Merge branch 'main' into 898_save_app_state3@main

.Rbuildignore

@@ -45,3 +45,6 @@ coverage.*
 ^\.pre-commit-config\.yaml$
 data-raw/data.R
 ^pkgdown$
+^.revdeprefs\.yaml$
+^revdep$
+^\.covrignore$

.github/workflows/check.yaml

@@ -28,8 +28,21 @@ jobs:
       additional-env-vars: |
         _R_CHECK_CRAN_INCOMING_REMOTE_=false
         _R_CHECK_EXAMPLE_TIMING_THRESHOLD_=10
-        NOT_CRAN=true
       additional-r-cmd-check-params: --as-cran
+  r-cmd-non-cran:
+    name: R CMD Check (non-CRAN) 🧬
+    uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+    with:
+      additional-env-vars: |
+        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
   coverage:
     name: Coverage 📔
     uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main
@@ -76,6 +89,8 @@ jobs:
     uses: insightsengineering/r.pkg.template/.github/workflows/style.yaml@main
     with:
       auto-update: true
+    secrets:
+      REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
   grammar:
     if: github.event_name != 'push'
     name: Grammar Check 🔤

.github/workflows/cla.yaml

@@ -0,0 +1,18 @@
+name: CLA 🔏
+
+on:
+  issue_comment:
+    types:
+      - created
+  # For PRs that originate from forks
+  pull_request_target:
+    types:
+      - opened
+      - closed
+      - synchronize
+
+jobs:
+  CLA:
+    name: CLA 📝
+    uses: insightsengineering/.github/.github/workflows/cla.yaml@main
+    secrets: inherit

.github/workflows/on-demand.yaml

@@ -0,0 +1,12 @@
+---
+name: On-demand 🧑‍🔬
+
+on:
+  schedule:
+    - cron: '45 3 * * 0'
+  workflow_dispatch:
+
+jobs:
+  revdepcheck:
+    name: revdepcheck ↩️
+    uses: insightsengineering/r.pkg.template/.github/workflows/revdepcheck.yaml@main

.gitignore

@@ -53,3 +53,5 @@ docs/
 
 # shinytest2: Ignore new debug snapshots for `$expect_values()`
 *_.new.png
+tests/testthat/_snaps/**/*.new.md
+tests/testthat/_snaps/**/*.new.svg

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ default_language_version:
   python: python3
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.0
+    rev: v0.4.2
     hooks:
       - id: style-files
         name: Style code with `styler`
@@ -59,6 +59,7 @@ repos:
           .*\.svg|
           .*\.xml|
           (.*/|)\_pkgdown.y[a]?ml|
+          (.*/|)\.covrignore|
           (.*/|)\.gitignore|
           (.*/|)\.gitlab-ci\.y[a]?ml|
           (.*/|)\.lintr|
@@ -122,7 +123,7 @@ repos:
           design/.*
           )$
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
       - id: check-added-large-files
         args: ["--maxkb=1000"]

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: teal.modules.hermes
 Title: RNA-Seq Analysis Modules to Add to a Teal Application
-Version: 0.1.6.9007
-Date: 2024-03-20
+Version: 0.1.6.9013
+Date: 2024-04-30
 Authors@R: c(
     person("Daniel", "Sabanés Bové", , "[email protected]", role = c("aut", "cre")),
     person("Nikolas", "Burkoff", role = "aut"),
@@ -29,39 +29,40 @@ URL: https://insightsengineering.github.io/teal.modules.hermes/,
 BugReports: 
     https://github.com/insightsengineering/teal.modules.hermes/issues
 Depends:
-    ggplot2,
     R (>= 4.1),
+    ggplot2,
     shiny,
     teal (>= 0.15.0)
 Imports:
-    checkmate,
     DT,
+    MultiAssayExperiment,
+    S4Vectors,
+    SummarizedExperiment,
+    checkmate,
     edgeR,
     forcats,
     hermes (>= 1.7.1),
     lifecycle,
-    MultiAssayExperiment,
     rtables (>= 0.5.1),
-    S4Vectors,
     shinyRadioMatrix (>= 0.2.1),
     shinyWidgets,
     stats,
     stringr,
-    SummarizedExperiment,
     teal.data (>= 0.3.0.9018),
     teal.logger (>= 0.1.3.9013),
     teal.reporter (>= 0.2.0),
     teal.widgets (>= 0.4.0),
-    tern (>= 0.7.10)
+    tern (>= 0.7.10),
+    utils
 Suggests:
     BiocStyle,
+    R6,
     covr,
     dplyr,
     globals,
     knitr,
     logger (>= 0.2.0),
     matrixStats,
-    R6,
     rmarkdown,
     rvest,
     shinytest2 (>= 0.2.0),
@@ -70,11 +71,11 @@ VignetteBuilder:
     knitr
 RdMacros:
     lifecycle
-biocViews:
 Config/Needs/website: insightsengineering/nesttemplate
 Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
+biocViews:

NAMESPACE

@@ -73,3 +73,4 @@ import(teal.data)
 importFrom(S4Vectors,DataFrame)
 importFrom(S4Vectors,setListElement)
 importFrom(lifecycle,deprecate_soft)
+importFrom(utils,str)

NEWS.md

@@ -1,4 +1,4 @@
-# teal.modules.hermes 0.1.6.9007
+# teal.modules.hermes 0.1.6.9013
 
 ### Miscellaneous
 * Added placeholders for `assaySpec`, `adtteSpec` and `geneSpec` inputs when no option is selected.

R/argument_convention.R

@@ -43,6 +43,7 @@
 #' @param plot_width (`list`)\cr list of integers to set the default, minimum,
 #'   and maximum plot width.
 #' @param filter_panel_api (`FilterPanelAPI`)\cr object describing the actual filter panel API.
+#' @param .test (`flag`)\cr whether to display the internal structure of the plot for testing purposes.
 #'
 #' @name module_arguments
 #' @keywords internal

R/barplot.R

@@ -34,29 +34,33 @@ tm_g_barplot <- function(label,
                            Max = matrixStats::colMaxs
                          ),
                          pre_output = NULL,
-                         post_output = NULL) {
+                         post_output = NULL,
+                         .test = FALSE) {
   message("Initializing tm_g_barplot")
   assert_string(label)
   assert_string(mae_name)
   assert_character(exclude_assays)
   assert_summary_funs(summary_funs)
   assert_tag(pre_output, null.ok = TRUE)
   assert_tag(post_output, null.ok = TRUE)
+  assert_flag(.test)
 
   module(
     label = label,
     server = srv_g_barplot,
     server_args = list(
       mae_name = mae_name,
       exclude_assays = exclude_assays,
-      summary_funs = summary_funs
+      summary_funs = summary_funs,
+      .test = .test
     ),
     ui = ui_g_barplot,
     ui_args = list(
       mae_name = mae_name,
       summary_funs = summary_funs,
       pre_output = pre_output,
-      post_output = post_output
+      post_output = post_output,
+      .test = .test
     ),
     datanames = mae_name
   )
@@ -69,7 +73,8 @@ ui_g_barplot <- function(id,
                          mae_name,
                          summary_funs,
                          pre_output,
-                         post_output) {
+                         post_output,
+                         .test = FALSE) {
   ns <- NS(id)
   teal.widgets::standard_layout(
     encoding = tags$div(
@@ -101,7 +106,10 @@ ui_g_barplot <- function(id,
         )
       )
     ),
-    output = teal.widgets::plot_with_settings_ui(ns("plot")),
+    output = div(
+      if (.test) verbatimTextOutput(ns("table")) else NULL,
+      teal.widgets::plot_with_settings_ui(ns("plot"))
+    ),
     pre_output = pre_output,
     post_output = post_output
   )
@@ -116,11 +124,13 @@ srv_g_barplot <- function(id,
                           reporter,
                           mae_name,
                           exclude_assays,
-                          summary_funs) {
+                          summary_funs,
+                          .test = FALSE) {
   with_reporter <- !missing(reporter) && inherits(reporter, "Reporter")
   assert_class(filter_panel_api, "FilterPanelAPI")
   checkmate::assert_class(data, "reactive")
   checkmate::assert_class(shiny::isolate(data()), "teal_data")
+  assert_flag(.test)
   moduleServer(id, function(input, output, session) {
     ns <- session$ns
 
@@ -191,6 +201,13 @@ srv_g_barplot <- function(id,
       plot_r = plot_r
     )
 
+    if (.test) {
+      table_r <- reactive({
+        utils::str(layer_data(plot_r()))
+      })
+      output$table <- renderPrint(table_r())
+    }
+
     ### REPORTER
     if (with_reporter) {
       card_fun <- function(comment, label) {
@@ -232,6 +249,7 @@ srv_g_barplot <- function(id,
           card$append_text("Comment", "header3")
           card$append_text(comment)
         }
+
         card
       }
       teal.reporter::simple_reporter_srv("simple_reporter", reporter = reporter, card_fun = card_fun)
@@ -248,14 +266,15 @@ srv_g_barplot <- function(id,
 #' if (interactive()) {
 #'   sample_tm_g_barplot()
 #' }
-sample_tm_g_barplot <- function() {
+sample_tm_g_barplot <- function(.test = FALSE) {
   data <- teal.data::teal_data(MAE = hermes::multi_assay_experiment)
   app <- teal::init(
     data = data,
     modules = teal::modules(
       tm_g_barplot(
         label = "barplot",
-        mae_name = "MAE"
+        mae_name = "MAE",
+        .test = .test
       )
     )
   )