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AI Agent Directives for Morphogenesis Ruby Project

This file contains project guidelines and context that AI coding agents should follow when working on this codebase.

Project Overview

Project Name: Morphogenesis
Language: Ruby
Goal: Explore morphogenesis through cellular automata using object-oriented design principles.

The project is inspired by the following research papers:

CA-NEAT: Evolved Compositional Pattern Producing Networks for Cellular Automata Morphogenesis and Replication
(Amos et al., GECCO 2018)

ARC-NCA: Towards Developmental Solutions to the Abstraction and Reasoning Corpus
(TBD et al., May 2025)

A key concept explored in this project is the French Flag Problem.

Core Principles

  1. Object-Oriented Design
    Use modular classes for cells, grids, patterns, and evolutionary operators.

  2. Extensibility
    Make it easy to add new automaton rules, fitness metrics, and mutation strategies.

  3. Test-Driven Development
    Write comprehensive tests using RSpec following BDD principles.

Directory Structure

.
├── lib/       # Ruby source files
├── spec/      # RSpec test files
├── AGENTS.md  # AI agent directives (this file)
└── README.md  # Project overview and usage instructions

Coding Standards

Style and Formatting

  • Use StandardRB for code formatting and style enforcement.
  • Run bundle exec standardrb to check for style issues.
  • Run bundle exec standardrb --fix to auto-fix issues before committing.
  • Always use double quotes for strings in Ruby code.
  • Add an empty line at the end of each file.
  • Wrap lines in Markdown and plain text files at a maximum width of 100 characters.

Testing with RSpec

  • Use RSpec.describe for top-level example groups.
  • Use let and let! to define test data and memoize it across examples.
  • Use the expect(...).to syntax for assertions.
  • Always use parentheses with eq: expect(...).to eq(value).
  • Use aggregate_failures when grouping multiple related expectations in one example.
  • Run tests with bundle exec rspec.

Git Workflow

  • Commit early and often with clear, descriptive messages.
  • Ensure all style checks and tests pass before committing.

Working with This Codebase

When making changes to this project:

  1. Understand the context by reading relevant tests and implementation files.
  2. Make minimal changes - only modify what's necessary to accomplish the task.
  3. Write tests first or ensure existing tests cover your changes.
  4. Run tests frequently to catch issues early.
  5. Follow the existing code style and patterns used in the project.
  6. Update documentation if your changes affect the public API or behavior.

This file provides guidance for AI coding agents. Keep it updated as project conventions evolve.