rettxidentity 0.2.0
Pure Python library for deterministic identity canonicalization and matching in the rettX ecosystem
License: MIT
Requires Python: >=3.10
Keywords: identity, matching, canonicalization, rett-syndrome, rare-disease

# rettxidentity

**Pure Python library for deterministic identity canonicalization and matching in the rettX ecosystem**

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## Overview

`rettxidentity` is a reusable identity canonicalization and matching engine for the rettX ecosystem. It enables deterministic comparison of a caregiver-entered Draft Identity against a Verified Identity extracted from medical reports, producing an explicit Match Decision (PASS, BORDERLINE, FAIL) with confidence scores and explainable reason codes.

The library is intentionally designed with:
- ✅ No database dependencies
- ✅ No network calls
- ✅ No secrets or configuration files
- ✅ Deterministic outputs (same inputs → same outputs)
- ✅ Thread-safe (all dataclasses frozen)
- ✅ Cross-platform (Linux, Windows, macOS)

## Key Features

- **Identity Comparison**: Compare draft vs verified identities with explicit match decisions
- **Cross-Script Matching**: Handle Greek, Georgian, and Cyrillic names seamlessly
- **Name Normalization**: Unicode-aware name normalization with diacritics handling
- **Canonicalization**: Versioned, deterministic identity representation
- **Explainability**: Every decision includes reason codes explaining the logic
- **Performance**: 1000+ comparisons/second on standard hardware

## Installation

```bash
pip install rettxidentity
```

## Quick Start

```python
from rettxidentity import (
    compare_identities, 
    Identity, 
    PersonName, 
    MatchDecision,
    MutationStatus  # New in v0.2.0
)

# Draft identity (from caregiver input with clinical diagnosis)
draft = Identity(
    name=PersonName(given="Maria", surname="Garcia"),
    date_of_birth="1985-03-15",
    country_of_birth="ES",
    mutation_status=MutationStatus.CLINICAL_ONLY,  # Clinical diagnosis
    mutation_key=None
)

# Verified identity (from medical report with genetic test)
verified = Identity(
    name=PersonName(given="María", surname="García López"),
    date_of_birth="1985-03-15",
    country_of_birth="Spain",
    mutation_status=MutationStatus.CONFIRMED,  # Lab-confirmed
    mutation_key="MECP2"
)

# Compare them
result = compare_identities(draft, verified)

# Check the decision
if result.decision == MatchDecision.PASS:
    print("✓ Identities match! Safe to proceed.")
    print(f"Confidence: {result.confidence:.2%}")
    print(f"Reason codes: {[rc.value for rc in result.reason_codes]}")
elif result.decision == MatchDecision.BORDERLINE:
    print("⚠ Requires admin review")
    print(f"Reason codes: {[rc.value for rc in result.reason_codes]}")
else:  # FAIL
    print("✗ Identities do not match. Request correction.")
    print(f"Reason codes: {[rc.value for rc in result.reason_codes]}")
```

### Mutation Status Classification (v0.2.0)

The library supports structured mutation classification:

```python
# Lab-confirmed mutation with genetic coordinates
identity_genetic = Identity(
    name=PersonName(given="Sarah", surname="Thompson"),
    mutation_status=MutationStatus.CONFIRMED,
    mutation_key="NM_004992.3:c.808C>T"
)

# Clinical diagnosis without genetic testing
identity_clinical = Identity(
    name=PersonName(given="Emma", surname="Johnson"),
    mutation_status=MutationStatus.CLINICAL_ONLY,
    mutation_key=None  # No genetic coordinates
)

# No mutation information
identity_no_mutation = Identity(
    name=PersonName(given="John", surname="Doe"),
    mutation_status=MutationStatus.UNKNOWN,  # Default
    mutation_key=None
)

# Hard gate only applies when BOTH identities have CONFIRMED status
# Allows matching between CONFIRMED and CLINICAL_ONLY (identity locking policy)
```

## Documentation

- **[Specification](specs/001-identity-matching-library/spec.md)** - Feature requirements and user scenarios
- **[Implementation Plan](specs/001-identity-matching-library/plan.md)** - Technical architecture and design decisions
- **[Quickstart Guide](specs/001-identity-matching-library/quickstart.md)** - Usage examples and patterns
- **[API Contract](specs/001-identity-matching-library/contracts/api.md)** - Complete API reference
- **[Matching Rules](specs/001-identity-matching-library/contracts/matching-rules.md)** - Decision logic details

## Development

### Setup

```bash
# Clone repository
git clone https://github.com/rettx/rettxidentity.git
cd rettxidentity

# Install with dev dependencies
pip install -e ".[dev]"
```

### Running Tests

```bash
# Run all tests with coverage (minimum 80% required)
pytest

# Run specific test categories
pytest -m unit              # Unit tests only
pytest -m contract          # Contract tests only
pytest -m integration       # Integration tests only

# Generate detailed coverage report
pytest --cov-report=html
```

### Code Quality

```bash
# Format code
ruff format src tests

# Lint with auto-fix
ruff check --fix src tests

# Type check
mypy src/rettxidentity --strict
```

### CI/CD

The project uses GitHub Actions for continuous integration and deployment:

- **CI Workflow**: Runs on every push and PR (linting, type checking, tests)
- **Publish Workflow**: Automatically publishes to PyPI when a release is created

See [.github/workflows/README.md](.github/workflows/README.md) for detailed CI/CD documentation.

## Design Principles

This library follows the [rettX Identity Constitution](specs/001-identity-matching-library/plan.md#constitution-check):

1. **Identity ≠ Identifier** - Never generates rettxid
2. **Verified Identity Only** - Canonical output from verified identity only
3. **Determinism** - Same inputs → same outputs (versioned)
4. **Explainability** - Structured reason codes in all outputs
5. **Script-Agnostic** - Native scripts first-class; transliteration for comparison
6. **DOB + Mutation Anchors** - Hard gates with clear rules
7. **No Lock** - Declares eligibility, never locks
8. **Borderline First-Class** - Preferred over FAIL in ambiguity
9. **Purity & Statelessness** - No DB, network, filesystem
10. **Minimal Surface Area** - Focused API
11. **Versioned Canonicalization** - All outputs include version
12. **Privacy by Construction** - No logging by default

## License

MIT License - see [LICENSE](LICENSE) file for details.

## Contributing

Contributions are welcome! Please read our contributing guidelines and code of conduct.

## Support

For questions and support, please open an issue on GitHub