Add automatic dependency setup to Makefile

Use Make's dependency system to automatically install dependencies
before building. This follows standard Make patterns:

- Create .setup_done sentinel file after successful setup
- Make render and run_nb depend on .setup_done
- Running 'make' will now automatically run setup if needed
- Setup only runs once (or after 'make clean')
- Add .setup_done to .gitignore

Now users can just run 'make' and everything works.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: tdhopper

.gitignore

@@ -1,3 +1,4 @@
 web/index.html
 web/img/plots/
-Examples.*.ipynb
+Examples.*.ipynb
+.setup_done

Makefile

@@ -11,31 +11,35 @@ clean:
 	rm -f Examples.*.ipynb
 	rm -f *.pyc
 	rm -f  .Rhistory
+	rm -f .setup_done
 
 travis: render
 
-setup:
+.setup_done:
 	@echo "Setting up development environment..."
 	@echo "1. Installing Python dependencies with uv..."
 	@command -v uv >/dev/null 2>&1 || { echo "Installing uv..."; curl -LsSf https://astral.sh/uv/install.sh | sh; }
 	uv pip install -r requirements.txt
 	@echo "2. Installing R packages..."
 	@./setup_r.sh
 	@echo "✓ Setup complete!"
+	@touch .setup_done
+
+setup: .setup_done
 
 test:
 	python -m pytest tests/
 
 qrender:
 	python render.py "Examples.ipynb"
 
-render: run_nb
+render: .setup_done run_nb
 	python render.py "Examples.$(GIT_COMMIT).ipynb"
 
 s3_upload:
 	s3cmd sync $(OUTPUTDIR)/ s3://$(S3_BUCKET) --acl-public --delete-removed --guess-mime-type --no-mime-magic --no-preserve
 
-run_nb:
+run_nb: .setup_done
 	jupyter nbconvert --to notebook --execute "Examples.ipynb" --output "Examples.$(GIT_COMMIT).ipynb"
 
 dev_environment: setup