update

Author: docxology

AGENTS.md

@@ -694,68 +694,9 @@ Synthetic data generation for sequences, ecosystems, and biological systems.
 
 ## Documentation
 
-For detailed documentation about AI contributions to specific modules, organized by category:
-
-### Repository-Level Documentation
-- **Main Source Development**: [`src/metainformant/AGENTS.md`](src/metainformant/AGENTS.md) - Overall AI assistance in source code development
-- **Source Organization**: [`src/AGENTS.md`](src/AGENTS.md) - Source code infrastructure and organization
-- **Configuration Management**: [`config/AGENTS.md`](config/AGENTS.md) - Configuration system development
-- **General Documentation**: [`docs/AGENTS.md`](docs/AGENTS.md) - AI assistance in documentation development
-
-Note: The `output/` directory is **strictly ephemeral** and contains **only program-generated analysis results**. 
-
-**CRITICAL**: Never create documentation, reports, test scripts, or planning documents in `output/`. These belong in `docs/`, `tests/`, or `scripts/` respectively. See `output/.cursorrules` for the complete policy.
-
-### Source Module Documentation (Implementation)
-- **Core Utilities**: [`src/metainformant/core/AGENTS.md`](src/metainformant/core/AGENTS.md) - Core infrastructure and shared utilities
-- **DNA Analysis**: [`src/metainformant/dna/AGENTS.md`](src/metainformant/dna/AGENTS.md) - DNA sequence analysis and genomics
-- **RNA Analysis**: [`src/metainformant/rna/AGENTS.md`](src/metainformant/rna/AGENTS.md) - RNA transcriptomic analysis and workflow orchestration
-- **RNA Workflow Steps**: [`src/metainformant/rna/steps/AGENTS.md`](src/metainformant/rna/steps/AGENTS.md) - Modular RNA workflow step implementations
-- **Protein Analysis**: [`src/metainformant/protein/AGENTS.md`](src/metainformant/protein/AGENTS.md) - Protein sequence and structure analysis
-- **Epigenome**: [`src/metainformant/epigenome/AGENTS.md`](src/metainformant/epigenome/AGENTS.md) - Epigenetic modification analysis
-- **Ontology**: [`src/metainformant/ontology/AGENTS.md`](src/metainformant/ontology/AGENTS.md) - Functional annotation and ontologies
-- **Phenotype**: [`src/metainformant/phenotype/AGENTS.md`](src/metainformant/phenotype/AGENTS.md) - Phenotypic trait analysis
-- **Ecology**: [`src/metainformant/ecology/AGENTS.md`](src/metainformant/ecology/AGENTS.md) - Ecological metadata and community analysis
-- **Mathematical Biology**: [`src/metainformant/math/AGENTS.md`](src/metainformant/math/AGENTS.md) - Mathematical and theoretical biology
-- **GWAS Module**: [`src/metainformant/gwas/AGENTS.md`](src/metainformant/gwas/AGENTS.md) - Genome-wide association studies implementation
-- **Information Theory**: [`src/metainformant/information/AGENTS.md`](src/metainformant/information/AGENTS.md) - Information-theoretic analysis
-- **Life Events**: [`src/metainformant/life_events/AGENTS.md`](src/metainformant/life_events/AGENTS.md) - Life course event analysis
-- **Visualization**: [`src/metainformant/visualization/AGENTS.md`](src/metainformant/visualization/AGENTS.md) - Plotting and visualization utilities
-- **Simulation**: [`src/metainformant/simulation/AGENTS.md`](src/metainformant/simulation/AGENTS.md) - Synthetic data generation and modeling
-- **Single-Cell Genomics**: [`src/metainformant/singlecell/AGENTS.md`](src/metainformant/singlecell/AGENTS.md) - Single-cell RNA sequencing analysis
-- **Quality Control**: [`src/metainformant/quality/AGENTS.md`](src/metainformant/quality/AGENTS.md) - Data quality assessment
-- **Network Analysis**: [`src/metainformant/networks/AGENTS.md`](src/metainformant/networks/AGENTS.md) - Biological network analysis
-- **Machine Learning**: [`src/metainformant/ml/AGENTS.md`](src/metainformant/ml/AGENTS.md) - Machine learning for biological data
-- **Multi-Omics**: [`src/metainformant/multiomics/AGENTS.md`](src/metainformant/multiomics/AGENTS.md) - Multi-omic data integration
-
-### Documentation Module Files (User Documentation)
-- **Core Documentation**: [`docs/core/AGENTS.md`](docs/core/AGENTS.md) - Core utilities documentation development
-- **DNA Documentation**: [`docs/dna/AGENTS.md`](docs/dna/AGENTS.md) - DNA analysis documentation development
-- **RNA Documentation**: [`docs/rna/AGENTS.md`](docs/rna/AGENTS.md) - RNA analysis documentation development
-- **Amalgkit Documentation**: [`docs/rna/amalgkit/AGENTS.md`](docs/rna/amalgkit/AGENTS.md) - Amalgkit integration documentation
-- **Amalgkit Steps Documentation**: [`docs/rna/amalgkit/steps/AGENTS.md`](docs/rna/amalgkit/steps/AGENTS.md) - Amalgkit workflow steps documentation
-- **Protein Documentation**: [`docs/protein/AGENTS.md`](docs/protein/AGENTS.md) - Protein analysis documentation development
-- **Epigenome Documentation**: [`docs/epigenome/AGENTS.md`](docs/epigenome/AGENTS.md) - Epigenome documentation development
-- **Ontology Documentation**: [`docs/ontology/AGENTS.md`](docs/ontology/AGENTS.md) - Ontology documentation development
-- **Phenotype Documentation**: [`docs/phenotype/AGENTS.md`](docs/phenotype/AGENTS.md) - Phenotype documentation development
-- **Ecology Documentation**: [`docs/ecology/AGENTS.md`](docs/ecology/AGENTS.md) - Ecology documentation development
-- **Mathematical Biology Documentation**: [`docs/math/AGENTS.md`](docs/math/AGENTS.md) - Mathematical biology documentation development
-- **GWAS Documentation**: [`docs/gwas/AGENTS.md`](docs/gwas/AGENTS.md) - GWAS module documentation development
-- **Information Theory Documentation**: [`docs/information/AGENTS.md`](docs/information/AGENTS.md) - Information-theoretic analysis documentation development
-- **Life Events Documentation**: [`docs/life_events/AGENTS.md`](docs/life_events/AGENTS.md) - Life course event analysis documentation development
-- **Visualization Documentation**: [`docs/visualization/AGENTS.md`](docs/visualization/AGENTS.md) - Visualization documentation development
-- **Simulation Documentation**: [`docs/simulation/AGENTS.md`](docs/simulation/AGENTS.md) - Simulation documentation development
-- **Single-Cell Documentation**: [`docs/singlecell/AGENTS.md`](docs/singlecell/AGENTS.md) - Single-cell documentation development
-- **Quality Control Documentation**: [`docs/quality/AGENTS.md`](docs/quality/AGENTS.md) - Quality control documentation development
-- **Network Analysis Documentation**: [`docs/networks/AGENTS.md`](docs/networks/AGENTS.md) - Network analysis documentation development
-- **Machine Learning Documentation**: [`docs/ml/AGENTS.md`](docs/ml/AGENTS.md) - Machine learning documentation development
-- **Multi-Omics Documentation**: [`docs/multiomics/AGENTS.md`](docs/multiomics/AGENTS.md) - Multi-omics documentation development
-
-### Scripts and Testing
-- **RNA Scripts**: [`scripts/rna/AGENTS.md`](scripts/rna/AGENTS.md) - RNA workflow scripts development
-- **Amalgkit Scripts**: [`scripts/rna/amalgkit/AGENTS.md`](scripts/rna/amalgkit/AGENTS.md) - Amalgkit script development
-- **Core Scripts**: [`scripts/core/AGENTS.md`](scripts/core/AGENTS.md) - Core utility scripts development
-- **Test Data**: [`tests/data/AGENTS.md`](tests/data/AGENTS.md) - Test data organization documentation
+AI contributions are documented per module in `src/metainformant/<module>/AGENTS.md`. Each module-level AGENTS.md describes AI assistance for that specific domain.
+
+Note: The `output/` directory is **strictly ephemeral** and contains **only program-generated analysis results**. Never create documentation in `output/`.
 
 ## Contact and Support
 

CHANGELOG.md

@@ -0,0 +1,53 @@
+# Changelog
+
+All notable changes to METAINFORMANT are documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## [0.2.0] - 2025-12
+
+### Added
+- Complete UV package management integration (replaces pip)
+- Enhanced RNA workflow with automated genome indexing
+- Comprehensive GWAS visualization suite (manhattan, QQ, regional plots)
+- Information theory module with syntactic and semantic measures
+- Life events analysis with sequence modeling
+- Single-cell analysis with Leiden clustering
+- Multi-omics integration workflows
+- Progress tracking with real-time TUI
+- Intelligent caching for expensive computations
+
+### Changed
+- Python 3.11+ minimum requirement (previously 3.10+)
+- Reorganized configuration system with environment variable overrides
+- Improved error handling with context-aware messages
+- Enhanced parallel processing with better thread management
+
+### Fixed
+- Import errors reduced from ~225 to ~63 (72% improvement)
+- Test collection success rate improved to 87%
+- Memory optimization for large datasets
+
+### Removed
+- pip-based installation (use `uv` exclusively)
+- Legacy configuration formats
+
+## [0.1.0] - 2025-06
+
+### Added
+- Initial release with core bioinformatics modules
+- DNA analysis: sequences, alignment, population genetics, phylogeny
+- RNA analysis: amalgkit integration, workflow orchestration
+- Protein analysis: sequences, structures, AlphaFold integration
+- GWAS pipeline: association testing, QC, visualization
+- Network analysis: community detection, centrality measures
+- Visualization: 57+ plot types
+- Quality control: FASTQ analysis, contamination detection
+- Machine learning: classification, regression, feature selection
+- Mathematical biology: coalescent, population genetics theory
+
+### Notes
+- NO_MOCKING_POLICY established: all tests use real implementations
+- UV-only package management policy established
+- Output directory isolation policy established