Merge branch 'main' into 112_documentation_derivation_error_in_safety_specsxlsx

Author: Fanny-Gautier

.github/PULL_REQUEST_TEMPLATE.md

@@ -10,6 +10,8 @@ Before you submit your pull request, take a look at the following checklist. Man
 - [ ] **Impact on Examples:** If your updates impact any examples, review locally for warnings or errors in the impacted example pages.
 - [ ] **Merge Conflicts:** Developers should address any merge conflicts and merge upon successful review.
 - [ ] **New Packages:** If new packages were used, ensure they are included in the `DESCRIPTION` file's `Imports` section.
+- [ ] **Landing Pages:** If new packages were added or removed, update the package tables in the [main landing page](../index.qmd) and the relevant section landing page(s) (`sdtm/index.qmd`, `adam/index.qmd`, `tlg/index.qmd`).
 - [ ] **Updated Examples:** If you added or updated an example, ensure it runs on the latest CRAN release versions of all packages used.
 - [ ] **Testing Instructions:** Provide instructions on how to test the code if necessary. 
 
+By default, a temporary website with the content of the PR is created. To avoid this add `[skip website]` to the title of the PR.

.github/workflows/docs.yaml

@@ -26,6 +26,7 @@ on:
 jobs:
   build-deploy:
     name: Build & Deploy Website
+    if: "github.event_name != 'pull_request' || !contains(github.event.pull_request.title, '[skip website]')"
     runs-on: ubuntu-latest
     steps:
       - name: Check out repository
@@ -40,6 +41,9 @@ jobs:
       - name: Set up Quarto
         uses: quarto-dev/quarto-actions/setup@v2
 
+      - name: Install Jupyter
+        run: python3 -m pip install jupyter
+
       - name: Setup R
         uses: r-lib/actions/setup-r@v2
 
@@ -51,32 +55,30 @@ jobs:
         with:
           to: html
 
-      # temporary!
-      # remove this step if closed (& relleased): https://github.com/quarto-ext/shinylive/issues/59
-      - name: Remove large WebR assets 🧹
-        run: |
-          packages_path <- sprintf("./_site/site_libs/quarto-contrib/shinylive-%s/shinylive/webr/packages", shinylive::assets_version())
-
-          # remove the dirs with size > 100 MB
-          for (x in list.dirs(packages_path)) {
-            x_files <- file.info(list.files(x, full.names = TRUE))
-            if (any(x_files$size > 100 * 1024^2)) {
-              print(x)
-              print(x_files)
-              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)
-        shell: Rscript {0}
-
       - name: Publish docs
+        # runs when main branch is updated, or when a PR is merged into main
         if: github.ref == 'refs/heads/main'
         uses: peaceiris/actions-gh-pages@v3
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}
           publish_dir: ./_site
+
+      - name: Publish PR docs in a subdirectory
+        # runs when a PR is opened or updated, but not when merged into main
+        if: github.event_name == 'pull_request' && github.base_ref == 'main'
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./_site
+          destination_dir: ${{ github.head_ref }}
+
+      - name: Create comment
+        # runs when a PR is opened or updated, but not when merged into main
+        if: github.event_name == 'pull_request' && github.base_ref == 'main'
+        uses: marocchino/sticky-pull-request-comment@v2
+        with:
+          header: "Documentation Website"
+          message: |
+            The website is available at https://${{ github.repository_owner }}.github.io/${{ github.event.repository.name }}/${{ github.head_ref }}.
+        env:
+          GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/link_check.yml

@@ -21,10 +21,6 @@ jobs:
           Rscript -e 'install.packages("fs")'
         shell: bash
 
-      - name: Switch .qmd to .md
-        run: Rscript R/switch.R
-        shell: bash
-
       - name: Link Checker
         uses: lycheeverse/lychee-action@v1.8.0
         with:

.github/workflows/remove_pr_website.yml

@@ -0,0 +1,65 @@
+name: Remove PR website
+
+on:
+  workflow_call:
+    secrets:
+      GITHUB_PAT:
+        required: false
+        description: GitHub API access token, which might be needed for downstream ops or rendering.
+  pull_request:
+    types:
+      - closed
+    branches:
+      - main
+
+permissions:
+  contents: write
+
+jobs:
+  delete-subfolder:
+    runs-on: ubuntu-latest
+    env:
+      BRANCH: ${{ github.event.pull_request.head.ref }}
+    steps:
+      - name: Checkout repository (default branch)
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          persist-credentials: true
+
+      - name: Ensure gh-pages exists and check it out
+        run: |
+          set -euo pipefail
+          if git ls-remote --heads origin gh-pages | grep -q 'refs/heads/gh-pages'; then
+            git fetch origin gh-pages:gh-pages
+            git checkout gh-pages
+          else
+            echo "gh-pages branch not found. Nothing to do."
+            exit 0
+          fi
+        shell: bash
+
+      - name: Remove subfolder named after merged branch (if present)
+        run: |
+          set -euo pipefail
+          SUBDIR="${BRANCH}"
+          echo "SUBDIR: ${SUBDIR}"
+          if [ -z "$SUBDIR" ]; then
+            echo "Branch name empty. Nothing to do."
+            exit 0
+          fi
+
+          if [ -d "$SUBDIR" ]; then
+            git rm -r --ignore-unmatch -- "$SUBDIR"
+            if [ -n "$(git status --porcelain)" ]; then
+              git config user.name "github-actions[bot]"
+              git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+              git commit -m "ci: remove gh-pages subfolder for merged branch ${BRANCH}"
+              git push origin gh-pages
+            else
+              echo "No changes to commit after removal."
+            fi
+          else
+            echo "Subfolder '$SUBDIR' does not exist on gh-pages. Nothing to do."
+          fi
+        shell: bash

DESCRIPTION

@@ -16,6 +16,7 @@ Authors@R:
     person("Aksel", "Thomsen", , "oath@novonordisk.com", role = "aut"),
     person("Shiyu", "Chen", , "shiyu.chen@atorusresearch.com", role = "aut"),
     person("Rammprasad", "Ganapathy", , "rammprasad.ganapathy@gene.com", role = "aut")
+    person("Alanah", "Jonas", , "alanah.x.jonas@gsk.com", role = "aut"),
 Description: This is not a package, but we just use this file to declare
     the dependencies of the site.
 URL: https://github.com/pharmaverse/examples
@@ -26,6 +27,7 @@ Imports:
     cards,
     dplyr,
     filters,
+    forcats,
     gtsummary,
     lubridate,
     labelled,
@@ -38,7 +40,6 @@ Imports:
     pharmaverseadam,
     pkglite,
     reactable,
-    reactablefmtr,
     rtables,
     rtables.officer,
     rlistings,
@@ -50,6 +51,7 @@ Imports:
     teal.modules.clinical,
     teal.modules.general,
     tern,
+    tfrmt,
     tidyr,
     xportr,
     logr,
@@ -58,6 +60,8 @@ Imports:
 Suggests:
     knitr,
     rmarkdown
+Remotes:
+    shinylive=posit-dev/r-shinylive
 Encoding: UTF-8
 Language: en-US
 

R/switch.R

@@ -1,51 +1,57 @@
-#' fixes link-check problem
-#' Finds whether any files use the string: "(.mailto:" for linking email adresses
-#' then just replaces with: "(mailto:" as is markdown standard
+#' Fixes link-check problem
+#' - Finds files that use the string "(.mailto:" and corrects to "(mailto:"
+#' - Updates links to `.qmd` files to point to `.md` files.
 #'
 #' @param file_list vector of filenames
 #'
-#' @return messages only. side effect is: changes files.
+#' @return messages. Side effect: modifies files.
 modify_files <- function(file_list) {
-  # Create an empty vector to store the file names that contain the string
+  # Create an empty vector to store file names that need modifications
   matching_files <- c()
 
-  # Iterate over each file in the directory
+  # Iterate over each file to check for issues
   for (file in file_list) {
     # Read the contents of the file
     file_contents <- readLines(file)
 
-    # Check if the file contains the string "(.mailto:"
-    if (any(grepl("\\(\\.mailto:", file_contents))) {
+    # Check if the file contains the string "(.mailto:" OR references to `.qmd` files
+    if (any(grepl("\\(\\.mailto:", file_contents)) || any(grepl("\\.qmd\\)", file_contents))) {
       # Add the file name to the vector
       matching_files <- c(matching_files, file)
     }
   }
 
-  # Iterate over the matching files
+  # Iterate over the matching files to apply fixes
   for (file in matching_files) {
     # Read the contents of the file
     file_contents <- readLines(file)
 
-    # Remove the "." from each line that contains the string
+    # Fix email links
     modified_contents <- gsub("\\(\\.mailto:", "(mailto:", file_contents)
 
+    # Update links to `.qmd` files to point to `.md` files
+    # Matches patterns like `[text](filename.qmd)` and replaces `.qmd` with `.md`
+    modified_contents <- gsub("\\.qmd\\)", ".md)", modified_contents)
+
     # Write the modified contents back to the file
     writeLines(modified_contents, file)
 
-    # Print a message indicating the modification has been made
+    # Print a message indicating what modifications have been made
     message("Modified file:", file, "\n")
   }
 
-  # Print the list of matching files
+  # Print a list of matching files that were modified
   message("Matching files:", matching_files, "\n")
 }
 
-# get all qmd files
+# Get all `.qmd` files
 all_qmd <- list.files(full.names = FALSE, all.files = FALSE, pattern = ".qmd$", recursive = TRUE)
 
-# modify if needed the link to email problem for link checker
+# Modify files to fix email links and update `.qmd` references
 modify_files(all_qmd)
-# get filenames ending with .md
+
+# Generate a list of `.md` filenames that will replace `.qmd` files
 all_md <- gsub(".qmd$", ".md", all_qmd)
-# rename all files
+
+# Rename all `.qmd` files to `.md`
 file.rename(all_qmd, all_md)

_extensions/quarto-ext/shinylive/shinylive.lua

@@ -458,6 +458,13 @@ return {
         el.attr.classes = pandoc.List()
         el.attr.classes:insert("shinylive-r")
       end
+      
+      el.text = 
+        "#| '!! shinylive warning !!': |\n"..
+        "#|   shinylive does not work in self-contained HTML documents.\n" .. 
+        "#|   Please set `embed-resources: false` in your metadata.\n" ..
+        el.text
+      
       return el
     end
   }

_quarto.yml

@@ -65,6 +65,17 @@ filters:
 
 format:
   html:
+    include-in-header:
+      text: |
+        <script type="text/javascript">
+        function googleTranslateElementInit() {
+          new google.translate.TranslateElement({pageLanguage: 'en', includedLanguages: 'zh-CN,fr,es,ja,hi'}, 'google_translate_element');
+        }
+        </script>
+        <script type="text/javascript" src="//translate.google.com/translate_a/element.js?cb=googleTranslateElementInit"></script>
+    include-before-body:
+      text: |
+        <div id="google_translate_element"></div>
     search: true
     theme:
       light:

adam/adae.qmd

@@ -1,6 +1,6 @@
 ---
 title: "ADAE"
-order: 7
+order: 3
 ---
 
 ```{r setup script, include=FALSE, purl=FALSE}