Revert "post-release-cleanup (#247)"

This reverts commit 78a5aab.

Author: vedhav

.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

@@ -5,8 +5,7 @@ Date: 2024-02-19
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "dawid.kaledkowski@roche.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-9533-457X")),
-    person("Kartikeya", "Kirar", , "kartikeya.kirar@businesspartner.roche.com", role = "aut",
-           comment = c(ORCID = "0009-0005-1258-4757")),
+    person("Kartikeya", "Kirar", , "kartikeya.kirar@businesspartner.roche.com", role = "aut"),
     person("Marcin", "Kosinski", , "marcin.kosinski.mk1@roche.com", role = "aut"),
     person("Maciej", "Nasinski", role = "aut"),
     person("Konrad", "Pagacz", role = "aut"),

R/AddCardModule.R

@@ -1,45 +1,10 @@
-#' Add card button module
-#'
+#' Add Card Button User Interface
 #' @description `r lifecycle::badge("experimental")`
-#'
-#' Provides a button to add views/cards to a report.
+#' button for adding views/cards to the Report.
 #'
 #' For more details see the vignette: `vignette("simpleReporter", "teal.reporter")`.
-#'
-#' @details
-#' The `card_fun` function is designed to create a new `ReportCard` instance and optionally customize it:
-#' - The `card` parameter allows for specifying a custom or default `ReportCard` instance.
-#' - Use the `comment` parameter to add a comment to the card via `card$append_text()` - if `card_fun` does not
-#' have the `comment` parameter, then `comment` from `Add Card UI` module will be added at the end of the content of the
-#' card.
-#' - The `label` parameter enables customization of the card's name and its content through `card$append_text()`-
-#' if `card_fun` does not have the `label` parameter, then card name will be set to the name passed in
-#' `Add Card UI` module, but no text will be added to the content of the `card`.
-#'
-#' This module supports using a subclass of [`ReportCard`] for added flexibility.
-#' A subclass instance should be passed as the default value of
-#' the `card` argument in the `card_fun` function.
-#' See below:
-#' ```{r}
-#' CustomReportCard <- R6::R6Class(
-#'   classname = "CustomReportCard",
-#'   inherit = teal.reporter::ReportCard
-#' )
-#'
-#' custom_function <- function(card = CustomReportCard$new()) {
-#'   card
-#' }
-#' ```
-#' @name add_card_button
-#'
-#' @param id (`character(1)`) this `shiny` module's id.
-#' @param reporter (`Reporter`) instance.
-#' @param card_fun (`function`) which returns a [`ReportCard`] instance. See `Details`.
-#'
-#' @return `NULL`.
-NULL
-
-#' @rdname add_card_button
+#' @param id `character(1)` this `shiny` module's id.
+#' @return `shiny::tagList`
 #' @export
 add_card_button_ui <- function(id) {
   ns <- shiny::NS(id)
@@ -81,7 +46,39 @@ add_card_button_ui <- function(id) {
   )
 }
 
-#' @rdname add_card_button
+#' Add Card Button Server
+#' @description `r lifecycle::badge("experimental")`
+#' server for adding views/cards to the Report.
+#'
+#' For more details see the vignette: `vignette("simpleReporter", "teal.reporter")`.
+#'
+#' @details
+#' This module allows using a child of [`ReportCard`] instead of [`ReportCard`].
+#' To properly support this, an instance of the child class must be passed
+#' as the default value of the `card` argument in the `card_fun` function.
+#' See below:
+#' ```{r}
+#' CustomReportCard <- R6::R6Class( # nolint: object_name_linter.
+#'   classname = "CustomReportCard",
+#'   inherit = teal.reporter::ReportCard
+#' )
+#'
+#' custom_function <- function(card = CustomReportCard$new()) {
+#'   card
+#' }
+#' ```
+#'
+#' @param id `character(1)` this `shiny` module's id.
+#' @param reporter [`Reporter`] instance.
+#' @param card_fun `function` which returns a [`ReportCard`] instance. It can have optional `card`, `comment` and
+#' `label` parameters. If `card` parameter is added, then the `ReportCard` instance is created for the user.
+#' Use `comment` parameter to pass it's value whenever you prefer with `card$append_text()` - if `card_fun` does not
+#' have `comment` parameter, then `comment` from `Add Card UI` module will be added at the end of the content of the
+#' card. If `label` parameter is provided, you can use it to customize appearance of the `card name` and use if to
+#' specify `card` content with `card$append_text()` - if `card_fun` does not have `label` parameter, then `card name`
+#' will be set to the name passed in `Add Card UI` module, but no text will be added to the content of the `card`.
+#'
+#' @return `shiny::moduleServer`
 #' @export
 add_card_button_srv <- function(id, reporter, card_fun) {
   checkmate::assert_function(card_fun)

R/Archiver.R

@@ -1,15 +1,11 @@
-#' @title `Archiver`: Base class for data archiving
-#' @docType class
-#' @description
-#' A base `R6` class for implementing data archiving functionality.
-#'
+#' @title `Archiver`
 #' @keywords internal
 Archiver <- R6::R6Class( # nolint: object_name_linter.
   classname = "Archiver",
   public = list(
-    #' @description Initialize an `Archiver` object.
+    #' @description Returns an `Archiver` object.
     #'
-    #' @return Object of class `Archiver`, invisibly.
+    #' @return an `Archiver` object
     #' @examples
     #' Archiver <- getFromNamespace("Archiver", "teal.reporter")
     #' Archiver$new()
@@ -20,14 +16,12 @@ Archiver <- R6::R6Class( # nolint: object_name_linter.
     finalize = function() {
       # destructor
     },
-    #' @description Reads data from the `Archiver`.
-    #' Pure virtual method that should be implemented by inherited classes.
+    #' @description Pure virtual method for reading an `Archiver`.
     read = function() {
       # returns Reporter instance
       stop("Pure virtual method.")
     },
-    #' @description Writes data to the `Archiver`.
-    #' Pure virtual method that should be implemented by inherited classes.
+    #' @description Pure virtual method for writing an `Archiver`.
     write = function() {
       stop("Pure virtual method.")
     }
@@ -36,20 +30,15 @@ Archiver <- R6::R6Class( # nolint: object_name_linter.
   lock_class = TRUE
 )
 
-#' @title `FileArchiver`: A File-based `Archiver`
-#' @docType class
-#' @description
-#' Inherits from `Archiver` to provide file-based archiving functionality.
-#' Manages an output directory for storing archived data.
-#'
+#' @title `RDSArchiver`
 #' @keywords internal
 FileArchiver <- R6::R6Class( # nolint: object_name_linter.
   classname = "FileArchiver",
   inherit = Archiver,
   public = list(
-    #' @description Initialize a `FileArchiver` object with a unique output directory.
+    #' @description Returns a `FileArchiver` object.
     #'
-    #' @return Object of class `FileArchiver`, invisibly.
+    #' @return a `FileArchiver` object
     #' @examples
     #' FileArchiver <- getFromNamespace("FileArchiver", "teal.reporter")
     #' FileArchiver$new()
@@ -61,11 +50,10 @@ FileArchiver <- R6::R6Class( # nolint: object_name_linter.
       invisible(self)
     },
     #' @description Finalizes a `FileArchiver` object.
-    #' Cleans up by removing the output directory and its contents.
     finalize = function() {
       unlink(private$output_dir, recursive = TRUE)
     },
-    #' @description Get `output_dir` field.
+    #' @description get `output_dir` field
     #'
     #' @return `character` a `output_dir` field path.
     #' @examples
@@ -80,34 +68,25 @@ FileArchiver <- R6::R6Class( # nolint: object_name_linter.
   )
 )
 
-#' @title `JSONArchiver`: A `JSON`-based `Archiver`
-#' @docType class
-#' @description
-#' Inherits from `FileArchiver` to implement `JSON`-based archiving functionality.
-#' Convert `Reporter` instances to and from `JSON` format.
-#'
+#' @title `JSONArchiver`
 #' @keywords internal
 JSONArchiver <- R6::R6Class( # nolint: object_name_linter.
   classname = "JSONArchiver",
   inherit = FileArchiver,
   public = list(
-    #' @description Write a `Reporter` instance in `JSON` file.
-    #' Serializes a given `Reporter` instance and saves it in the `Archiver`'s output directory,
-    #' to this `JSONArchiver` object.
+    #' @description write a `Reporter` instance in to this `JSONArchiver` object.
     #'
-    #' @param reporter (`Reporter`) instance.
+    #' @param reporter `Reporter` instance.
     #'
-    #' @return `self`.
+    #' @return invisibly self
     #' @examples
-    #' library(ggplot2)
-    #'
     #' ReportCard <- getFromNamespace("ReportCard", "teal.reporter")
     #' card1 <- ReportCard$new()
     #'
     #' card1$append_text("Header 2 text", "header2")
     #' card1$append_text("A paragraph of default text", "header2")
     #' card1$append_plot(
-    #'  ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
+    #'  ggplot2::ggplot(iris, ggplot2::aes(x = Petal.Length)) + ggplot2::geom_histogram()
     #' )
     #'
     #' Reporter <- getFromNamespace("Reporter", "teal.reporter")
@@ -124,22 +103,19 @@ JSONArchiver <- R6::R6Class( # nolint: object_name_linter.
       reporter$to_jsondir(private$output_dir)
       self
     },
-    #' @description Read a `Reporter` instance from a `JSON` file.
-    #' Converts a `Reporter` instance from the `JSON` file in the `JSONArchiver`'s output directory.
+    #' @description read a `Reporter` instance from a directory with `JSONArchiver`.
     #'
-    #' @param path (`character(1)`) a path to the directory with all proper files.
+    #' @param path `character(1)` a path to the directory with all proper files.
     #'
     #' @return `Reporter` instance.
     #' @examples
-    #' library(ggplot2)
-    #'
     #' ReportCard <- getFromNamespace("ReportCard", "teal.reporter")
     #' card1 <- ReportCard$new()
     #'
     #' card1$append_text("Header 2 text", "header2")
     #' card1$append_text("A paragraph of default text", "header2")
     #' card1$append_plot(
-    #'  ggplot(iris, aes(x = Petal.Length)) + geom_histogram()
+    #'  ggplot2::ggplot(iris, ggplot2::aes(x = Petal.Length)) + ggplot2::geom_histogram()
     #' )
     #'
     #' Reporter <- getFromNamespace("Reporter", "teal.reporter")

R/ContentBlock.R

@@ -1,18 +1,13 @@
-#' @title `ContentBlock`: A building block for report content
-#' @docType class
-#' @description This class represents a basic content unit in a report,
-#' such as text, images, or other multimedia elements.
-#' It serves as a foundation for constructing complex report structures.
-#'
+#' @title `ContentBlock`
 #' @keywords internal
 ContentBlock <- R6::R6Class( # nolint: object_name_linter.
   classname = "ContentBlock",
   public = list(
-    #' @description Initialize a `ContentBlock` object.
+    #' @description Returns a `ContentBlock` object.
     #'
     #' @details Returns a `ContentBlock` object with no content and the default style.
     #'
-    #' @return Object of class `ContentBlock`, invisibly.
+    #' @return `ContentBlock`
     #' @examples
     #' ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter")
     #' ContentBlock$new()
@@ -23,9 +18,9 @@ ContentBlock <- R6::R6Class( # nolint: object_name_linter.
     },
     #' @description Sets content of this `ContentBlock`.
     #'
-    #' @param content (`character(0)` or `character(1)`) string or file path assigned to this `ContentBlock`
+    #' @param content (`character(0)` or `character(1)`) a string literal or a file path assigned to this `ContentBlock`
     #'
-    #' @return `self`, invisibly.
+    #' @return invisibly self
     #' @examples
     #' ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter")
     #' block <- ContentBlock$new()
@@ -36,9 +31,9 @@ ContentBlock <- R6::R6Class( # nolint: object_name_linter.
       private$content <- content
       invisible(self)
     },
-    #' @description Retrieves the content assigned to this block.
+    #' @description Returns the absolute path to content of this `ContentBlock`
     #'
-    #' @return `character` string or file path assigned to this `ContentBlock`.
+    #' @return `character` content of this `ContentBlock`
     #' @examples
     #' ContentBlock <- getFromNamespace("ContentBlock", "teal.reporter")
     #' block <- ContentBlock$new()
@@ -49,10 +44,10 @@ ContentBlock <- R6::R6Class( # nolint: object_name_linter.
     },
     #' @description Create the `ContentBlock` from a list.
     #'
-    #' @param x (`named list`) with two fields `text` and `style`.
+    #' @param x `named list` with two fields `c("text", "style")`.
     #' Use the `get_available_styles` method to get all possible styles.
     #'
-    #' @return `self`, invisibly.
+    #' @return invisibly self
     from_list = function(x) {
       invisible(self)
     },
@@ -67,7 +62,7 @@ ContentBlock <- R6::R6Class( # nolint: object_name_linter.
     content = character(0),
     # @description The copy constructor.
     #
-    # @param name (`character(1)`) the name of the field
+    # @param name `character(1)` the name of the field
     # @param value the value assigned to the field
     #
     # @return the value of the copied field