AGENTS.md@docs/pymdp git:20260907.ae194c2A

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# PyMDP Framework Documentation Agents

## Overview

This document provides agent scaffolding for the PyMDP Framework documentation subsystem. The documentation is organized into specialized agent modules, each responsible for specific aspects of the PyMDP Framework system.

**Status**: ✅ Documentation  
**Version**: 1.0  

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## Purpose

Documentation for the pymdp 1.0.0 (JAX-first) active inference framework
integration with GNN. pymdp 1.0.0 replaces the pre-1.0 NumPy Agent surface with
a JAX/equinox Agent that takes batched `list[jax.Array]` models and requires
explicit PRNG key / empirical-prior carry-through.

## Documentation Organization

The PyMDP Framework documentation system is part of the broader GNN (Generalized Notation Notation) pipeline and ecosystem.

### Related Systems
- **Main Documentation**: [docs/README.md](../README.md)
- **GNN Documentation**: [gnn/AGENTS.md](../gnn/AGENTS.md)
- **Pipeline Reference**: [src/gnn/AGENTS.md](../../src/gnn/AGENTS.md)
- **Active Inference**: [activeinference.org](https://activeinference.org)

## Subsystems

- **gnn_pymdp.md**: GNN → PyMDP integration contract
- **pymdp_1_0_0_alignment_matrix.md**: upstream 1.0.0 vs local wiring
- **pymdp_performance_guide.md**: performance notes and **Systematic Scaling Studies**
- **run_pymdp_gnn_scaling_analysis.py**: automated study orchestrator agent
- **pymdp_advanced_tutorials.md**: supplementary notes
- **pymdp_pomdp/**: reference scripts and README

**Last Updated**: 2026-04-14

## Quick Navigation

- **Get Started**: See [README.md](README.md)
- **Pipeline Overview**: [src/gnn/AGENTS.md](../../src/gnn/AGENTS.md)
- **Full Documentation Index**: [docs/README.md](../README.md)

## Documentation Standards

All documentation in this subsystem follows the professional standards established in the GNN documentation system:

- **Clarity**: Concrete examples, technical accuracy
- **Functionality**: Shows what code actually does
- **Evidence-Based**: Specific metrics and real examples
- **Professional**: Clear structure, no promotional language

## Integration

This documentation integrates with the 25-step GNN processing pipeline:

1. **Pipeline Initialization** (Step 0): Template setup
2. **Environment Setup** (Step 1): Dependency installation
3. **Testing** (Step 2): Quality assurance
4. **Core Processing** (Steps 3-9): GNN parsing and validation
5. **Simulation** (Steps 10-16): Model execution and analysis
6. **Integration** (Steps 17-24): Output and reporting

See [src/gnn/AGENTS.md](../../src/gnn/AGENTS.md) for complete pipeline documentation.

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**Status**: ✅ Production Ready  
**Compliance**: Professional documentation standards  
**Maintenance**: Regular updates with new features