Changelog

All notable changes to the PBI project will be documented in this file.

The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

[Unreleased]

Added

• Comprehensive documentation restructuring
• Dedicated Docker guide with troubleshooting
• Local installation guide with step-by-step instructions
• Database overview with schema documentation
• API reference with work-in-progress status
• Command reference/cheatsheet for common operations
• Guides overview for navigation

Changed

• Reorganized documentation structure for clarity
• Moved old documentation to archive for review
• Improved index page with clear status and roadmap

Fixed

• Documentation navigation and discoverability

[0.1.0] - 2024

Added

• Initial database integration from PhageScope
• 9-table star schema with DuckDB
• Snakemake pipeline for data processing
• Basic API with FastAPI
• Docker support for pipeline and API
• Validation reports and data quality checks
• FASTA sequence indexing with pyfaidx

Features

• ~873,000 phage genomes integrated
• ~43 million protein annotations
• Support for 14+ phage databases
• Optimized analytical queries
• REST API endpoints for data access

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Version History Summary

• v0.1.0 (2024): Initial release with database integration and basic API
• Unreleased: Documentation improvements and refinements

Upcoming

See the project status and roadmap for planned features.