Start

External Repositories & Clone Management

The START project integrates with several Active Inference and computational neuroscience repositories to provide comprehensive educational resources and examples. These can be optionally cloned into src/_clones/ for local development and curriculum enhancement.

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: Used as reference material for comprehensive curriculum content and concept validation

RxInferExamples.jl (Bayesian Inference Examples)

• URL: github.com/docxology/RxInferExamples.jl
• Destination: src/_clones/RxInferExamples.jl
• Purpose: Practical examples of Bayesian inference and probabilistic programming
• Integration: Source of hands-on exercises and computational examples for technical curricula

Implementation Resources

ActiveInference.jl (Julia Implementation)

• URL: github.com/docxology/ActiveInference.jl/tree/textbook
• Destination: src/_clones/ActiveInference.jl
• Branch: textbook (educational focus)
• Purpose: Julia-based Active Inference implementation with educational documentation
• Integration: Technical reference and code examples for programming-focused curricula

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: Hands-on programming exercises and computational examples

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: src/repos/clone_repo.py

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 python src/repos/clone_repo.py --url https://github.com/ActiveInferenceInstitute/cognitive --dest src/_clones/cognitive --shallow

# Bayesian inference examples
uv run python src/repos/clone_repo.py --url https://github.com/docxology/RxInferExamples.jl --dest src/_clones/RxInferExamples.jl --shallow

# Julia Active Inference (textbook branch)
uv run python src/repos/clone_repo.py --url https://github.com/docxology/ActiveInference.jl --dest src/_clones/ActiveInference.jl --branch textbook --shallow

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

# Lean theorem proving (LeanNiche)
uv run python src/repos/clone_repo.py --url https://github.com/docxology/lean_niche --dest src/_clones/lean_niche --shallow

# Research manuscript template (Thin Orchestrator)
uv run python src/repos/clone_repo.py --url https://github.com/docxology/template --dest src/_clones/template --shallow

# VERSES AXIOM
uv run python src/repos/clone_repo.py --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.jl

# 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
• Used by domain analysis scripts to validate Active Inference concepts
• Enhances curriculum content with authoritative concept definitions

Code Example Integration

• pymdp and ActiveInference.jl provide working code examples
• Integrated into hands-on curriculum sections
• Used for generating programming exercises and computational labs

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
├── RxInferExamples.jl/       # Bayesian inference examples
│   ├── notebooks/            # Jupyter notebooks with examples
│   └── scripts/              # Standalone example scripts
├── ActiveInference.jl/       # 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

Usage in Curriculum Development

Content Enhancement

• Reference cloned repositories for authoritative Active Inference content
• Adapt examples from implementation repositories for specific domains
• Use knowledge graph structure to ensure comprehensive concept coverage

Technical Integration

• Import code examples into curriculum programming sections
• Generate domain-specific computational exercises
• Provide working implementations for hands-on learning

Quality Assurance

• Validate curriculum content against authoritative sources
• Ensure technical accuracy using reference implementations
• 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.jl
uv run python src/repos/clone_repo.py --url https://github.com/docxology/ActiveInference.jl --dest src/_clones/ActiveInference.jl --branch textbook --shallow

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