cognitive/project_structure.md

Project Structure

Overview

This document outlines the comprehensive organization of the cognitive modeling framework, detailing the purpose and relationships between different components.

Core Directories

📁 knowledge_base/

Core knowledge organization and theoretical foundations

Cognitive Domain

• cognitive/ - Core cognitive concepts
  • active_inference/ - Active Inference framework
  • belief_updating/ - Belief update mechanisms
  • policy_selection/ - Action selection algorithms
  • free_energy/ - Free Energy calculations
  • predictive_processing/ - Predictive processing theory

Mathematical Domain

• mathematics/ - Mathematical foundations
  • probability/ - Probability theory
  • information_theory/ - Information theoretic concepts
  • optimization/ - Optimization methods
  • dynamical_systems/ - System dynamics

Implementation Domain

• implementations/ - Concrete examples
  • navigation/ - Navigation tasks
  • foraging/ - Resource foraging
  • coordination/ - Multi-agent coordination
  • learning/ - Learning scenarios

📁 src/

Source code implementation

Core Components

• models/ - Core modeling components
  • active_inference/ - Active Inference implementation
    • generative_model.py
    • belief_updater.py
    • policy_selector.py
  • state_estimation/ - State estimation tools
  • optimization/ - Optimization algorithms

Utility Functions

• utils/ - Utility functions
  • visualization/ - Visualization tools
    • state_space.py
    • belief_plots.py
    • network_viz.py
  • validation/ - Validation utilities
    • matrix_validation.py
    • model_checks.py
  • data_processing/ - Data handling

Analysis Tools

• analysis/ - Analysis tools
  • metrics/ - Performance metrics
  • network_analysis/ - Network analysis
  • simulations/ - Simulation frameworks

📁 tests/

Comprehensive test suite

Test Categories

• unit/ - Unit tests
  • test_matrix_ops.py
  • test_belief_updates.py
  • test_policy_selection.py
• integration/ - Integration tests
  • test_agent_environment.py
  • test_learning_scenarios.py
• visualization/ - Visualization tests
  • test_state_plots.py
  • test_network_viz.py

📁 docs/

Project documentation

Documentation Types

• theory/ - Theoretical foundations
  • active_inference.md
  • free_energy.md
  • predictive_processing.md
• implementation/ - Implementation details
  • api_reference.md
  • class_documentation.md
  • function_specifications.md
• examples/ - Usage examples
  • quickstart.md
  • tutorials/
  • case_studies/

📁 templates/

Reusable templates and patterns

Template Categories

• concepts/ - Concept templates
  • cognitive_template.md
  • mathematical_template.md
  • implementation_template.md
• documentation/ - Documentation templates
  • api_template.md
  • example_template.md
  • tutorial_template.md

File Organization

Naming Conventions

• Use lowercase with underscores
• Include category prefixes
• Be descriptive and concise

File Structure

• Include header metadata
• Follow consistent organization
• Maintain clear dependencies

Version Control

• Use meaningful commits
• Group related changes
• Track dependencies

Development Workflow

1. Knowledge Development

1. Create concept documentation
2. Establish relationships
3. Validate theoretical consistency
4. Update dependencies

2. Implementation

1. Write core functionality
2. Add unit tests
3. Create integration tests
4. Document API

3. Validation

1. Run test suite
2. Check coverage
3. Validate relationships
4. Review documentation

4. Deployment

1. Update version
2. Generate documentation
3. Create release notes
4. Deploy changes

Quality Assurance

Documentation Standards

• Complete API documentation
• Clear usage examples
• Comprehensive guides
• Up-to-date references

Testing Requirements

• High test coverage
• Integration testing
• Property-based tests
• Performance benchmarks

Code Quality

• Follow style guide
• Use type hints
• Write clear comments
• Maintain modularity

References

Documentation

• Project style guide
• API documentation
• Testing guide
• Contribution guide

Dependencies

• requirements.txt
• setup.py
• environment.yml
• Dockerfile