gnn-pipeline

name	gnn-pipeline
description	Generalized Notation Notation (GNN) processing pipeline for Active Inference generative models. Use when working with GNN files, running the 25-step pipeline, parsing model specifications, generating simulations, or producing visualizations and reports from GNN model definitions.

GNN Pipeline Skill

GNN (Generalized Notation Notation) is a text-based specification language for Active Inference generative models. This repository implements a 25-step processing pipeline (steps 0–24) that transforms GNN specifications into executable simulations, visualizations, analysis reports, and more.

When to Use This Skill

• Parsing or authoring .md GNN model files
• Running the full pipeline or individual steps
• Generating simulation code (PyMDP, RxInfer.jl, JAX, DisCoPy, ActiveInference.jl, PyTorch, NumPyro, Stan, bnlearn)
• Creating visualizations, exports, or reports from GNN models
• Working with Active Inference ontology annotations

Quick Start

# Using just (recommended task runner)
just                     # List recipes
just test                # Fast test suite
just pipeline            # Full 25-step pipeline
just render-health       # Check all 9 renderer backends

# Run full pipeline directly
python src/main.py --target-dir input/gnn_files --verbose

# Run specific steps only
python src/main.py --only-steps "3,5,11,12" --verbose

# Run a single step directly
python src/3_gnn.py --target-dir input/gnn_files --output-dir output --verbose

# Run tests
pytest src/tests/ -v

# Setup environment
uv sync && uv run python src/main.py --target-dir input/gnn_files --verbose

Architecture: Thin Orchestrator Pattern

Every pipeline step follows the same pattern:

src/N_module.py          → Thin orchestrator (<150 lines): CLI args, logging, delegation
src/module/              → Module directory: all domain logic
  ├── __init__.py        → Public API exports
  ├── processor.py       → Core processing logic
  ├── mcp.py             → MCP tool registration (if applicable)
  ├── AGENTS.md          → Module documentation
  ├── README.md          → Usage guide
  ├── SPEC.md            → Module specification
  └── SKILL.md           → This skill format (Claude Code activation)

25-Step Pipeline

Phase	Steps	Purpose
Core (0–9)	Template, Setup, Tests, GNN Parse, Registry, Type Check, Validation, Export, Viz, Advanced Viz	Parse GNN files, validate, export, visualize
Simulation (10–16)	Ontology, Render, Execute, LLM, ML, Audio, Analysis	Generate and run simulations, analyze results
Output (17–24)	Integration, Security, Research, Website, MCP, GUI, Report, Intelligent Analysis	Produce deliverables and reports

GNN File Format

GNN files are Markdown documents with structured sections:

## GNNSection
ActInfPOMDP

## ModelName
My Model

## StateSpaceBlock
A[3,3,type=float]   # Likelihood matrix
B[3,3,3,type=float] # Transition matrix
s[3,1,type=float]   # Hidden state

## Connections
D>s    # D feeds into s (directed)
s-A    # s connects to A (undirected)

## InitialParameterization
A={(0.9,0.05,0.05), (0.05,0.9,0.05), (0.05,0.05,0.9)}

## ActInfOntologyAnnotation
A=LikelihoodMatrix
s=HiddenState

Framework Selection

# Execute specific frameworks
python src/12_execute.py --frameworks "pymdp,jax" --verbose

# Lite preset (PyMDP, JAX, DisCoPy)
python src/12_execute.py --frameworks "lite" --verbose

# All frameworks (default)
python src/12_execute.py --frameworks "all" --verbose

Module Skills

Each src/module/ directory contains its own SKILL.md with module-specific instructions. See src/AGENTS.md for the complete module registry.

Testing

# Full test suite; refresh collect/pass counts before publishing them
uv run --extra dev python -m pytest src/tests/ -q --tb=no \
  --ignore=src/tests/llm/test_llm_ollama.py \
  --ignore=src/tests/llm/test_llm_ollama_integration.py

# Test a specific module
pytest src/tests/gnn/test_gnn_overall.py -v

# With coverage
pytest src/tests/ --cov=src -v

References

• CLAUDE.md — Claude Code project guidance
• AGENTS.md — Master agent scaffolding
• ARCHITECTURE.md — System architecture
• SECURITY.md — Security policy and remediation
• SETUP_GUIDE.md — Environment setup guide
• src/SPEC.md — Source specification
• doc/gnn/README.md — GNN documentation index
• doc/gnn/reference/gnn_syntax.md — GNN syntax reference
• doc/gnn/tutorials/gnn_examples_doc.md — Example GNN models