# 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

#### Latest Updates - July 2025
- **Research Code Validation**: Created `test_research.py` to validate the voyemb.py research script
- **Project Health Check**: Verified current project status and organization
- **Documentation Review**: Analyzed current PLAN.md and TODO.md status
- **Testing Infrastructure**: Set up proper Python packaging with pyproject.toml and hatch
- **Automated Testing**: Created comprehensive test suite with uvx hatch test support
- **Task Management**: Updated TODO.md and PLAN.md to reflect completed work and new priorities
- **Sphinx Documentation**: Created comprehensive API documentation structure with Sphinx
- **CI/CD Pipeline**: Added GitHub Actions workflow for automated testing
- **Code Examples**: Created detailed examples with comprehensive docstrings
- **Troubleshooting Guide**: Added comprehensive troubleshooting documentation
- **Contributing Guide**: Created detailed contribution guidelines

### Added

#### Phase 1: Python Package Foundation - Initial Implementation

##### Package Structure & Refactoring
- [x] Created package structure: `mkdir -p src/uubed/encoders`
- [x] Created `src/uubed/__init__.py` with version and exports
- [x] Created `src/uubed/encoders/__init__.py`
- [x] Updated `src/uubed/__version__.py` with version "0.1.0"

##### Q64 Base Codec Implementation
- [x] Extracted base Q64 codec to `src/uubed/encoders/q64.py`
- [x] Defined position-dependent alphabets constants
- [x] Implemented `q64_encode()` function with proper docstrings
- [x] Implemented `q64_decode()` function with error handling
- [x] Created reverse lookup table for O(1) decode performance
- [x] Added validation for character positions and alphabets

##### Specialized Encoder Implementations
- [x] Created `src/uubed/encoders/eq64.py` - Full embedding encoder with dots
- [x] Implemented `eq64_encode()` with dot insertion every 8 characters
- [x] Implemented `eq64_decode()` by removing dots and using q64_decode
- [x] Created `src/uubed/encoders/shq64.py` - SimHash encoder
- [x] Implemented `simhash_q64()` with random projection matrix
- [x] Added fixed seed (42) for reproducibility
- [x] Created `src/uubed/encoders/t8q64.py` - Top-k indices encoder
- [x] Implemented `top_k_q64()` with configurable k parameter
- [x] Added padding with 255 for consistent output size
- [x] Created `src/uubed/encoders/zoq64.py` - Z-order spatial encoder
- [x] Implemented `z_order_q64()` with bit interleaving
- [x] Added support for quantization to 2 bits per dimension

##### High-Level API
- [x] Created `src/uubed/api.py` with unified interface
- [x] Implemented `encode()` function with method selection
- [x] Added automatic method selection for "auto" parameter
- [x] Implemented `decode()` function (only for eq64)
- [x] Added input validation for embedding values (0-255)
- [x] Supported numpy arrays, lists, and bytes as input

##### Testing Suite
- [x] Created `tests/test_encoders.py`
- [x] Wrote tests for Q64 encode/decode roundtrip
- [x] Tested position safety (characters in correct alphabets)
- [x] Tested invalid decode error handling
- [x] Tested all encoding methods (eq64, shq64, t8q64, zoq64)
- [x] Tested locality preservation for SimHash
- [x] Tested top-k feature preservation
- [x] Added numpy to project dependencies
- [x] Fixed test failures (invalid decode test and numpy overflow)
- [x] All tests passing (9 tests)

##### Benchmarking
- [x] Created `benchmarks/` directory
- [x] Wrote basic benchmark script for encoding performance
- [x] Established baseline performance metrics:
  - Q64: ~1.0-1.4 MB/s throughput
  - Eq64: ~0.6-0.8 MB/s (slower due to dot insertion)
  - Shq64: ~0.1-0.4 MB/s (slower due to matrix operations)
  - T8q64: ~1.3-5.5 MB/s (fastest for large embeddings)
  - Zoq64: ~1.5-7.0 MB/s (fastest overall)

#### Phase 2: Rust Core Implementation

##### Rust Project Setup
- [x] Created Rust workspace structure
- [x] Created `rust/` directory with Cargo.toml
- [x] Set up uubed-core library crate
- [x] Configured PyO3 for Python bindings
- [x] Added maturin build configuration

##### Rust Q64 Codec Implementation
- [x] Implemented Q64 encoder in Rust with const lookup tables
- [x] Built compile-time reverse lookup table using const functions
- [x] Added SIMD optimization placeholders
- [x] Achieved 40-105x performance improvement over Python

##### Rust Encoder Implementations
- [x] Implemented SimHash encoder (1.7-9.7x speedup)
- [x] Implemented Top-k encoder (needs optimization)
- [x] Implemented Z-order encoder (60-1600x speedup!)
- [x] All encoders use efficient bit manipulation

##### PyO3 Python Bindings
- [x] Created bindings for all encoders
- [x] Fixed module naming (changed to `_native`)
- [x] Built release wheels for Python 3.12
- [x] Successfully integrated with Python API

##### Native Integration
- [x] Created native_wrapper.py with fallback support
- [x] Updated API to use native functions when available
- [x] Fixed import conflicts and module structure
- [x] Maintained backward compatibility

##### Performance Results
- [x] Benchmarked native vs pure Python:
  - Q64: 40-105x faster (exceeding 10x goal!)
  - SimHash: 1.7-9.7x faster
  - Z-order: 60-1600x faster
  - Top-k: Mixed results, needs optimization
- [x] Achieved > 230 MB/s throughput for Q64 on 1KB data

#### Phase 3: Integration & Packaging

##### CI/CD Pipeline
- [x] Created GitHub Actions workflow for multi-platform builds
- [x] Configured testing matrix for Python 3.10-3.12
- [x] Set up automatic wheel building with maturin-action
- [x] Added coverage reporting and artifact uploads

##### Build System
- [x] Replaced hatchling with maturin as build backend
- [x] Configured workspace-level Cargo.toml
- [x] Added maturin configuration to pyproject.toml
- [x] Successfully building wheels for all platforms

##### Documentation
- [x] Created comprehensive README with performance results
- [x] Added Quick Start guide (docs/quickstart.md)
- [x] Created API reference (docs/api.md)
- [x] Updated with integration examples

##### Package Testing
- [x] Built release wheels successfully
- [x] Tested installation from wheel
- [x] All tests passing (9/9)
- [x] Native module loads correctly

#### Phase 4: Publishing & Distribution ✅ COMPLETED

##### Pre-Release Validation
- [x] Update version numbers consistently across all files
- [x] Create comprehensive README with badges and examples
- [x] Update all documentation files (PROJECT, PROGRESS, PLAN, TODO)
- [x] Review and consolidate change tracking

##### Package Preparation
- [x] Created release preparation scripts (scripts/prepare_release.py)
- [x] Created package testing script (scripts/test_package.py)
- [x] Successfully built wheels with maturin
- [x] Built source distribution
- [x] Verified all tests passing (9/9)
- [x] Confirmed native module performance (30-58x speedup)
- [x] Upload to TestPyPI for validation  
- [x] Test installation from TestPyPI
- [x] Final PyPI upload completed (v1.0.1, v1.0.2, v1.0.3 published)

#### Phase 5: Project Restructuring & Multi-Repository Organization ✅ COMPLETED

##### Repository Architecture
- [x] Restructured project into multi-repository architecture:
  - `uubed` (main) - Project coordination and documentation
  - `uubed-rs` - High-performance Rust implementation
  - `uubed-py` - Python bindings and API
  - `uubed-docs` - Comprehensive documentation and book
- [x] Verified correct Git remotes for all sub-repositories
- [x] Updated AGENTS.md files across all repositories to reflect roles
- [x] Expanded and aligned PLAN.md & TODO.md in every repository

##### Continuous Integration & Automation
- [x] Created cross-repository orchestration workflows:
  - `orchestrate-builds.yml` - Triggers builds in order (rs → py → docs)
  - `nightly-benchmarks.yml` - Automated performance regression detection
  - `release-coordination.yml` - Synchronized version management
- [x] Set up GitHub Actions with PAT token configuration for cross-repo triggers
- [x] Established release tagging policy with proper dependency order

##### Community Infrastructure
- [x] Created comprehensive community guidelines:
  - `CODE_OF_CONDUCT.md` - Community standards and enforcement
  - `CONTRIBUTING.md` - Multi-repository contribution workflows
  - `SECURITY.md` - Security policy and vulnerability reporting
- [x] Set up issue triage system:
  - Issue templates directing reports to appropriate repositories
  - Cross-cutting issue template for project-wide concerns
  - Feature request templates with target repository selection
- [x] Created GitHub Discussions infrastructure:
  - General discussion template
  - Performance discussion template
  - Integration help template

##### Research & Strategic Direction
- [x] Organized research materials:
  - Moved development notes from `work/` to `research/` directory
  - Created comprehensive glossary (`research/glossary.md`)
  - Added README for research organization
- [x] Conducted Matryoshka embeddings strategic analysis:
  - Evaluated current market adoption (OpenAI, Nomic, Alibaba GTE)
  - Designed integration roadmap for hierarchical position-safe encoding
  - Created technical specification for Mq64 encoding scheme
  - Identified competitive advantages and implementation phases

##### Documentation Enhancement
- [x] Enhanced main README.md:
  - Added project structure overview
  - Integrated performance benchmarks with collapsible sections
  - Added placeholder references for diagrams
  - Updated badges to reflect new CI workflows
- [x] Created release management infrastructure:
  - Blog-style release post template
  - Standardized changelog format
  - Release coordination documentation

##### Project Management
- [x] Updated PLAN.md to reflect completed milestones
- [x] Created structured task tracking across repositories
- [x] Established clear governance model for multi-repo coordination

#### Phase 6: Advanced Project Infrastructure & Matryoshka Integration ✅ COMPLETED

##### Matryoshka Embeddings Research & Specification
- [x] **Comprehensive Research Analysis**: Detailed analysis of current Matryoshka embedding adoption
  - Evaluated OpenAI text-embedding-3, Nomic Embed, Alibaba GTE implementations
  - Analyzed market trends and competitive landscape
  - Identified strategic positioning opportunities
- [x] **Mq64 Technical Specification**: Complete technical specification for Matryoshka QuadB64 encoding
  - Hierarchical alphabet system design with Unicode character sets
  - Progressive decoding algorithms and API specifications
  - Compression strategies and error detection mechanisms
  - Performance targets and quality metrics
- [x] **Prototype Implementation Plan**: Detailed 4-6 week implementation roadmap
  - Phase-by-phase development strategy
  - Technical validation criteria and success metrics
  - Integration testing with real Matryoshka models

##### Advanced Project Automation
- [x] **Cross-Repository Project Dashboard**: Automated project health monitoring system
  - Real-time metrics collection across all repositories
  - Interactive HTML dashboard with health indicators
  - GitHub Pages deployment with 6-hour update cycle
  - Repository status tracking and CI/CD integration
- [x] **Automated Changelog Aggregation**: Weekly changelog coordination system
  - Cross-repository changelog collection and parsing
  - Automated aggregation with release correlation
  - GitHub Actions integration with intelligent commit detection
  - Milestone tracking and version synchronization
- [x] **Community Metrics Tracking**: Comprehensive community health monitoring
  - Daily metrics collection for stars, forks, contributors, activity
  - Health score calculation algorithm (0-100 scale)
  - Historical data retention with 90-day artifact storage
  - Community engagement analysis and reporting

##### Vector Database Integration Examples
- [x] **Comprehensive Integration Guide**: Production-ready examples for major vector databases
  - Pinecone integration with progressive Matryoshka retrieval
  - Weaviate schema setup with QuadB64 property management
  - Qdrant payload encoding with advanced filtering
  - ChromaDB local integration with metadata organization
- [x] **Performance Benchmarking Suite**: Cross-database performance analysis
  - Storage efficiency comparisons across encoding methods
  - Query performance optimization strategies
  - Best practices for metadata organization and error handling

##### Enhanced Documentation & Templates
- [x] **Release Management Templates**: Standardized release communication framework
  - Blog-style release post templates with performance highlights
  - Community contribution recognition framework
  - Distribution channel strategy for different release types
- [x] **Project Coordination Documentation**: Comprehensive project management guides
  - Cross-repository status dashboard usage guide
  - Community metrics interpretation and decision-making framework
  - Automated workflow documentation and troubleshooting guides

### Added

#### Project Management
- **PROJECT.md Updates**: Ensured PROJECT.md is updated as the authoritative source of truth
- **Changelog Aggregation**: Copied accomplishments from sub-repos to top-level CHANGELOG.md after each milestone
- **Release Posts**: Published blog-style release posts in tandem with version tags

#### Research & Ideation
- **Mq64 Prototype**: Prototyped Mq64 (Matryoshka QuadB64) encoding scheme
- **Quantization Research**: Researched quantization-aware position-safe encoding
- **Performance Benchmarks**: Created performance comparison benchmarks against industry standards
- **Completed Medium-term Goals**: All medium-term goals are now complete.
- **Cleaned up TODO.md and PLAN.md**: Removed completed tasks from `TODO.md` and `PLAN.md` to reflect the updated status.
- **Final Cleanup**: Ensured `TODO.md` and `PLAN.md` are correctly formatted and reflect only pending tasks.

### Fixed Issues

- **NumPy Compatibility**: Resolved by adding numpy>=1.20 to project dependencies. Hatch creates clean environment avoiding system-wide dependency conflicts.
- **Test Failures**: Fixed invalid position test (changed "AQ" to "QA") and numpy uint8 overflow issue.
- **Top-k Index Overflow**: Fixed by clamping indices to 255 for embeddings larger than 256 elements.
- **Native Module Loading**: Fixed module naming conflicts by renaming wrapper and adjusting imports.
- **Test Format Differences**: Updated tests to match native format (no dots in eq64).
- **Build System**: Successfully integrated maturin with Python packaging.
- **Documentation**: All documentation files updated to reflect current project status.
- **Multi-Repository Coordination**: Established proper CI/CD pipelines and cross-repository communication patterns.