Changelog
=========

All notable changes to IDEAL-GENOM will be documented in this file.

Version 1.0.0 (Current)
-----------------------

**Released:** January 2026

**Major Changes:**

- Complete redesign of configuration system from JSON to YAML
- Unified pipeline framework with step-based execution
- New command-line interface with subcommands (run, validate, template)
- Package renamed from ideal-genom-qc to ideal-genom

**New Features:**

- **GWAS Pipeline**: Complete GWAS workflow with GLM and GLMM support
- **VCF Processing**: Post-imputation VCF processing and PLINK conversion
- **Population Analysis**: Enhanced population structure tools (PCA, UMAP, t-SNE, Fst)
- **Pipeline Executor**: Automated pipeline execution with dependency management
- **Configuration Validation**: Built-in YAML configuration validation
- **Variable Substitution**: Support for dynamic variable references in configurations

**Improvements:**

- Enhanced error handling and logging
- Improved memory management for large datasets
- Parallel processing support across all modules
- Better documentation with comprehensive examples
- Rich reporting and visualization capabilities
- Docker support with pre-configured environment

**API Changes:**

- YAML configuration replaces JSON configuration files
- New Python API with consistent class interfaces
- Module reorganization: ``ideal_genom.qc``, ``ideal_genom.gwas``, ``ideal_genom.post_imputation``
- Simplified class initialization patterns

**Bug Fixes:**

- Fixed kinship calculation memory issues
- Improved VCF parsing for large files
- Corrected reference genome download paths
- Fixed PCA projection edge cases

**Dependencies:**

- Python 3.11+ required (up from 3.8+)
- PLINK 2.0 now required alongside PLINK 1.9
- GCTA 1.95.0 or higher
- BCFtools 1.10+ for VCF processing

Version 0.1.0
-------------

**Released:** 2024

**Initial Release:**

- Basic QC pipeline (Sample QC, Ancestry QC, Variant QC)
- JSON-based configuration
- Command-line interface for basic operations
- Integration with PLINK 1.9
- 1000 Genomes reference panel support
- Basic UMAP visualization

Migration Guide (0.1.0 → 0.2.0)
--------------------------------

**Configuration Files:**

Old (JSON)::

    {
        "sample_qc": {
            "mind": 0.1,
            "maf": 0.01
        }
    }

New (YAML)::

    pipeline:
      steps:
        - name: "sample_qc"
          module: "ideal_genom.qc.sample_qc"
          class: "SampleQC"
          execute_params:
            mind: 0.1
            maf: 0.01

**Command-Line Interface:**

Old::

    python -m ideal_genom_qc \
        --path_params parameters.json \
        --file_folders paths.json \
        --steps steps.json

New::

    ideal-genom run --config pipeline.yaml

**Python API:**

Old::

    from ideal_genom_qc import SampleQC

    qc = SampleQC(...)
    qc.run(...)

New::

    from ideal_genom.qc.sample_qc import SampleQC

    qc = SampleQC(...)
    qc.execute_sample_qc_pipeline(...)

For detailed migration instructions, see the :doc:`getting_started` guide.

Contributing
------------

We welcome contributions! Please see :doc:`contributing` for guidelines.

For bug reports and feature requests, please use our `GitHub Issues <https://github.com/cge-tubingens/ideal-genom-qc/issues>`_.