External Repositories & Clone Management¶

The START project can optionally clone several Active Inference and computational neuroscience repositories into src/_clones/ for local inspection and curriculum development. Cloned content is reference material only: it is not automatically treated as verified evidence, imported into generated curricula, or included in the release bundle.

Repository Ecosystem¶

Core Knowledge Resources¶

cognitive (Active Inference Institute Knowledge Graph)¶

• URL: github.com/ActiveInferenceInstitute/cognitive
• Destination: src/_clones/cognitive
• Purpose: Knowledge graph backing for curriculum development, providing structured Active Inference concepts and relationships
• Integration: Optional reference material; any use in a published artifact must be cited and reviewed

gnn (Generalized Notation Notation)¶

• URL: github.com/ActiveInferenceInstitute/GeneralizedNotationNotation
• Destination: src/_clones/gnn
• Purpose: Generalized Notation Notation (GNN) project by the Active Inference Institute
• Integration: Optional reference material; generated claims require independent source review

cerebrum (CEREBRUM)¶

• URL: github.com/ActiveInferenceInstitute/CEREBRUM
• Destination: src/_clones/cerebrum
• Purpose: CEREBRUM project by the Active Inference Institute
• Integration: Optional reference material; generated claims require independent source review

rxinfer (RxInfer.jl Examples)¶

• URL: github.com/docxology/RxInferExamples.jl
• Destination: src/_clones/rxinfer
• Purpose: Practical examples of Bayesian inference and probabilistic programming
• Integration: Optional source of examples; copied material requires licensing and technical review

Implementation Resources¶

activeinference (ActiveInference.jl)¶

• URL: github.com/docxology/ActiveInference.jl/tree/textbook
• Destination: src/_clones/activeinference
• Branch: textbook (educational focus)
• Purpose: Julia-based Active Inference implementation with educational documentation
• Integration: Optional technical reference; generated claims require independent source review

pymdp (Python Active Inference)¶

• URL: github.com/docxology/pymdp/tree/textbook
• Destination: src/_clones/pymdp
• Branch: textbook (educational focus)
• Purpose: Python implementation of Active Inference and Free Energy Principle
• Integration: Optional implementation reference; generated examples require execution and review

lean_niche (Lean Theorem Proving & Verification)¶

• URL: github.com/docxology/lean_niche
• Destination: src/_clones/lean_niche
• Purpose: Lean environment for formal methods, proofs, and verification
• Integration: Formal verification examples and references for rigorous curricula

template (Thin Orchestrator Research Template)¶

• URL: github.com/docxology/template
• Destination: src/_clones/template
• Purpose: Research manuscript utilities using thin orchestrator pattern
• Integration: Reference for TDD-first pipelines and PDF generation

axiom (VERSES AXIOM)¶

• URL: github.com/VersesTech/axiom
• Destination: src/_clones/axiom
• Purpose: Knowledge operating system components and interfaces
• Integration: Reference architecture and potential data integration

Clone Management¶

Steps

• Select repository (knowledge, implementation, examples)
• If not present, run clone utility
• If present, update via git pull
• Verify destination and integration
• Use in pipeline (concept validation, examples, exercises)

Links

• Clone utility: uv run start-clone (the module is also importable as a Python API)

Interactive (recommended)¶

Use the Repository Manager from the main runner for a guided flow:

./run.sh
# Choose: "Repository Manager"

Automated Cloning¶

Use the integrated clone utility for consistent repository management:

# Core knowledge graph
uv run start-clone --url https://github.com/ActiveInferenceInstitute/cognitive --dest src/_clones/cognitive --shallow

# Generalized Notation Notation (GNN)
uv run start-clone --url https://github.com/ActiveInferenceInstitute/GeneralizedNotationNotation --dest src/_clones/gnn --shallow

# CEREBRUM
uv run start-clone --url https://github.com/ActiveInferenceInstitute/CEREBRUM --dest src/_clones/cerebrum --shallow

# Bayesian inference examples (RxInfer.jl)
uv run start-clone --url https://github.com/docxology/RxInferExamples.jl --dest src/_clones/rxinfer --shallow

# Julia Active Inference (textbook branch)
uv run start-clone --url https://github.com/docxology/ActiveInference.jl --dest src/_clones/activeinference --branch textbook --shallow

# Python Active Inference (textbook branch)  
uv run start-clone --url https://github.com/docxology/pymdp --dest src/_clones/pymdp --branch textbook --shallow

# Lean theorem proving (LeanNiche)
uv run start-clone --url https://github.com/docxology/lean_niche --dest src/_clones/lean_niche --shallow

# Research manuscript template (Thin Orchestrator)
uv run start-clone --url https://github.com/docxology/template --dest src/_clones/template --shallow

# VERSES AXIOM
uv run start-clone --url https://github.com/VersesTech/axiom --dest src/_clones/axiom --shallow

Manual Repository Management¶

# Clone with specific options
git clone --shallow-since="2023-01-01" --branch textbook https://github.com/docxology/ActiveInference.jl src/_clones/activeinference

# Update existing clones
cd src/_clones/cognitive && git pull origin main
cd src/_clones/pymdp && git pull origin textbook

Integration with Curriculum Pipeline¶

Knowledge Graph Integration¶

• cognitive repository provides structured concept relationships
• Available for manual inspection when explicitly cloned
• Does not by itself make generated content authoritative or independently verified

Code Example Integration¶

• pymdp and ActiveInference.jl provide working code examples
• May inform hands-on sections when explicitly selected by a human
• Examples must be tested, attributed, and checked against their license requirements

Educational Resource Enhancement¶

• RxInferExamples.jl provides practical Bayesian inference examples
• Textbook branches focus on educational content and clear explanations
• Examples adapted for domain-specific curriculum applications

Repository Structure After Cloning¶

src/_clones/
├── cognitive/                 # Knowledge graph and concept definitions
│   ├── content/              # Structured Active Inference content
│   └── ontologies/           # Formal concept relationships
├── gnn/                       # Generalized Notation Notation
├── cerebrum/                  # CEREBRUM
├── rxinfer/                   # Bayesian inference examples (RxInfer.jl)
│   ├── notebooks/            # Jupyter notebooks with examples
│   └── scripts/              # Standalone example scripts
├── activeinference/           # Julia Active Inference implementation
│   ├── docs/                 # Educational documentation
│   ├── examples/             # Code examples and tutorials
│   └── src/                  # Core implementation
├── pymdp/                     # Python Active Inference
│   ├── notebooks/            # Educational notebooks
│   ├── examples/             # Example scripts and demonstrations
│   └── pymdp/                # Core Python package
├── lean_niche/                # Lean theorem proving & verification environment
│   ├── src/                  # Lean and Python sources
│   ├── docs/                 # Project docs and verification workflows
│   └── examples/             # Example proofs and verification scripts
├── template/                  # Thin orchestrator research manuscript template
└── axiom/                     # VERSES AXIOM knowledge operating system

Usage in Curriculum Development¶

Content Enhancement¶

• Consult cloned repositories as candidate sources for Active Inference content
• Adapt examples only after checking provenance, license, version, and technical behavior
• Use graph structure as an organizing aid, not as independent validation

Technical Integration¶

• Import code examples only through an explicit, reviewed workflow
• Generate domain-specific exercises only after executing or otherwise validating them
• Provide working implementations with source attribution and version metadata

Quality Assurance¶

• Validate curriculum content against cited, independently reviewed sources
• Check technical accuracy using reference implementations without treating them as proof
• Maintain consistency with Active Inference Institute standards

Verification & Maintenance¶

Verify Clone Integrity¶

# Path exists and is a git repo
test -d src/_clones/cognitive/.git && echo OK

# Show remote and branch
git -C src/_clones/cognitive remote -v
git -C src/_clones/cognitive branch --show-current

Update Clones Safely¶

git -C src/_clones/cognitive fetch --prune
git -C src/_clones/cognitive pull --ff-only origin main

git -C src/_clones/pymdp fetch --prune
git -C src/_clones/pymdp pull --ff-only origin textbook

Re-clone When Needed¶

rm -rf src/_clones/activeinference
uv run start-clone --url https://github.com/docxology/ActiveInference.jl --dest src/_clones/activeinference --branch textbook --shallow