UniProt MCP Server

# Changelog All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ## [Unreleased] ### Added - Initial documentation improvements ## [0.1.0] - 2025-10-27 ### Added - Initial public release - MCP server with stdio and HTTP transports - Five core tools for UniProt data access: - `fetch_entry`: Retrieve complete protein entries - `get_sequence`: Fetch protein sequences - `search_uniprot`: Full-text search with advanced filters - `map_ids`: Convert between 200+ database identifier types - `fetch_entry_flatfile`: Access historical entry versions - Two MCP resources: - `uniprot://uniprotkb/{accession}`: Raw entry JSON - `uniprot://help/search`: Search documentation - One MCP prompt: - "Summarize Protein": Generate structured protein summaries - Retry logic with exponential backoff for API resilience - Progress reporting for long-running ID mapping jobs - CORS support for browser-based clients - Prometheus metrics endpoint - Comprehensive test suite with 77% coverage - Type-safe Pydantic models for all responses - Published to PyPI as `uniprot-mcp` - Published to MCP Registry as `io.github.josefdc/uniprot-mcp` ### Infrastructure - CI/CD with GitHub Actions (lint, type-check, test) - Automated PyPI publishing on version tags - Automated MCP Registry updates - Development tooling with uv, ruff, mypy - VCR-based integration tests ### Documentation - Comprehensive README with quickstart and examples - Contributing guidelines - Code of Conduct (Contributor Covenant 2.1) - Security policy - Developer documentation - Registry publishing guide ## Release Process To create a new release: 1. Update version in `pyproject.toml` and `server.json` 2. Update this CHANGELOG with release notes 3. Commit changes: `git commit -m "chore: bump version to X.Y.Z"` 4. Create and push tag: `git tag vX.Y.Z && git push origin vX.Y.Z` 5. GitHub Actions will automatically: - Build and publish to PyPI - Update MCP Registry - Create GitHub Release ## Version History [0.1.0]: https://github.com/josefdc/Uniprot-MCP/releases/tag/v0.1.0 [Unreleased]: https://github.com/josefdc/Uniprot-MCP/compare/v0.1.0...HEAD