Merge branch 'main' into 1187_decorate_output@main

insightsengineering · Oct 30, 2024 · dfce86b · dfce86b
2 parents 30bb248 + 977ea9e
commit dfce86b
Show file tree

Hide file tree

Showing 24 changed files with 633 additions and 239 deletions.
diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
@@ -42,6 +42,14 @@ jobs:
         checking top-level files .* NOTE
       unit-test-report-brand: >-
         https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/thumbs/teal.png
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal.data
+        insightsengineering/teal.slice
+        insightsengineering/teal.code
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
   r-cmd-non-cran:
     name: R CMD Check (non-CRAN) 🧬
     uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
@@ -63,6 +71,14 @@ jobs:
         checking Rd .usage sections .* NOTE
         checking for unstated dependencies in vignettes .* NOTE
         checking top-level files .* NOTE
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal.data
+        insightsengineering/teal.slice
+        insightsengineering/teal.code
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
   coverage:
     name: Coverage 📔
     uses: insightsengineering/r.pkg.template/.github/workflows/test-coverage.yaml@main
@@ -71,6 +87,14 @@ jobs:
     with:
       additional-env-vars: |
         NOT_CRAN=true
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal.data
+        insightsengineering/teal.slice
+        insightsengineering/teal.code
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
   linter:
     if: github.event_name != 'push'
     name: SuperLinter 🦸‍♀️
@@ -82,6 +106,14 @@ jobs:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
       auto-update: true
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal.data
+        insightsengineering/teal.slice
+        insightsengineering/teal.code
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
   gitleaks:
     name: gitleaks 💧
     uses: insightsengineering/r.pkg.template/.github/workflows/gitleaks.yaml@main

diff --git a/.github/workflows/docs.yaml b/.github/workflows/docs.yaml
@@ -42,3 +42,11 @@ jobs:
     with:
       default-landing-page: latest-tag
       additional-unit-test-report-directories: unit-test-report-non-cran
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal.data
+        insightsengineering/teal.slice
+        insightsengineering/teal.code
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -16,12 +16,29 @@ jobs:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
       default-landing-page: latest-tag
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal.data
+        insightsengineering/teal.slice
+        insightsengineering/teal.code
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
   validation:
     name: R Package Validation report 📃
     needs: release
     uses: insightsengineering/r.pkg.template/.github/workflows/validation.yaml@main
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
+    with:
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal.data
+        insightsengineering/teal.slice
+        insightsengineering/teal.code
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
   release:
     name: Create release 🎉
     uses: insightsengineering/r.pkg.template/.github/workflows/release.yaml@main
@@ -46,6 +63,14 @@ jobs:
         checking top-level files .* NOTE
       unit-test-report-brand: >-
         https://raw.githubusercontent.com/insightsengineering/hex-stickers/main/thumbs/teal.png
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal.data
+        insightsengineering/teal.slice
+        insightsengineering/teal.code
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
   coverage:
     name: Coverage 📔
     needs: [release, docs]
@@ -55,6 +80,14 @@ jobs:
     with:
       additional-env-vars: |
         NOT_CRAN=true
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/teal.data
+        insightsengineering/teal.slice
+        insightsengineering/teal.code
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
   wasm:
     name: Build WASM packages 🧑‍🏭
     needs: release

diff --git a/.github/workflows/scheduled.yaml b/.github/workflows/scheduled.yaml
@@ -56,6 +56,14 @@ jobs:
       )
     name: revdepcheck ↩️
     uses: insightsengineering/r.pkg.template/.github/workflows/revdepcheck.yaml@main
+    with:
+      lookup-refs: |
+        insightsengineering/teal.data
+        insightsengineering/teal.slice
+        insightsengineering/teal.code
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.widgets
   rhub:
     if: >
       github.event_name == 'schedule' || (

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,7 +1,7 @@
 ---
 # 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:

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: teal
 Title: Exploratory Web Apps for Analyzing Clinical Trials Data
-Version: 0.15.2.9067
-Date: 2024-10-03
+Version: 0.15.2.9078
+Date: 2024-10-28
 Authors@R: c(
     person("Dawid", "Kaledkowski", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-9533-457X")),
@@ -37,7 +37,7 @@ BugReports: https://github.com/insightsengineering/teal/issues
 Depends:
     R (>= 4.0),
     shiny (>= 1.8.1),
-    teal.data (> 0.6.0.9007),
+    teal.data (>= 0.6.0.9014),
     teal.slice (>= 0.5.1.9009)
 Imports:
     checkmate (>= 2.1.0),
@@ -48,7 +48,7 @@ Imports:
     rlang (>= 1.0.0),
     shinyjs,
     stats,
-    teal.code (>= 0.5.0),
+    teal.code (>= 0.5.0.9011),
     teal.logger (>= 0.2.0),
     teal.reporter (>= 0.3.1.9004),
     teal.widgets (>= 0.4.0),
@@ -59,16 +59,17 @@ Suggests:
     mirai (>= 1.1.1),
     MultiAssayExperiment,
     R6,
-    renv (>= 1.0.7),
+    renv (>= 1.0.11),
     rmarkdown (>= 2.23),
-    rvest,
+    rvest (>= 1.0.0),
     shinytest2,
     shinyvalidate,
-    testthat (>= 3.1.5),
+    testthat (>= 3.2.0),
     withr (>= 2.1.0),
     yaml (>= 1.1.0)
 VignetteBuilder:
-    knitr
+    knitr,
+    rmarkdown
 RdMacros:
     lifecycle
 Config/Needs/verdepcheck: rstudio/shiny, insightsengineering/teal.data,

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# teal 0.15.2.9067
+# teal 0.15.2.9078
 
 ### New features
 

diff --git a/R/module_filter_data.R b/R/module_filter_data.R
@@ -56,9 +56,9 @@ srv_filter_data <- function(id, datasets, active_datanames, data_rv, is_active)
     data,
     paste0(
       ".raw_data <- list2env(list(",
-      toString(sprintf("%1$s = %1$s", datanames)),
+      toString(sprintf("%1$s = %1$s", sapply(datanames, as.name))),
       "))\n",
-      "lockEnvironment(.raw_data) #@linksto .raw_data" # this is environment and it is shared by qenvs. CAN'T MODIFY!
+      "lockEnvironment(.raw_data) # @linksto .raw_data" # this is environment and it is shared by qenvs. CAN'T MODIFY!
     )
   )
   filtered_code <- .get_filter_expr(datasets = datasets, datanames = datanames)
@@ -74,7 +74,7 @@ srv_filter_data <- function(id, datasets, active_datanames, data_rv, is_active)
   filter_changed <- reactive({
     req(inherits(datasets(), "FilteredData"))
     new_signature <- c(
-      teal.data::get_code(data_rv()),
+      teal.code::get_code(data_rv()),
       .get_filter_expr(datasets = datasets(), datanames = active_datanames())
     )
     if (!identical(previous_signature(), new_signature)) {

diff --git a/R/module_init_data.R b/R/module_init_data.R
@@ -126,11 +126,18 @@ srv_init_data <- function(id, data) {
   vapply(
     datanames,
     function(dataname, datasets) {
-      hash <- rlang::hash(data[[dataname]])
+      x <- data[[dataname]]
+
+      code <- if (is.function(x) && !is.primitive(x)) {
+        x <- deparse1(x)
+        bquote(rlang::hash(deparse1(.(as.name(dataname)))))
+      } else {
+        bquote(rlang::hash(.(as.name(dataname))))
+      }
       sprintf(
         "stopifnot(%s == %s) # @linksto %s",
-        deparse1(bquote(rlang::hash(.(as.name(dataname))))),
-        deparse1(hash),
+        deparse1(code),
+        deparse1(rlang::hash(x)),
         dataname
       )
     },