tweak graph render to output where Jekyll does

docs/diagrams/index.md

@@ -8,6 +8,7 @@ title: Plankton ML - workflow diagrams
 
 # Workflow Diagrams
 
+
 ![From imaging instrument to cloud storage](as_is/instrument_to_store.svg) - as is
 ![From imaging instrument to cloud storage](could_be/instrument_to_store.svg) - as is
 

scripts/render_diagrams.sh

@@ -3,19 +3,23 @@
 
 # Set the directory path
 DIR="./docs/diagrams/"
+SITE="_site/"
 
 # Loop through each subdirectory
 for sub_dir in "$DIR"*/; do
     # Loop through each dot file in the subdirectory
     for dotfile in "$sub_dir"*.dot; do
         # Get the base name without extension
         base_name=$(basename "$dotfile" .dot)
-
+        dir_path=${sub_dir//docs/docs\/_site}
+        mkdir -p $dir_path
+        output="$dir_path$base_name.svg"
+
         # Render the dot file to SVG
-        dot -Tsvg "$dotfile" -o "$sub_dir$base_name.svg"
+        dot -Tsvg "$dotfile" -o $output
 
         # Print a success message
-        echo "Rendered $dotfile to $sub_dir$base_name.svg"
+        echo "Rendered $dotfile to $output"
     done
 done