Add Jupyter Specification UI Documentation

[stevehanstudio]

Summary

This PR adds documentation for the CompuCell3D Jupyter Specification UI widget to the cc3d_python.rst file. The documentation provides users with a complete guide to using the interactive Jupyter widget for configuring CompuCell3D simulations.

This documentation accompanies the CompuCell3D PR: "Add Interactive Jupyter Widget for CompuCell3D Simulation Configuration".

Project Background

This project was developed through the Advanced Technology Technician Training (AT3) program by Steve Han and Jinyao Huang under the guidance of Dr. T.J. Sego.

Changes Made

Documentation Added

• New section: "CompuCell3D Jupyter Specification UI" in docs/cc3d_python.rst
• Comprehensive coverage of all widget features and functionality
• Two usage methods: Quickstart and Granular Control approaches
• Configuration persistence: JSON save/load functionality with example
• Integration examples: Shows how the widget produces cc3d.core.PyCoreSpecs objects

Key Features Documented

• Interactive tabs for Metadata, Potts Core, Cell Types, and Plugins
• Volume/Surface constraints and Contact/Adhesion energy configuration
• Blob initializer with region controls
• Live visualization and run/pause controls
• JSON configuration format with complete example

Structure

1. Overview - Introduction to the widget and its capabilities
2. Features - Detailed list of supported functionality
3. Quick Start - Simple usage with ui.run_and_visualize()
4. Using the UI in Two Ways - Quickstart and Granular Control methods
5. Quickstart Method - ui.run_and_visualize() details
6. Configuration Persistence - JSON save/load with example format
7. Granular Control Method - Manual setup for advanced users
8. What ui.specs Returns - Specification objects explanation

Work-in-Progress Note

Added appropriate note indicating that some advanced features (Plugins, Initializers, Steppables) are still under development with "not implemented yet" placeholders.

Testing

• Documentation builds successfully with make html
• Viewed and validated docs/_build/html/cc3d_python.html in browser
• All RST formatting validated
• No linter errors introduced

Files Modified

• docs/cc3d_python.rst - Added Jupyter Specification UI section

Files Added

The documentation references 2 images that should be added to docs/images/:

• SpecificationSetupUIwidget.jpg - Widget overview
• cell_sorting_initial_output.png - Simulation visualization

This documentation provides users with what they need to understand and use the Jupyter Specification UI widget effectively.