Merge branch 'main' into 518_incorrect_soft_dep@main

.github/workflows/check.yaml

@@ -51,12 +51,10 @@ jobs:
       additional-env-vars: |
         _R_CHECK_EXAMPLE_TIMING_THRESHOLD_=11
         TESTING_DEPTH=5
+        NOT_CRAN=true
       enforce-note-blocklist: true
-      publish-unit-test-report-gh-pages: false
-      junit-xml-comparison: false
       concurrency-group: non-cran
-      disable-unit-test-reports: true
-      skip-r-cmd-install: true
+      unit-test-report-directory: unit-test-report-non-cran
       note-blocklist: |
         checking dependencies in R code .* NOTE
         checking R code for possible problems .* NOTE
@@ -71,6 +69,9 @@ jobs:
     uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+    with:
+      additional-env-vars: |
+        NOT_CRAN=true
   linter:
     if: github.event_name != 'push'
     name: SuperLinter 🦸‍♀️

.github/workflows/docs.yaml

@@ -41,3 +41,4 @@ jobs:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
       default-landing-page: latest-tag
+      additional-unit-test-report-directories: unit-test-report-non-cran

.github/workflows/release.yaml

@@ -52,3 +52,10 @@ jobs:
     uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+    with:
+      additional-env-vars: |
+        NOT_CRAN=true
+  wasm:
+    name: Build WASM packages 🧑‍🏭
+    needs: release
+    uses: insightsengineering/r.pkg.template/.github/workflows/wasm.yaml@main

.github/workflows/scheduled.yaml

@@ -5,9 +5,26 @@ on:
   schedule:
     - cron: '45 3 * * 0'
   workflow_dispatch:
+    inputs:
+      chosen-workflow:
+        description: |
+          Select which workflow you'd like to run
+        required: true
+        type: choice
+        default: rhub
+        options:
+          - rhub
+          - dependency-test
+          - branch-cleanup
+          - revdepcheck
 
 jobs:
   dependency-test:
+    if: >
+      github.event_name == 'schedule' || (
+        github.event_name == 'workflow_dispatch' &&
+        inputs.chosen-workflow == 'dependency-test'
+      )
     strategy:
       fail-fast: false
       matrix:
@@ -22,7 +39,54 @@ jobs:
       additional-env-vars: |
         PKG_SYSREQS_DRY_RUN=true
   branch-cleanup:
+    if: >
+      github.event_name == 'schedule' || (
+        github.event_name == 'workflow_dispatch' &&
+        inputs.chosen-workflow == 'branch-cleanup'
+      )
     name: Branch Cleanup 🧹
     uses: insightsengineering/r.pkg.template/.github/workflows/branch-cleanup.yaml@main
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+  revdepcheck:
+    if: >
+      github.event_name == 'schedule' || (
+        github.event_name == 'workflow_dispatch' &&
+        inputs.chosen-workflow == 'revdepcheck'
+      )
+    name: revdepcheck ↩️
+    uses: insightsengineering/r.pkg.template/.github/workflows/revdepcheck.yaml@main
+    with:
+      lookup-refs: |
+        insightsengineering/roxy.shinylive
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.slice
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/tern
+        insightsengineering/rtables
+  rhub:
+    if: >
+      github.event_name == 'schedule' || (
+        github.event_name == 'workflow_dispatch' &&
+        inputs.chosen-workflow == 'rhub'
+      )
+    name: R-hub 🌐
+    uses: insightsengineering/r.pkg.template/.github/workflows/rhub.yaml@main
+    with:
+      lookup-refs: |
+        insightsengineering/roxy.shinylive
+        insightsengineering/teal
+        insightsengineering/teal.transform
+        insightsengineering/teal.code
+        insightsengineering/teal.data
+        insightsengineering/teal.slice
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
+        insightsengineering/tern
+        insightsengineering/rtables

.gitignore

@@ -29,3 +29,5 @@ vignettes/*.R
 coverage.*
 tests/testthat/_snaps/**/*.new.md
 tests/testthat/_snaps/**/*.new.svg
+/doc/
+/Meta/

.pre-commit-config.yaml

@@ -1,12 +1,12 @@
 ---
 # All available hooks: https://pre-commit.com/hooks.html
 # R specific hooks: https://github.com/lorenzwalthert/precommit
-default_stages: [commit]
+default_stages: [pre-commit]
 default_language_version:
   python: python3
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.2
+    rev: v0.4.3.9003
     hooks:
       - id: style-files
         name: Style code with `styler`
@@ -18,8 +18,6 @@ repos:
           - ggmosaic
           - ggplot2
           - shiny
-          - teal
-          - teal.transform
           - checkmate
           - dplyr
           - DT
@@ -33,6 +31,9 @@ repos:
           - shinyWidgets
           - stats
           - stringr
+          - insightsengineering/roxy.shinylive
+          - insightsengineering/teal
+          - insightsengineering/teal.transform
           - insightsengineering/teal.code
           - insightsengineering/teal.data
           - insightsengineering/teal.logger

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.modules.general
 Title: General Modules for 'teal' Applications
-Version: 0.3.0.9038
-Date: 2024-06-27
+Version: 0.3.0.9054
+Date: 2024-11-08
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre")),
     person("Pawel", "Rucki", , "[email protected]", role = "aut"),
@@ -27,8 +27,8 @@ Depends:
     ggplot2 (>= 3.4.0),
     R (>= 3.6),
     shiny (>= 1.6.0),
-    teal (>= 0.15.1),
-    teal.transform (>= 0.5.0)
+    teal (>= 0.15.2.9079),
+    teal.transform (>= 0.5.0.9015)
 Imports:
     broom (>= 0.7.10),
     checkmate (>= 2.1.0),
@@ -49,8 +49,8 @@ Imports:
     shinyWidgets (>= 0.5.1),
     stats,
     stringr (>= 1.4.1),
-    teal.code (>= 0.5.0),
-    teal.data (>= 0.5.0),
+    teal.code (>= 0.5.0.9012),
+    teal.data (>= 0.6.0.9015),
     teal.logger (>= 0.2.0.9004),
     teal.reporter (>= 0.3.0),
     teal.widgets (>= 0.4.0),
@@ -72,14 +72,16 @@ Suggests:
     pkgload,
     rlang (>= 1.0.0),
     rmarkdown (>= 2.23),
+    roxy.shinylive,
     rtables (>= 0.6.8),
     rvest,
     shinytest2,
     sparkline,
     testthat (>= 3.1.9),
     withr (>= 2.0.0)
 VignetteBuilder:
-    knitr
+    knitr,
+    rmarkdown
 Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
     rstudio/shiny, insightsengineering/teal,
     insightsengineering/teal.transform, mllg/checkmate, tidyverse/dplyr,
@@ -91,15 +93,14 @@ Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
     insightsengineering/tern, tidyverse/tibble, tidyverse/tidyr,
     tidymodels/broom, daattali/colourpicker, daattali/ggExtra,
     aphalo/ggpmisc, aphalo/ggpp, slowkow/ggrepel, baddstats/goftest,
-    gridExtra, ramnathv/htmlwidgets, jeroen/jsonlite, yihui/knitr,
-    daroczig/logger, deepayan/lattice, MASS,
-    insightsengineering/nestcolor, r-lib/rlang, rstudio/rmarkdown,
-    insightsengineering/rtables, tidyverse/rvest, sparkline,
-    rstudio/shinytest2, insightsengineering/teal.data, r-lib/testthat,
-    r-lib/withr
+    ramnathv/htmlwidgets, jeroen/jsonlite, yihui/knitr, daroczig/logger,
+    deepayan/lattice, insightsengineering/nestcolor, r-lib/pkgload,
+    r-lib/rlang, rstudio/rmarkdown, insightsengineering/roxy.shinylive,
+    insightsengineering/rtables, tidyverse/rvest, htmlwidgets/sparkline,
+    rstudio/shinytest2, r-lib/testthat, r-lib/withr
 Config/Needs/website: insightsengineering/nesttemplate
 Encoding: UTF-8
 Language: en-US
 LazyData: true
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+Roxygen: list(markdown = TRUE, packages = c("roxy.shinylive"))
+RoxygenNote: 7.3.2

NEWS.md

@@ -1,14 +1,17 @@
-# teal.modules.general 0.3.0.9038
+# teal.modules.general 0.3.0.9054
 
 * Removed `Show Warnings` modals from modules.
 
 ### Enhancements
 * Added `teal.logger` functionality for logging changes in shiny inputs in all modules.
 
+### Bug fixes
+* Fixed a bug in `tm_missing_data` in "Group by Subject" that was not using reactive data call.
+
 # teal.modules.general 0.3.0
 
 ### Enhancements
-* Updated the package docs and vignettes with the new way of specifying data for `teal::init()`. The `data` argument will accept a `teal_data` object
+* Updated the package docs and vignettes with the new way of specifying data for `teal::init()`. The `data` argument will accept a `teal_data` object.
 
 ### Bug fixes
 * Outlier labels no longer appear out of bounds in `tm_a_regression`.

R/tm_a_pca.R

@@ -18,18 +18,18 @@
 #'
 #' @inherit shared_params return
 #'
+#' @examplesShinylive
+#' library(teal.modules.general)
+#' interactive <- function() TRUE
+#' {{ next_example }}
 #' @examples
-#' library(teal.widgets)
-#'
 #' # general data example
 #' data <- teal_data()
 #' data <- within(data, {
 #'   require(nestcolor)
 #'   USArrests <- USArrests
 #' })
 #'
-#' datanames(data) <- "USArrests"
-#'
 #' app <- init(
 #'   data = data,
 #'   modules = modules(
@@ -45,9 +45,6 @@
 #'           multiple = TRUE
 #'         ),
 #'         filter = NULL
-#'       ),
-#'       ggplot2_args = ggplot2_args(
-#'         labs = list(subtitle = "Plot generated by PCA Module")
 #'       )
 #'     )
 #'   )
@@ -56,14 +53,18 @@
 #'   shinyApp(app$ui, app$server)
 #' }
 #'
+#' @examplesShinylive
+#' library(teal.modules.general)
+#' interactive <- function() TRUE
+#' {{ next_example }}
+#' @examples
 #' # CDISC data example
 #' data <- teal_data()
 #' data <- within(data, {
 #'   require(nestcolor)
 #'   ADSL <- rADSL
 #' })
-#' datanames(data) <- "ADSL"
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,
@@ -80,9 +81,6 @@
 #'           multiple = TRUE
 #'         ),
 #'         filter = NULL
-#'       ),
-#'       ggplot2_args = ggplot2_args(
-#'         labs = list(subtitle = "Plot generated by PCA Module")
 #'       )
 #'     )
 #'   )

R/tm_a_regression.R

@@ -42,16 +42,17 @@
 #'
 #' @inherit shared_params return
 #'
+#' @examplesShinylive
+#' library(teal.modules.general)
+#' interactive <- function() TRUE
+#' {{ next_example }}
 #' @examples
 #' # general data example
-#' library(teal.widgets)
-#'
 #' data <- teal_data()
 #' data <- within(data, {
 #'   require(nestcolor)
 #'   CO2 <- CO2
 #' })
-#' datanames(data) <- c("CO2")
 #'
 #' app <- init(
 #'   data = data,
@@ -77,9 +78,6 @@
 #'           multiple = TRUE,
 #'           fixed = FALSE
 #'         )
-#'       ),
-#'       ggplot2_args = ggplot2_args(
-#'         labs = list(subtitle = "Plot generated by Regression Module")
 #'       )
 #'     )
 #'   )
@@ -88,16 +86,18 @@
 #'   shinyApp(app$ui, app$server)
 #' }
 #'
+#' @examplesShinylive
+#' library(teal.modules.general)
+#' interactive <- function() TRUE
+#' {{ next_example }}
+#' @examples
 #' # CDISC data example
-#' library(teal.widgets)
-#'
 #' data <- teal_data()
 #' data <- within(data, {
 #'   require(nestcolor)
 #'   ADSL <- rADSL
 #' })
-#' datanames(data) <- "ADSL"
-#' join_keys(data) <- default_cdisc_join_keys[datanames(data)]
+#' join_keys(data) <- default_cdisc_join_keys[names(data)]
 #'
 #' app <- init(
 #'   data = data,
@@ -123,9 +123,6 @@
 #'           multiple = TRUE,
 #'           fixed = FALSE
 #'         )
-#'       ),
-#'       ggplot2_args = ggplot2_args(
-#'         labs = list(subtitle = "Plot generated by Regression Module")
 #'       )
 #'     )
 #'   )