From 24678ffa3da664c3f1c06e0bfff3a1694ab9b3f5 Mon Sep 17 00:00:00 2001
From: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Date: Wed, 14 Aug 2024 15:49:23 +0200
Subject: [PATCH] Config/Needs/verdepcheck cleanup; init() cleanup (#1313)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Signed-off-by: Pawel Rucki <12943682+pawelru@users.noreply.github.com>
Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
Co-authored-by: Dawid Kałędkowski <6959016+gogonzo@users.noreply.github.com>
---
 DESCRIPTION                    |  9 +++---
 R/init.R                       | 55 +++++++++++++++++-----------------
 man/init.Rd                    | 44 +++++++++++++--------------
 man/module_bookmark_manager.Rd |  6 ++--
 man/module_filter_data.Rd      |  6 ++--
 man/module_init_data.Rd        | 10 +++----
 man/module_teal.Rd             | 22 +++++++-------
 man/module_teal_module.Rd      |  6 ++--
 man/module_teal_with_splash.Rd | 22 +++++++-------
 man/modules_depth.Rd           |  2 +-
 10 files changed, 88 insertions(+), 94 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 48f3071be5..6ed8623eb8 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -75,13 +75,12 @@ RdMacros:
 Config/Needs/verdepcheck: rstudio/shiny, insightsengineering/teal.data,
     insightsengineering/teal.slice, mllg/checkmate,
     HenrikBengtsson/future, jeroen/jsonlite, r-lib/lifecycle,
-    daroczig/logger, tidyverse/magrittr, rstudio/promises, rstudio/renv,
-    r-lib/rlang, daattali/shinyjs, insightsengineering/teal.logger,
+    daroczig/logger, rstudio/promises, rstudio/renv,
+    r-lib/rlang, daattali/shinyjs, insightsengineering/teal.code, insightsengineering/teal.logger,
     insightsengineering/teal.reporter, insightsengineering/teal.widgets,
     rstudio/bslib, yihui/knitr, bioc::MultiAssayExperiment, r-lib/R6,
-    rstudio/rmarkdown, rstudio/shinyvalidate,
-    insightsengineering/teal.code, r-lib/testthat, r-lib/withr,
-    yaml=vubiostat/r-yaml
+    rstudio/rmarkdown, tidyverse/rvest, rstudio/shinytest2, rstudio/shinyvalidate,
+    r-lib/testthat, r-lib/withr, yaml=vubiostat/r-yaml
 Config/Needs/website: insightsengineering/nesttemplate
 Encoding: UTF-8
 Language: en-US
diff --git a/R/init.R b/R/init.R
index 092c263dd5..baf8ffcd90 100644
--- a/R/init.R
+++ b/R/init.R
@@ -10,32 +10,29 @@
 #' End-users: This is the most important function for you to start a
 #' `teal` app that is composed of `teal` modules.
 #'
-#' @details
-#' When initializing the `teal` app, if `datanames` are not set for the `teal_data` object,
-#' defaults from the `teal_data` environment will be used.
-#'
 #' @param data (`teal_data` or `teal_data_module`)
-#' For constructing the data object, refer to [teal_data()] and [teal_data_module()].
+#'   For constructing the data object, refer to [teal_data()] and [teal_data_module()].
+#'   If `datanames` are not set for the `teal_data` object, defaults from the `teal_data` environment will be used.
 #' @param modules (`list` or `teal_modules` or `teal_module`)
-#'   nested list of `teal_modules` or `teal_module` objects or a single
+#'   Nested list of `teal_modules` or `teal_module` objects or a single
 #'   `teal_modules` or `teal_module` object. These are the specific output modules which
 #'   will be displayed in the `teal` application. See [modules()] and [module()] for
 #'   more details.
-#' @param filter (`teal_slices`)
-#'   Specifies the initial filter using [teal_slices()].
-#' @param title (`shiny.tag` or `character(1)`)
-#'   The browser window title. Defaults to a title "teal app" with the icon of NEST.
+#' @param filter (`teal_slices`) Optionally,
+#'   specifies the initial filter using [teal_slices()].
+#' @param title (`shiny.tag` or `character(1)`) Optionally,
+#'   the browser window title. Defaults to a title "teal app" with the icon of NEST.
 #'   Can be created using the `build_app_title()` or
 #'   by passing a valid `shiny.tag` which is a head tag with title and link tag.
-#' @param header (`shiny.tag` or `character(1)`)
-#'   The header of the app.
-#' @param footer (`shiny.tag` or `character(1)`)
-#'   The footer of the app.
-#' @param id (`character`) optional
-#'   string specifying the `shiny` module id in cases it is used as a `shiny` module
+#' @param header (`shiny.tag` or `character(1)`) Optionally,
+#'   the header of the app.
+#' @param footer (`shiny.tag` or `character(1)`) Optionally,
+#'   the footer of the app.
+#' @param id (`character`) Optionally,
+#'   a string specifying the `shiny` module id in cases it is used as a `shiny` module
 #'   rather than a standalone `shiny` app. This is a legacy feature.
-#' @param landing_popup (`teal_module`) optional
-#'   A `landing_popup_module` to show up as soon as the teal app is initialized.
+#' @param landing_popup (`teal_module_landing`) Optionally,
+#'   a `landing_popup_module` to show up as soon as the teal app is initialized.
 #'
 #' @return Named list containing server and UI functions.
 #'
@@ -45,13 +42,12 @@
 #'
 #' @examples
 #' app <- init(
-#'   data = teal_data(
-#'     new_iris = transform(iris, id = seq_len(nrow(iris))),
-#'     new_mtcars = transform(mtcars, id = seq_len(nrow(mtcars))),
-#'     code = "
+#'   data = within(
+#'     teal_data(),
+#'     {
 #'       new_iris <- transform(iris, id = seq_len(nrow(iris)))
 #'       new_mtcars <- transform(mtcars, id = seq_len(nrow(mtcars)))
-#'     "
+#'     }
 #'   ),
 #'   modules = modules(
 #'     module(
@@ -89,7 +85,7 @@
 #'   ),
 #'   title = "App title",
 #'   header = tags$h1("Sample App"),
-#'   footer = tags$p("Copyright 2017 - 2023")
+#'   footer = tags$p("Sample footer")
 #' )
 #' if (interactive()) {
 #'   shinyApp(app$ui, app$server)
@@ -166,9 +162,8 @@ init <- function(data,
   if (length(landing) == 1L) {
     landing_popup <- landing[[1L]]
     modules <- drop_module(modules, "teal_module_landing")
-    # TODO: verify the version before release.
     lifecycle::deprecate_soft(
-      when = "0.16",
+      when = "0.15.3",
       what = "landing_popup_module()",
       details = paste(
         "Pass `landing_popup_module` to the `landing_popup` argument of the `init` ",
@@ -249,8 +244,12 @@ init <- function(data,
   res <- list(
     ui = function(request) {
       ui_teal(
-        id = ns("teal"), data = if (inherits(data, "teal_data_module")) data,
-        modules = modules, title = title, header = header, footer = footer
+        id = ns("teal"),
+        data = if (inherits(data, "teal_data_module")) data,
+        modules = modules,
+        title = title,
+        header = header,
+        footer = footer
       )
     },
     server = function(input, output, session) {
diff --git a/man/init.Rd b/man/init.Rd
index 974dd9801a..328c0b9179 100644
--- a/man/init.Rd
+++ b/man/init.Rd
@@ -17,34 +17,35 @@ init(
 }
 \arguments{
 \item{data}{(\code{teal_data} or \code{teal_data_module})
-For constructing the data object, refer to \code{\link[=teal_data]{teal_data()}} and \code{\link[=teal_data_module]{teal_data_module()}}.}
+For constructing the data object, refer to \code{\link[=teal_data]{teal_data()}} and \code{\link[=teal_data_module]{teal_data_module()}}.
+If \code{datanames} are not set for the \code{teal_data} object, defaults from the \code{teal_data} environment will be used.}
 
 \item{modules}{(\code{list} or \code{teal_modules} or \code{teal_module})
-nested list of \code{teal_modules} or \code{teal_module} objects or a single
+Nested list of \code{teal_modules} or \code{teal_module} objects or a single
 \code{teal_modules} or \code{teal_module} object. These are the specific output modules which
 will be displayed in the \code{teal} application. See \code{\link[=modules]{modules()}} and \code{\link[=module]{module()}} for
 more details.}
 
-\item{filter}{(\code{teal_slices})
-Specifies the initial filter using \code{\link[=teal_slices]{teal_slices()}}.}
+\item{filter}{(\code{teal_slices}) Optionally,
+specifies the initial filter using \code{\link[=teal_slices]{teal_slices()}}.}
 
-\item{title}{(\code{shiny.tag} or \code{character(1)})
-The browser window title. Defaults to a title "teal app" with the icon of NEST.
+\item{title}{(\code{shiny.tag} or \code{character(1)}) Optionally,
+the browser window title. Defaults to a title "teal app" with the icon of NEST.
 Can be created using the \code{build_app_title()} or
 by passing a valid \code{shiny.tag} which is a head tag with title and link tag.}
 
-\item{header}{(\code{shiny.tag} or \code{character(1)})
-The header of the app.}
+\item{header}{(\code{shiny.tag} or \code{character(1)}) Optionally,
+the header of the app.}
 
-\item{footer}{(\code{shiny.tag} or \code{character(1)})
-The footer of the app.}
+\item{footer}{(\code{shiny.tag} or \code{character(1)}) Optionally,
+the footer of the app.}
 
-\item{id}{(\code{character}) optional
-string specifying the \code{shiny} module id in cases it is used as a \code{shiny} module
+\item{id}{(\code{character}) Optionally,
+a string specifying the \code{shiny} module id in cases it is used as a \code{shiny} module
 rather than a standalone \code{shiny} app. This is a legacy feature.}
 
-\item{landing_popup}{(\code{teal_module}) optional
-A \code{landing_popup_module} to show up as soon as the teal app is initialized.}
+\item{landing_popup}{(\code{teal_module_landing}) Optionally,
+a \code{landing_popup_module} to show up as soon as the teal app is initialized.}
 }
 \value{
 Named list containing server and UI functions.
@@ -55,19 +56,14 @@ Named list containing server and UI functions.
 End-users: This is the most important function for you to start a
 \code{teal} app that is composed of \code{teal} modules.
 }
-\details{
-When initializing the \code{teal} app, if \code{datanames} are not set for the \code{teal_data} object,
-defaults from the \code{teal_data} environment will be used.
-}
 \examples{
 app <- init(
-  data = teal_data(
-    new_iris = transform(iris, id = seq_len(nrow(iris))),
-    new_mtcars = transform(mtcars, id = seq_len(nrow(mtcars))),
-    code = "
+  data = within(
+    teal_data(),
+    {
       new_iris <- transform(iris, id = seq_len(nrow(iris)))
       new_mtcars <- transform(mtcars, id = seq_len(nrow(mtcars)))
-    "
+    }
   ),
   modules = modules(
     module(
@@ -105,7 +101,7 @@ app <- init(
   ),
   title = "App title",
   header = tags$h1("Sample App"),
-  footer = tags$p("Copyright 2017 - 2023")
+  footer = tags$p("Sample footer")
 )
 if (interactive()) {
   shinyApp(app$ui, app$server)
diff --git a/man/module_bookmark_manager.Rd b/man/module_bookmark_manager.Rd
index 1a6a1e1d8b..abfdcffcfc 100644
--- a/man/module_bookmark_manager.Rd
+++ b/man/module_bookmark_manager.Rd
@@ -20,12 +20,12 @@ get_bookmarking_option()
 need_bookmarking(modules)
 }
 \arguments{
-\item{id}{(\code{character}) optional
-string specifying the \code{shiny} module id in cases it is used as a \code{shiny} module
+\item{id}{(\code{character}) Optionally,
+a string specifying the \code{shiny} module id in cases it is used as a \code{shiny} module
 rather than a standalone \code{shiny} app. This is a legacy feature.}
 
 \item{modules}{(\code{list} or \code{teal_modules} or \code{teal_module})
-nested list of \code{teal_modules} or \code{teal_module} objects or a single
+Nested list of \code{teal_modules} or \code{teal_module} objects or a single
 \code{teal_modules} or \code{teal_module} object. These are the specific output modules which
 will be displayed in the \code{teal} application. See \code{\link[=modules]{modules()}} and \code{\link[=module]{module()}} for
 more details.}
diff --git a/man/module_filter_data.Rd b/man/module_filter_data.Rd
index a7c6915e9c..e2dfe310f4 100644
--- a/man/module_filter_data.Rd
+++ b/man/module_filter_data.Rd
@@ -17,8 +17,8 @@ srv_filter_data(id, datasets, active_datanames, data_rv, is_active)
 .observe_active_filter_changed(datasets, is_active, active_datanames, data_rv)
 }
 \arguments{
-\item{id}{(\code{character}) optional
-string specifying the \code{shiny} module id in cases it is used as a \code{shiny} module
+\item{id}{(\code{character}) Optionally,
+a string specifying the \code{shiny} module id in cases it is used as a \code{shiny} module
 rather than a standalone \code{shiny} app. This is a legacy feature.}
 
 \item{datasets}{(\code{reactive} returning \code{FilteredData} or \code{NULL})
@@ -30,7 +30,7 @@ which implies in filter-panel to be "global". When \code{NULL} then filter-panel
 \item{data_rv}{(\code{reactive} returning \code{teal_data})}
 
 \item{modules}{(\code{list} or \code{teal_modules} or \code{teal_module})
-nested list of \code{teal_modules} or \code{teal_module} objects or a single
+Nested list of \code{teal_modules} or \code{teal_module} objects or a single
 \code{teal_modules} or \code{teal_module} object. These are the specific output modules which
 will be displayed in the \code{teal} application. See \code{\link[=modules]{modules()}} and \code{\link[=module]{module()}} for
 more details.}
diff --git a/man/module_init_data.Rd b/man/module_init_data.Rd
index 8370aefcd0..d61bb48e7a 100644
--- a/man/module_init_data.Rd
+++ b/man/module_init_data.Rd
@@ -11,8 +11,8 @@ ui_init_data(id, data)
 srv_init_data(id, data, modules, filter = teal_slices())
 }
 \arguments{
-\item{id}{(\code{character}) optional
-string specifying the \code{shiny} module id in cases it is used as a \code{shiny} module
+\item{id}{(\code{character}) Optionally,
+a string specifying the \code{shiny} module id in cases it is used as a \code{shiny} module
 rather than a standalone \code{shiny} app. This is a legacy feature.}
 
 \item{data}{(\code{teal_data}, \code{teal_data_module}, or \code{reactive} returning \code{teal_data})
@@ -22,13 +22,13 @@ The \code{data} argument in the \code{ui} is included solely for the \verb{$ui}
 the reactive data of the enclosing application.}
 
 \item{modules}{(\code{list} or \code{teal_modules} or \code{teal_module})
-nested list of \code{teal_modules} or \code{teal_module} objects or a single
+Nested list of \code{teal_modules} or \code{teal_module} objects or a single
 \code{teal_modules} or \code{teal_module} object. These are the specific output modules which
 will be displayed in the \code{teal} application. See \code{\link[=modules]{modules()}} and \code{\link[=module]{module()}} for
 more details.}
 
-\item{filter}{(\code{teal_slices})
-Specifies the initial filter using \code{\link[=teal_slices]{teal_slices()}}.}
+\item{filter}{(\code{teal_slices}) Optionally,
+specifies the initial filter using \code{\link[=teal_slices]{teal_slices()}}.}
 }
 \value{
 A \code{reactive} object that returns:
diff --git a/man/module_teal.Rd b/man/module_teal.Rd
index bbe43e80b0..29cab0645c 100644
--- a/man/module_teal.Rd
+++ b/man/module_teal.Rd
@@ -18,12 +18,12 @@ ui_teal(
 srv_teal(id, data, modules, filter = teal_slices())
 }
 \arguments{
-\item{id}{(\code{character}) optional
-string specifying the \code{shiny} module id in cases it is used as a \code{shiny} module
+\item{id}{(\code{character}) Optionally,
+a string specifying the \code{shiny} module id in cases it is used as a \code{shiny} module
 rather than a standalone \code{shiny} app. This is a legacy feature.}
 
 \item{modules}{(\code{list} or \code{teal_modules} or \code{teal_module})
-nested list of \code{teal_modules} or \code{teal_module} objects or a single
+Nested list of \code{teal_modules} or \code{teal_module} objects or a single
 \code{teal_modules} or \code{teal_module} object. These are the specific output modules which
 will be displayed in the \code{teal} application. See \code{\link[=modules]{modules()}} and \code{\link[=module]{module()}} for
 more details.}
@@ -34,19 +34,19 @@ The \code{data} argument in the \code{ui} is included solely for the \verb{$ui}
 \code{teal_data_module}. Otherwise, it can be disregarded, ensuring that \code{ui_teal} does not depend on
 the reactive data of the enclosing application.}
 
-\item{title}{(\code{shiny.tag} or \code{character(1)})
-The browser window title. Defaults to a title "teal app" with the icon of NEST.
+\item{title}{(\code{shiny.tag} or \code{character(1)}) Optionally,
+the browser window title. Defaults to a title "teal app" with the icon of NEST.
 Can be created using the \code{build_app_title()} or
 by passing a valid \code{shiny.tag} which is a head tag with title and link tag.}
 
-\item{header}{(\code{shiny.tag} or \code{character(1)})
-The header of the app.}
+\item{header}{(\code{shiny.tag} or \code{character(1)}) Optionally,
+the header of the app.}
 
-\item{footer}{(\code{shiny.tag} or \code{character(1)})
-The footer of the app.}
+\item{footer}{(\code{shiny.tag} or \code{character(1)}) Optionally,
+the footer of the app.}
 
-\item{filter}{(\code{teal_slices})
-Specifies the initial filter using \code{\link[=teal_slices]{teal_slices()}}.}
+\item{filter}{(\code{teal_slices}) Optionally,
+specifies the initial filter using \code{\link[=teal_slices]{teal_slices()}}.}
 }
 \value{
 \code{NULL} invisibly
diff --git a/man/module_teal_module.Rd b/man/module_teal_module.Rd
index 01ad3f947d..b5bb015f81 100644
--- a/man/module_teal_module.Rd
+++ b/man/module_teal_module.Rd
@@ -64,12 +64,12 @@ srv_teal_module(
 )
 }
 \arguments{
-\item{id}{(\code{character}) optional
-string specifying the \code{shiny} module id in cases it is used as a \code{shiny} module
+\item{id}{(\code{character}) Optionally,
+a string specifying the \code{shiny} module id in cases it is used as a \code{shiny} module
 rather than a standalone \code{shiny} app. This is a legacy feature.}
 
 \item{modules}{(\code{list} or \code{teal_modules} or \code{teal_module})
-nested list of \code{teal_modules} or \code{teal_module} objects or a single
+Nested list of \code{teal_modules} or \code{teal_module} objects or a single
 \code{teal_modules} or \code{teal_module} object. These are the specific output modules which
 will be displayed in the \code{teal} application. See \code{\link[=modules]{modules()}} and \code{\link[=module]{module()}} for
 more details.}
diff --git a/man/module_teal_with_splash.Rd b/man/module_teal_with_splash.Rd
index 5d75a51b89..4fa6ba3e3e 100644
--- a/man/module_teal_with_splash.Rd
+++ b/man/module_teal_with_splash.Rd
@@ -17,8 +17,8 @@ ui_teal_with_splash(
 srv_teal_with_splash(id, data, modules, filter = teal_slices())
 }
 \arguments{
-\item{id}{(\code{character}) optional
-string specifying the \code{shiny} module id in cases it is used as a \code{shiny} module
+\item{id}{(\code{character}) Optionally,
+a string specifying the \code{shiny} module id in cases it is used as a \code{shiny} module
 rather than a standalone \code{shiny} app. This is a legacy feature.}
 
 \item{data}{(\code{teal_data}, \code{teal_data_module}, or \code{reactive} returning \code{teal_data})
@@ -27,25 +27,25 @@ The \code{data} argument in the \code{ui} is included solely for the \verb{$ui}
 \code{teal_data_module}. Otherwise, it can be disregarded, ensuring that \code{ui_teal} does not depend on
 the reactive data of the enclosing application.}
 
-\item{title}{(\code{shiny.tag} or \code{character(1)})
-The browser window title. Defaults to a title "teal app" with the icon of NEST.
+\item{title}{(\code{shiny.tag} or \code{character(1)}) Optionally,
+the browser window title. Defaults to a title "teal app" with the icon of NEST.
 Can be created using the \code{build_app_title()} or
 by passing a valid \code{shiny.tag} which is a head tag with title and link tag.}
 
-\item{header}{(\code{shiny.tag} or \code{character(1)})
-The header of the app.}
+\item{header}{(\code{shiny.tag} or \code{character(1)}) Optionally,
+the header of the app.}
 
-\item{footer}{(\code{shiny.tag} or \code{character(1)})
-The footer of the app.}
+\item{footer}{(\code{shiny.tag} or \code{character(1)}) Optionally,
+the footer of the app.}
 
 \item{modules}{(\code{list} or \code{teal_modules} or \code{teal_module})
-nested list of \code{teal_modules} or \code{teal_module} objects or a single
+Nested list of \code{teal_modules} or \code{teal_module} objects or a single
 \code{teal_modules} or \code{teal_module} object. These are the specific output modules which
 will be displayed in the \code{teal} application. See \code{\link[=modules]{modules()}} and \code{\link[=module]{module()}} for
 more details.}
 
-\item{filter}{(\code{teal_slices})
-Specifies the initial filter using \code{\link[=teal_slices]{teal_slices()}}.}
+\item{filter}{(\code{teal_slices}) Optionally,
+specifies the initial filter using \code{\link[=teal_slices]{teal_slices()}}.}
 }
 \value{
 Returns a \code{reactive} expression containing a \code{teal_data} object when data is loaded or \code{NULL} when it is not.
diff --git a/man/modules_depth.Rd b/man/modules_depth.Rd
index 4501141cb2..f3b9e057c1 100644
--- a/man/modules_depth.Rd
+++ b/man/modules_depth.Rd
@@ -8,7 +8,7 @@ modules_depth(modules, depth = 0L)
 }
 \arguments{
 \item{modules}{(\code{list} or \code{teal_modules} or \code{teal_module})
-nested list of \code{teal_modules} or \code{teal_module} objects or a single
+Nested list of \code{teal_modules} or \code{teal_module} objects or a single
 \code{teal_modules} or \code{teal_module} object. These are the specific output modules which
 will be displayed in the \code{teal} application. See \code{\link[=modules]{modules()}} and \code{\link[=module]{module()}} for
 more details.}