use setup-r-dependencies action

.github/workflows/check.yml

@@ -20,34 +20,59 @@ jobs:
     if: github.event_name != 'push'
     name: Audit Dependencies 🕵️‍♂️
     uses: insightsengineering/r.pkg.template/.github/workflows/audit.yaml@main
-  r-cmd:
+  r-cmd-dev:
     if: github.event_name != 'push'
     name: R CMD Check (development) 🧬
-    uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
+    uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@bci_params
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
-      install-deps-from-package-repositories: "R-universe=https://pharmaverse.r-universe.dev/,CRAN=https://cloud.r-project.org/"
       package-subdirectory: package
       additional-env-vars: |
         NOT_CRAN=true
         QUARTO_PROFILE=development
         TLG_CATALOG_PKG_BUILD_RENDER=TRUE
       concurrency-group: development
+      deps-installation-method: setup-r-dependencies
+      lookup-refs: |
+        insightsengineering/random.cdisc.data
+        insightsengineering/formatters
+        insightsengineering/rlistings
+        insightsengineering/rtables
+        insightsengineering/tern
+        insightsengineering/tern.mmrm
+        insightsengineering/tern.rbmi
+        insightsengineering/teal.data
+        insightsengineering/teal.code
+        insightsengineering/teal.logger
+        insightsengineering/teal.reporter
+        insightsengineering/teal.slice
+        insightsengineering/teal.transform
+        insightsengineering/teal.widgets
+        insightsengineering/teal
+        insightsengineering/teal.modules.general
+        insightsengineering/teal.modules.clinical
+      skip-desc-dev: true
+      repository-list: "https://pharmaverse.r-universe.dev/, PPM@latest"
+      cache-version: "dev"
   r-cmd-stable:
     if: github.event_name != 'push'
     name: R CMD Check (stable) 🧬
-    uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@main
+    uses: insightsengineering/r.pkg.template/.github/workflows/build-check-install.yaml@bci_params
     secrets:
       REPO_GITHUB_TOKEN: ${{ secrets.REPO_GITHUB_TOKEN }}
     with:
-      install-deps-from-package-repositories: "R-universe=https://insightsengineering.r-universe.dev/,CRAN=https://cloud.r-project.org/"
       package-subdirectory: package
       additional-env-vars: |
         NOT_CRAN=true
         QUARTO_PROFILE=stable
         TLG_CATALOG_PKG_BUILD_RENDER=TRUE
       concurrency-group: stable
+      deps-installation-method: setup-r-dependencies
+      skip-desc-dev: true
+      skip-desc-branch: true
+      repository-list: "https://insightsengineering.r-universe.dev/, PPM@latest"
+      cache-version: "stable"
   linter:
     if: github.event_name != 'push'
     name: SuperLinter 🦸‍♀️

.github/workflows/docs.yml

@@ -16,6 +16,7 @@ on:
   push:
     branches:
       - main
+      - use_setup_r_deps
   schedule:
     - cron: "17 17 * * 3,6"
 
@@ -61,7 +62,6 @@ jobs:
         uses: actions/cache@v4
         with:
           path: |
-            ~/package/.staged.dependencies
             book/_freeze
           key: ${{ runner.os }}-tlg-catalog-dev
 
@@ -70,14 +70,15 @@ jobs:
           echo "gchat_webhook=${{ secrets.GCHAT_WEBHOOK }}" >> $GITHUB_ENV
         shell: bash
 
-      - name: Run Staged dependencies 🎦
-        uses: insightsengineering/staged-dependencies-action@v1
-        env:
-          GITHUB_PAT: ${{ secrets.REPO_GITHUB_TOKEN }}
+      - name: Setup R dependencies 🎦
+        uses: insightsengineering/setup-r-dependencies@named_repos
         with:
-          path: "./package"
-          enable-check: false
-          direction: upstream
+          github-token: ${{ secrets.REPO_GITHUB_TOKEN }}
+          repository-path: "./package"
+          skip-desc-branch: true
+          skip-desc-dev: true
+          repository-list: "https://pharmaverse.r-universe.dev/, PPM@latest"
+          cache-version: "dev"
 
       - name: Render catalog 🖨
         run: |
@@ -98,7 +99,7 @@ jobs:
         with:
           name: site-development
           path: site.zip
-        
+
       - name: Remove large WebR assets 🧹
         run: |
           packages_path <- sprintf("./book/_site/site_libs/quarto-contrib/shinylive-%s/shinylive/webr/packages", shinylive::assets_version())
@@ -112,28 +113,28 @@ jobs:
               unlink(x, recursive = TRUE)
             }
           }
-          
+
           # refresh the `metadata.rds` file
           metadata_path <- file.path(packages_path, "metadata.rds")
           metadata <- readRDS(metadata_path)
           new_metadata <- metadata[intersect(names(metadata), list.dirs(packages_path, full.names = FALSE))]
-          saveRDS(new_metadata, metadata_path)        
+          saveRDS(new_metadata, metadata_path)
         shell: Rscript {0}
 
-      - name: Publish docs 📔
-        uses: peaceiris/actions-gh-pages@v3
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./book/_site
-          destination_dir: development
+      #- name: Publish docs 📔
+      #  uses: peaceiris/actions-gh-pages@v3
+      #  with:
+      #    github_token: ${{ secrets.GITHUB_TOKEN }}
+      #    publish_dir: ./book/_site
+      #    destination_dir: development
 
-      - name: GChat notification 🔔
-        if: (failure() || cancelled()) && env.gchat_webhook != ''
-        uses: insightsengineering/google-chat-notification@master
-        with:
-          name: ${{ github.event.repository.name }} - development
-          url: ${{ secrets.GCHAT_WEBHOOK }}
-          status: ${{ job.status }}
+      #- name: GChat notification 🔔
+      #  if: (failure() || cancelled()) && env.gchat_webhook != ''
+      #  uses: insightsengineering/google-chat-notification@master
+      #  with:
+      #    name: ${{ github.event.repository.name }} - development
+      #    url: ${{ secrets.GCHAT_WEBHOOK }}
+      #    status: ${{ job.status }}
 
   publish-stable:
     name: Build & Deploy TLGC (stable) 📖
@@ -161,11 +162,15 @@ jobs:
           echo "gchat_webhook=${{ secrets.GCHAT_WEBHOOK }}" >> $GITHUB_ENV
         shell: bash
 
-      - name: Install packages 🎦
-        run: |
-          devtools::install_dev_deps(".", repos = c("https://insightsengineering.r-universe.dev/", "https://cloud.r-project.org/"))
-        shell: Rscript {0}
-        working-directory: package
+      - name: Setup R dependencies 🎦
+        uses: insightsengineering/setup-r-dependencies@named_repos
+        with:
+          github-token: ${{ secrets.REPO_GITHUB_TOKEN }}
+          repository-path: "./package"
+          skip-desc-branch: true
+          skip-desc-dev: true
+          repository-list: "https://insightsengineering.r-universe.dev/, PPM@latest"
+          cache-version: "stable"
 
       - name: Render catalog 🖨
         run: |
@@ -179,7 +184,7 @@ jobs:
           zip -r9 ../../site.zip *
         shell: bash
         working-directory: book/_site
-        
+
       - name: Remove large WebR assets 🧹
         run: |
           packages_path <- sprintf("./book/_site/site_libs/quarto-contrib/shinylive-%s/shinylive/webr/packages", shinylive::assets_version())
@@ -193,36 +198,35 @@ jobs:
               unlink(x, recursive = TRUE)
             }
           }
-          
+
           # refresh the `metadata.rds` file
           metadata_path <- file.path(packages_path, "metadata.rds")
           metadata <- readRDS(metadata_path)
           new_metadata <- metadata[intersect(names(metadata), list.dirs(packages_path, full.names = FALSE))]
-          saveRDS(new_metadata, metadata_path)        
+          saveRDS(new_metadata, metadata_path)
         shell: Rscript {0}
 
-
       - name: Upload docs ⬆
         if: startsWith(github.ref, 'refs/tags/v')
         uses: actions/upload-artifact@v4
         with:
           name: site-stable
           path: site.zip
 
-      - name: Publish docs 📔
-        uses: peaceiris/actions-gh-pages@v3
-        with:
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          publish_dir: ./book/_site
-          destination_dir: stable
+      #- name: Publish docs 📔
+      #  uses: peaceiris/actions-gh-pages@v3
+      #  with:
+      #    github_token: ${{ secrets.GITHUB_TOKEN }}
+      #    publish_dir: ./book/_site
+      #    destination_dir: stable
 
-      - name: GChat notification 🔔
-        if: (failure() || cancelled()) && env.gchat_webhook != ''
-        uses: insightsengineering/google-chat-notification@master
-        with:
-          name: ${{ github.event.repository.name }} - stable
-          url: ${{ secrets.GCHAT_WEBHOOK }}
-          status: ${{ job.status }}
+      #- name: GChat notification 🔔
+      #  if: (failure() || cancelled()) && env.gchat_webhook != ''
+      #  uses: insightsengineering/google-chat-notification@master
+      #  with:
+      #    name: ${{ github.event.repository.name }} - stable
+      #    url: ${{ secrets.GCHAT_WEBHOOK }}
+      #    status: ${{ job.status }}
 
   upload-release-assets:
     name: Upload assets 🔼

book/_extensions/coatless/webr/_extension.yml

@@ -1,8 +1,8 @@
 name: webr
 title: Embedded webr code cells
 author: James Joseph Balamuta
-version: 0.4.2-dev.3
-quarto-required: ">=1.2.198"
+version: 0.4.3-dev.2
+quarto-required: ">=1.4.554"
 contributes:
   filters:
     - webr.lua

book/_extensions/coatless/webr/qwebr-cell-initialization.js

@@ -78,6 +78,10 @@ qwebrInstance.then(
           break;
         case 'setup':
           const activeDiv = document.getElementById(`qwebr-noninteractive-setup-area-${qwebrCounter}`);
+
+          // Store code in history
+          qwebrLogCodeToHistory(cellCode, entry.options);
+
           // Run the code in a non-interactive state with all output thrown away
           await mainWebR.evalRVoid(`${cellCode}`);
           break;