Auto-generated model diagrams from spec

[jc-macdonald]

Summary

Generate compartmental flow diagrams automatically from a parsed op_system specification.

Problem

Users currently have no way to visualize the model structure defined by their YAML spec. For presentations, documentation, and debugging, a visual representation of states and transitions is essential. Model diagrams are currently hand-drawn or produced with external tools.

Scope

• Accept a NormalizedRhs (or raw spec dict) and produce a directed graph of states and transitions
• Support at least one output format (e.g., Graphviz DOT, Mermaid markdown, or matplotlib figure)
• Label edges with rate expressions
• Optionally collapse axis-expanded states back to template form for readability
• Handle chain-generated stages (show the chain as a grouped subgraph or linear chain)
• Consider a CLI entry point or utility function: op_system diagram spec.yaml -o model.png

Non-Goals (for now)

• Interactive/web-based visualization
• Real-time state trajectory animation

Related

• Listed as "Proposed" in InsightNet talk slide 4
• Model specification guide: defining compartmental systems #45 — model specification guide (diagrams would complement the guide)