add a claude.md file for those of us that like the help

Author: larrybabb

CLAUDE.md

@@ -0,0 +1,67 @@
+# CLAUDE.md
+
+This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
+
+## Project Overview
+
+VRS-Python is the reference implementation of the GA4GH Variation Representation Specification (VRS), providing Python language support for representing genomic variation data consistently and uniquely.
+
+## Development Commands
+
+### Environment Setup
+- `make devready` - Create Python 3.12 venv, install dev dependencies, setup pre-commit hooks
+- `make nbready` - Create Python 3.12 venv, install notebook dependencies for Jupyter usage
+- `source venv/3.12/bin/activate` - Activate the virtual environment (required before development)
+
+### Development Tasks
+- `make test` - Run pytest test suite
+- `make lint` - Static analysis with ruff (auto-fix enabled)
+- `make format` - Code formatting with ruff
+- `pytest tests/path/to/specific_test.py` - Run individual test files
+- `pytest tests/path/to/specific_test.py::test_function_name` - Run specific test functions
+
+### Docker Services
+- `docker-compose up` - Start external dependencies (seqrepo-rest-service on port 5000, UTA database on port 5432)
+- Required for full functionality of VRS translation and normalization features
+
+### Package Installation
+- `pip install -e .[dev,extras,notebooks]` - Install in development mode with all dependencies
+- `pip install -e .[extras]` - Install with core extras (SeqRepo, HGVS tools, etc.)
+
+## Code Architecture
+
+### Core Components
+- **`src/ga4gh/vrs/models.py`** - Pydantic models for VRS objects (Allele, Location, etc.)
+- **`src/ga4gh/vrs/normalize.py`** - Allele normalization algorithms per VRS specification
+- **`src/ga4gh/vrs/dataproxy.py`** - Abstract interface and SeqRepo implementation for sequence data access
+- **`src/ga4gh/vrs/enderef.py`** - Converting between inlined and referenced VRS object forms
+
+### Key Modules
+- **`src/ga4gh/vrs/extras/translator.py`** - Translates between VRS and external formats (HGVS, SPDI, gnomAD, Beacon)
+- **`src/ga4gh/vrs/extras/annotator/`** - VCF annotation tools with VRS identifiers
+- **`src/ga4gh/vrs/utils/hgvs_tools.py`** - HGVS parsing and validation utilities
+- **`src/ga4gh/core/`** - Core GA4GH models and identifier generation
+
+### Testing Structure
+- **`tests/`** - Main test directory with pytest configuration
+- **`tests/validation/`** - VRS specification compliance tests
+- **`tests/extras/`** - Tests for translator and annotator functionality
+- **`tests/cassettes/`** - VCR.py cassettes for external API mocking
+
+## Development Notes
+
+### Dependencies
+- Requires Python >= 3.10 (Python 3.12 required for development)
+- External services: SeqRepo (sequence data), UTA (transcript alignments)
+- Key libraries: Pydantic 2.x, bioutils, HGVS, requests
+
+### Testing Environment
+- Uses pytest with coverage reporting
+- VCR.py for API response caching
+- Test data includes local SeqRepo instance at `tests/data/seqrepo/`
+- Set `SEQREPO_ROOT_DIR=tests/data/seqrepo/latest` for tests
+
+### Pre-commit Configuration
+- Ruff linting and formatting
+- Automatic code quality checks before commits
+- Install with `pre-commit install` (done automatically by `make develop`)