#120 test update switch for relative links

Author: jeffreyad

.github/workflows/link_check.yml

@@ -11,24 +11,31 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up R  # Install R from CRAN
+      - name: Set up R
         uses: r-lib/actions/setup-r@v2
         with:
-          r-version: '4.4.3' # You can specify a different R version if needed
+          r-version: '4.4.3'
 
       - name: Install R packages
         run: |
           Rscript -e 'install.packages("fs")'
         shell: bash
 
-      - name: Switch .qmd to .md
+      - name: Switch .qmd to .md and Update Links
         run: Rscript R/switch.R
         shell: bash
 
+      - name: Verify .qmd Conversion
+        run: |
+          if ls **/*.qmd; then
+            echo "Error: .qmd files still exist after switch.R!"
+            exit 1
+          fi
+          echo "All .qmd files successfully converted to .md."
+
       - name: Link Checker
         uses: lycheeverse/lychee-action@v1.8.0
         with:
           fail: true
-          exclude-paths: "**/*.qmd"
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

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
-file.rename(all_qmd, all_md)
+
+# Rename all `.qmd` files to `.md`
+file.rename(all_qmd, all_md)