From e6e63dfd200492b56ee50baf66f42abd32111def Mon Sep 17 00:00:00 2001
From: Jo Walsh <jowals@ceh.ac.uk>
Date: Thu, 11 Jul 2024 11:03:48 +0100
Subject: [PATCH] tweak graph render to output where Jekyll does

---
 docs/diagrams/index.md     |  1 +
 scripts/render_diagrams.sh | 10 +++++++---
 2 files changed, 8 insertions(+), 3 deletions(-)

diff --git a/docs/diagrams/index.md b/docs/diagrams/index.md
index 566b09c..a819b0c 100644
--- a/docs/diagrams/index.md
+++ b/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
 
diff --git a/scripts/render_diagrams.sh b/scripts/render_diagrams.sh
index 68093e7..7cb583b 100644
--- a/scripts/render_diagrams.sh
+++ b/scripts/render_diagrams.sh
@@ -3,6 +3,7 @@
 
 # Set the directory path
 DIR="./docs/diagrams/"
+SITE="_site/"
 
 # Loop through each subdirectory
 for sub_dir in "$DIR"*/; do
@@ -10,12 +11,15 @@ for sub_dir in "$DIR"*/; do
     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