjustments are needed.

----
This branch utilizes the functionality provided by the 'formatR' package
to automatically add spaces and indentations to the code. However, it
does create a strong dependency on the 'formatR' package. If the package
is not installed, the output will be generated without any formatting.

Additionally, this branch introduces the following changes:

- It exposes Knitr options to users through the functions
'download_report_button_srv', 'reporter_previewer_srv,'
'simple_reporter_srv,' and the R6 renderer.
- The Roxygen documentation has been updated to reflect these
modifications.

changes in reports are observed as follows.

branch: main
<img width="613" alt="image"
src="https://github.com/insightsengineering/teal.reporter/assets/6700955/84998f72-1676-46bc-aff1-e376b68e2c22">

branch: 169_wrap_rcode@main
<img width="582" alt="image"
src="https://github.com/insightsengineering/teal.reporter/assets/6700955/be027ece-c2b8-45c0-85cc-719c7ee306f6">

---------

Signed-off-by: kartikeya kirar <[email protected]>
Co-authored-by: kartikeya <[email protected]>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Marcin <[email protected]>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>

.lintr

@@ -1,5 +1,6 @@
 linters: linters_with_defaults(
   line_length_linter = line_length_linter(120),
   cyclocomp_linter = NULL,
-  object_usage_linter = NULL
+  object_usage_linter = NULL,
+  indentation_linter = NULL
   )

DESCRIPTION

@@ -31,6 +31,7 @@ Imports:
     zip (>= 1.1.0)
 Suggests:
     DT (>= 0.13),
+    formatR (>= 1.5),
     ggplot2 (>= 3.4.0),
     lattice (>= 0.18-4),
     png,
@@ -44,8 +45,8 @@ RdMacros:
 Config/Needs/verdepcheck: rstudio/bslib, mllg/checkmate,
     rstudio/htmltools, yihui/knitr, r-lib/lifecycle, r-lib/R6,
     rstudio/rmarkdown, rstudio/shiny, dreamRs/shinyWidgets,
-    yaml=vubiostat/r-yaml, r-lib/zip, davidgohel/flextable, rstudio/DT,
-    tidyverse/ggplot2, deepayan/lattice, cran/png,
+    yaml=vubiostat/r-yaml, r-lib/zip, davidgohel/flextable, rstudio/DT, 
+    yihui/formatR, tidyverse/ggplot2, deepayan/lattice, cran/png,
     insightsengineering/rtables, r-lib/testthat, rstudio/tinytex
 Config/Needs/website: insightsengineering/nesttemplate
 Encoding: UTF-8

NEWS.md

@@ -2,6 +2,8 @@
 
 * `add_card_button_srv` allows to specify `card_fun` with `label` parameter for card's title & content customization.
 
+* Supports automatic `Rcode` formatting using the suggested `formatR` package in reports.
+
 # teal.reporter 0.2.1
 
 ### Miscellaneous

R/DownloadModule.R

@@ -33,11 +33,16 @@ download_report_button_ui <- function(id) {
 #' For more details see the vignette: `vignette("simpleReporter", "teal.reporter")`.
 #' @param id `character(1)` this `shiny` module's id.
 #' @param reporter [`Reporter`] instance.
+#' @param global_knitr `list` a of `knitr` parameters (passed to `knitr::opts_chunk$set`)
+#'  for customizing the rendering process.
 #' @inheritParams reporter_download_inputs
 #' @return `shiny::moduleServer`
+#' @details `r global_knitr_details()`
+#'
 #' @export
 download_report_button_srv <- function(id,
                                        reporter,
+                                       global_knitr = getOption("teal.reporter.global_knitr"),
                                        rmd_output = c(
                                          "html" = "html_document", "pdf" = "pdf_document",
                                          "powerpoint" = "powerpoint_presentation", "word" = "word_document"
@@ -48,6 +53,7 @@ download_report_button_srv <- function(id,
                                          toc = FALSE
                                        )) {
   checkmate::assert_class(reporter, "Reporter")
+  checkmate::assert_subset(names(global_knitr), names(knitr::opts_chunk$get()))
   checkmate::assert_subset(
     rmd_output,
     c(
@@ -134,8 +140,7 @@ download_report_button_srv <- function(id,
           shiny::showNotification("Rendering and Downloading the document.")
           input_list <- lapply(names(rmd_yaml_args), function(x) input[[x]])
           names(input_list) <- names(rmd_yaml_args)
-          global_knitr <- list()
-          if (is.logical(input$showrcode)) global_knitr <- list(echo = input$showrcode)
+          if (is.logical(input$showrcode)) global_knitr[["echo"]] <- input$showrcode
           report_render_and_compress(reporter, input_list, global_knitr, file)
         },
         contentType = "application/zip"

R/Previewer.R

@@ -31,10 +31,15 @@ reporter_previewer_ui <- function(id) {
 #' For more details see the vignette: `vignette("previewerReporter", "teal.reporter")`.
 #' @param id `character(1)` this `shiny` module's id.
 #' @param reporter `Reporter` instance
+#' @param global_knitr `list` a of `knitr` parameters (passed to `knitr::opts_chunk$set`)
+#'  for customizing the rendering process.
 #' @inheritParams reporter_download_inputs
+#' @details `r global_knitr_details()`
+#'
 #' @export
 reporter_previewer_srv <- function(id,
                                    reporter,
+                                   global_knitr = getOption("teal.reporter.global_knitr"),
                                    rmd_output = c(
                                      "html" = "html_document", "pdf" = "pdf_document",
                                      "powerpoint" = "powerpoint_presentation",
@@ -45,6 +50,7 @@ reporter_previewer_srv <- function(id,
                                      toc = FALSE
                                    )) {
   checkmate::assert_class(reporter, "Reporter")
+  checkmate::assert_subset(names(global_knitr), names(knitr::opts_chunk$get()))
   checkmate::assert_subset(
     rmd_output,
     c(
@@ -179,8 +185,7 @@ reporter_previewer_srv <- function(id,
           shiny::showNotification("Rendering and Downloading the document.")
           input_list <- lapply(names(rmd_yaml_args), function(x) input[[x]])
           names(input_list) <- names(rmd_yaml_args)
-          global_knitr <- list()
-          if (is.logical(input$showrcode)) global_knitr <- list(echo = input$showrcode)
+          if (is.logical(input$showrcode)) global_knitr[["echo"]] <- input$showrcode
           report_render_and_compress(reporter, input_list, global_knitr, file)
         },
         contentType = "application/zip"

R/Renderer.R

@@ -22,14 +22,16 @@ Renderer <- R6::R6Class( # nolint: object_name_linter.
     #' @description getting the `Rmd` text which could be easily rendered later.
     #'
     #' @param blocks `list` of `c("TextBlock", "PictureBlock", "NewpageBlock")` objects.
-    #' @param yaml_header `character` a `rmarkdown` `yaml` header.
-    #' @param global_knitr `list` a global `knitr` parameters, like echo.
-    #' But if local parameter is set it will have priority.
-    #' Defaults to empty `list()`.
+    #' @param yaml_header `character` an `rmarkdown` `yaml` header.
+    #' @param global_knitr `list` a of `knitr` parameters (passed to `knitr::opts_chunk$set`)
+    #'  for customizing the rendering process.
+    #' @details `r global_knitr_details()`
     #'
     #' @return `character` a `Rmd` text (`yaml` header + body), ready to be rendered.
-    renderRmd = function(blocks, yaml_header, global_knitr = list()) {
+    renderRmd = function(blocks, yaml_header, global_knitr = getOption("teal.reporter.global_knitr")) {
       checkmate::assert_list(blocks, c("TextBlock", "PictureBlock", "NewpageBlock", "TableBlock", "RcodeBlock"))
+      checkmate::assert_subset(names(global_knitr), names(knitr::opts_chunk$get()))
+
       if (missing(yaml_header)) {
         yaml_header <- md_header(yaml::as.yaml(list(title = "Report")))
       }
@@ -84,13 +86,13 @@ Renderer <- R6::R6Class( # nolint: object_name_linter.
     #'
     #' @param blocks `list` of `c("TextBlock", "PictureBlock", "NewpageBlock")` objects.
     #' @param yaml_header `character` an `rmarkdown` `yaml` header.
-    #' @param global_knitr `list` a global `knitr` parameters, like echo.
-    #' But if local parameter is set it will have priority.
-    #' Defaults to empty `list()`.
-    #' @param ... `rmarkdown::render` arguments, `input` and `output_dir` should not be updated.z
+    #' @param global_knitr `list` a of `knitr` parameters (passed to `knitr::opts_chunk$set`)
+    #'  for customizing the rendering process.
+    #' @param ... `rmarkdown::render` arguments, `input` and `output_dir` should not be updated.
+    #' @details `r global_knitr_details()`
     #'
     #' @return `character` path to the output
-    render = function(blocks, yaml_header, global_knitr = list(), ...) {
+    render = function(blocks, yaml_header, global_knitr = getOption("teal.reporter.global_knitr"), ...) {
       args <- list(...)
       input_path <- self$renderRmd(blocks, yaml_header, global_knitr)
       args <- append(args, list(

R/ReportCard.R

@@ -60,7 +60,7 @@ ReportCard <- R6::R6Class( # nolint: object_name_linter.
       self$append_content(TextBlock$new(text, style))
       invisible(self)
     },
-    #' @description Appends a `rmarkdown` R chunk to this `ReportCard`.
+    #' @description Appends an `rmarkdown` R chunk to this `ReportCard`.
     #'
     #' @param text (`character(0)` or `character(1)`) the text
     #' @param ... any `rmarkdown` R chunk parameter and its value.

R/SimpleReporter.R

@@ -46,12 +46,16 @@ simple_reporter_ui <- function(id) {
 #' @param reporter [`Reporter`] instance.
 #' @param card_fun `function` which returns a [`ReportCard`] instance,
 #' the function has a `card` argument and an optional `comment` argument.
+#' @param global_knitr `list` a global `knitr` parameters for customizing the rendering process.
 #' @inheritParams reporter_download_inputs
+#' @details `r global_knitr_details()`
+#'
 #' @return `shiny::moduleServer`
 #' @export
 simple_reporter_srv <- function(id,
                                 reporter,
                                 card_fun,
+                                global_knitr = getOption("teal.reporter.global_knitr"),
                                 rmd_output = c(
                                   "html" = "html_document", "pdf" = "pdf_document",
                                   "powerpoint" = "powerpoint_presentation", "word" = "word_document"
@@ -68,6 +72,7 @@ simple_reporter_srv <- function(id,
       download_report_button_srv(
         "download_button_simple",
         reporter = reporter,
+        global_knitr = global_knitr,
         rmd_output = rmd_output,
         rmd_yaml_args = rmd_yaml_args
       )

R/utils.R

@@ -277,3 +277,21 @@ split_text_block <- function(x, n) {
   ind <- rep(1:nblocks, each = n)[seq_along(lines)]
   unname(lapply(split(lines, ind), paste, collapse = "\n"))
 }
+
+#' Retrieve text details for global_knitr options
+#' This function returns a character string describing the default settings for the global_knitr options.
+#' @noRd
+#'
+#' @keywords internal
+global_knitr_details <- function() {
+  paste0(
+    c(
+      " To access the default values for the `global_knitr` parameter,",
+      "  use `getOption('teal.reporter.global_knitr')`. These defaults include:",
+      " - `echo = TRUE`",
+      " - `tidy.opts = list(width.cutoff = 60)`",
+      " - `tidy = TRUE`  if `formatR` package is installed, `FALSE` otherwise"
+    ),
+    collapse = "\n"
+  )
+}

R/zzz.R

@@ -0,0 +1,22 @@
+.onLoad <- function(libname, pkgname) {
+  op <- options()
+  default_global_knitr <- list(teal.reporter.global_knitr = list(
+    echo = TRUE,
+    tidy.opts = list(width.cutoff = 60),
+    tidy = requireNamespace("formatR", quietly = TRUE)
+  ))
+
+  if (!("teal.reporter.global_knitr" %in% names(op))) {
+    options(default_global_knitr)
+  }
+
+  invisible()
+}
+
+.onAttach <- function(libname, pkgname) {
+  packageStartupMessage(
+    if (!requireNamespace("formatR", quietly = TRUE)) {
+      "For better code formatting, consider installing the formatR package."
+    }
+  )
+}