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 # AID2E Framework - Installation Guide
 
 ## Overview
 
 The AID2E Framework is a modular project containing the CLI, optimizers, schedulers, and utilities for AI-assisted detector design for the EIC. All modules are organized within the `src/aid2e/` directory structure.
 
 ## Installation
 
 ### Install with Core Dependencies
 
 ```bash
 pip install -e .
 ```
 
 This installs the framework with core dependencies:
 - `pyyaml>=5.4` - YAML configuration parsing
 - `pydantic>=2.0` - Data validation
 - `click>=8.0` - CLI framework
 
 ### Install with Development Tools
 
 ```bash
 pip install -e ".[dev]"
 ```
 
 Installs development tools for testing and code quality:
 - `pytest>=6.0` - Testing framework
 - `pytest-cov>=2.12` - Code coverage
 - `black>=21.0` - Code formatter
 - `flake8>=3.9` - Linter
 - `isort>=5.9` - Import sorting
 - `mypy>=0.910` - Type checking
 
 ### Install with Documentation Tools
 
 ```bash
 pip install -e ".[docs]"
 ```
 
 Installs documentation generation tools:
 - `mkdocs>=1.2` - Documentation generator
 - `mkdocs-material>=7.1` - Material theme
 - `mkdocstrings>=0.18` - API documentation
 - `mkdocstrings-python>=1.0.0` - Python docstring support
 
 ### Install Everything
 
 ```bash
 pip install -e ".[dev,docs]"
 ```
 
 ## Project Structure
 
 ```
 AID2E-framework/
 ├── src/aid2e/                     # Main source package
 │   ├── __init__.py
 │   ├── cli/                       # Command-line interface
 │   │   ├── __init__.py
 │   │   └── aid2e_cli.py
 │   ├── optimizers/                # Optimization algorithms
 │   │   └── __init__.py
 │   ├── schedulers/                # Job schedulers
 │   │   └── __init__.py
 │   └── utilities/                 # Utility modules
 │       ├── __init__.py
 │       ├── configurations/        # Configuration loading
 │       │   ├── __init__.py
 │       │   ├── base_models.py
 │       │   ├── design_config.py
 │       │   ├── problem_config.py
 │       │   ├── optimization_config.py
 │       │   ├── optimization_registry.py
 │       │   └── full_config.py
 │       └── epic_utils/            # EIC physics utilities
 │           ├── __init__.py
 │           ├── epic_design_config.py
 │           ├── epic_env_config.py
 │           └── epic_problem_config.py
 │
 ├── tests/                         # Test suite
 │   ├── __init__.py
 │   ├── conftest.py
 │   ├── test_integration.py
 │   ├── test_cli/
 │   │   ├── test_cli_module.py
 │   │   └── test_cli.py
 │   ├── test_optimizers/
 │   │   └── test_optimizers_module.py
 │   ├── test_schedulers/
 │   │   └── test_schedulers_module.py
 │   ├── test_utilities/
 │   │   ├── test_utilities_module.py
 │   │   ├── test_configurations/
 │   │   │   ├── test_config_file_loading.py
 │   │   │   └── test_configurations_module.py
 │   │   └── test_epic_utils/
 │   │       ├── test_epic_design_config.py
 │   │       └── test_epic_utils_module.py
 │   └── integration/
 │       └── test_integration_example.py
 │
 ├── docs/                          # Documentation (MkDocs)
 │   ├── README.md
 │   ├── docs-guide.md
 │   ├── user-guide/
 │   │   └── overview.md
 │   └── api-reference/
 │       ├── cli.md
 │       ├── optimizers.md
 │       ├── schedulers.md
 │       └── utilities.md
 │
 ├── examples/                      # Configuration examples
 │   ├── basic/
 │   │   ├── design.params
 │   │   ├── full_example.yml
 │   │   ├── optimizer.config
 │   │   ├── problem.config
 │   │   └── slurm.template
 │   └── configurations/
 │       ├── dtlz2_optimization.yml
 │       ├── epic_tracking_optimization.yml
 │       └── README.md
 │
 ├── scripts/                       # Helper scripts
 │   ├── docs-build.sh
 │   ├── docs-deploy-ghpages.sh
 │   └── docs-serve.sh
 │
 ├── .github/
 │   └── instructions/              # Project instructions
 │       └── project-def.instructions.md
 │
 ├── pyproject.toml                 # Project configuration
 ├── pytest.ini                     # Pytest configuration
 ├── mkdocs.yml                     # Documentation configuration
 ├── README.md                      # Project overview
 └── INSTALLATION.md                # This file
 ```
 
 ## Using the AID2E CLI
 
 After installation, the `aid2e` command-line tool is available:
 
 ```bash
 # Display version
 aid2e --version
 
 # Show available commands
 aid2e --help
 
 # Load and display configuration
 aid2e load examples/basic/full_example.yml
 
 # Show configuration details
 aid2e info examples/basic/full_example.yml
 ```
 
 ## Import Examples
 
 ### Using Modules in Python
 
 ```python
 # CLI module
 from aid2e.cli import cli
 
 # Optimizers module
 from aid2e.optimizers import SomeOptimizer
 
 # Schedulers module
 from aid2e.schedulers import SomeScheduler
 
 # Configuration utilities
 from aid2e.utilities.configurations import load_config, FullConfig
 from aid2e.utilities.epic_utils import some_function
 ```
 
 ### Loading Configurations
 
 ```python
 from aid2e.utilities.configurations import load_config
 
 # Load a full configuration
 config = load_config('examples/basic/full_example.yml')
 
 # Access configuration components
 print(config.design)
 print(config.problem)
 print(config.optimization)
 ```
 
 ## Development Workflow
 
 ### Setting Up for Development
 
 ```bash
 # Clone the repository
 git clone https://github.com/aid2e/AID2E-framework.git
 cd AID2E-framework
 
 # Create a virtual environment
 python -m venv .venv
 source .venv/bin/activate  # On Windows: .venv\Scripts\activate
 
 # Install with all development tools
 pip install -e ".[dev,docs]"
 ```
 
 ### Running Tests
 
 ```bash
 # Run all tests
 pytest tests/
 
 # Run with verbose output
 pytest tests/ -v
 
 # Run with coverage report
 pytest tests/ --cov=src/aid2e --cov-report=html
 
 # Run specific test file
 pytest tests/test_cli/test_aid2e_cli.py
 ```
 
 ### Building Documentation Locally
 
 ```bash
 # Build static site
 mkdocs build
 
 # Serve documentation locally (with live reload)
 mkdocs serve
 ```
 
 The documentation will be available at `http://localhost:8000/`
 
 ### Code Quality
 
 ```bash
 # Format code with black
 black src/ tests/
 
 # Check code style with flake8
 flake8 src/ tests/
 
 # Sort imports with isort
 isort src/ tests/
 
 # Type checking with mypy
 mypy src/
 ```
 
 ### Making Changes
 
 1. **Create a branch** for your changes:
    ```bash
    git checkout -b feature/your-feature-name
    ```
 
 2. **Make changes** to files in `src/aid2e/`
 
 3. **Write tests** in the corresponding `tests/` directory
 
 4. **Run tests** to ensure everything works:
    ```bash
    pytest tests/ -v
    ```
 
 5. **Format and lint** your code:
    ```bash
    black src/ tests/
    isort src/ tests/
    flake8 src/ tests/
    ```
 
 6. **Commit and push**:
    ```bash
    git add .
    git commit -m "Description of changes"
    git push origin feature/your-feature-name
    ```
 
 7. **Open a Pull Request** on GitHub

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