Reorganized repo structure, added github workflows

scripts/notebooks_to_readme.sh

@@ -0,0 +1,35 @@
+#!/bin/bash
+
+# Exit on error
+set -e
+
+NOTEBOOKS_DIR="notebooks"
+README_FILE="README.md"
+EXAMPLES_NOTEBOOK="$NOTEBOOKS_DIR/examples.ipynb"
+PICTURES_DIR="pictures/README"
+
+# Check if examples.ipynb exists
+if [ ! -f "$EXAMPLES_NOTEBOOK" ]; then
+  echo "examples.ipynb not found in $NOTEBOOKS_DIR. Exiting."
+  exit 1
+fi
+
+# Create pictures/README directory if it doesn't exist
+mkdir -p "$PICTURES_DIR"
+
+# Export examples.ipynb to markdown, putting images in pictures/README
+jupyter nbconvert --to markdown "$EXAMPLES_NOTEBOOK" --output temp_readme --output-dir "$PICTURES_DIR"
+
+# Move the markdown file to the root as README.md
+mv "$PICTURES_DIR/temp_readme.md" "$README_FILE"
+
+# Move all images to pictures/README (they are already there, but this ensures they stay organized)
+# (No-op if already in place)
+
+# Update image links in README.md to point to pictures/README/
+sed -i '' 's|(temp_readme_files/|(pictures/README/temp_readme_files/|g' "$README_FILE"
+
+# Optionally, clean up any old temp_readme_files in root
+# rm -rf temp_readme_files
+
+echo "README.md has been replaced with the markdown export of $EXAMPLES_NOTEBOOK, and images are in $PICTURES_DIR."