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Code Style

Coding standards for Zygotrix.

Python (Backend)​

Formatting​

Use Black for formatting:

black app/

Use isort for imports:

isort app/

Style Guidelines​

# Good: Descriptive names
def calculate_punnett_square(parent1_genotype: str, parent2_genotype: str) -> CrossResult:
    """Calculate offspring genotypes from genetic cross."""
    ...

# Bad: Unclear names
def calc(p1, p2):
    ...

Type Hints​

Always use type hints:

def get_user_by_email(email: str) -> Optional[User]:
    ...

Docstrings​

Use Google-style docstrings:

def run_gwas_analysis(
    snps: List[Dict],
    samples: List[Dict],
    analysis_type: str
) -> Dict[str, Any]:
    """
    Run GWAS analysis on provided data.
    
    Args:
        snps: List of SNP information dictionaries.
        samples: List of sample data dictionaries.
        analysis_type: Type of analysis (linear, logistic).
    
    Returns:
        Dictionary containing analysis results.
    
    Raises:
        HTTPException: If analysis fails.
    """

TypeScript/JavaScript (Frontend)​

Formatting​

Use Prettier:

npx prettier --write src/

Style Guidelines​

// Good: Typed components
interface PunnettSquareProps {
  parent1: string;
  parent2: string;
  onCalculate: (result: CrossResult) => void;
}

const PunnettSquare: React.FC<PunnettSquareProps> = ({ parent1, parent2, onCalculate }) => {
  // ...
};

C++ (Engine)​

Formatting​

Use clang-format:

clang-format -i src/*.cpp

Style Guidelines​

// Good: Clear naming, const correctness
std::vector<CrossResult> calculateCross(
    const std::string& parent1,
    const std::string& parent2
) const;

// Good: RAII for resource management
class FileHandler {
public:
    explicit FileHandler(const std::string& path);
    ~FileHandler();
    // ...
};

File Organization​

Python​

backend/app/
├── routes/          # API endpoints only
├── services/        # Business logic
├── repositories/    # Data access
├── schema/          # Pydantic models
└── core/            # Utilities

TypeScript​

src/
├── components/      # React components
├── hooks/           # Custom hooks
├── services/        # API calls
├── types/           # TypeScript types
└── utils/           # Helper functions