Update github workflow

Attempt to resolve that not all R packages should manually be added.

Author: loprtq

.github/workflows/publish.yml

@@ -31,9 +31,15 @@ jobs:
 
       - name: Install R packages
         run: |
-          install.packages(c("rmarkdown", "knitr", "reticulate"))
+          install.packages(c("quarto", "rmarkdown", "knitr", "reticulate"))
         shell: Rscript {0}
 
+      - name: Extract R dependencies from .qmd files
+        run: Rscript package_dependencies.R
+
+      - name: Install detected R dependencies
+        run: Rscript -e 'pak::pkg_install(scan("quarto-packages.txt", character()))'
+
       - name: Install R Dependencies
         uses: r-lib/actions/setup-r-dependencies@v2
 

package_dependencies.R

@@ -0,0 +1,13 @@
+# Get files
+files <- list.files(pattern = "\\.qmd$", recursive = TRUE)
+
+## Read files
+lines <- unlist(lapply(files, readLines))
+
+## Extract package names
+pkgs <- unique(unlist(regmatches(lines, gregexpr("library\\(['\"]?([A-Za-z0-9\\.]+)['\"]?\\)", lines))))
+pkgs <- gsub("library\\(['\"]?|['\"]?\\)", "", pkgs)
+pkgs <- pkgs[pkgs != ""]
+
+# Save package names to a text file
+writeLines(pkgs, "quarto-packages.txt")