feat: Academic-grade package overhaul with scientific precision

- Add explicit float64 dtype and VALIDATION_TOLERANCE constants
- Add bounds validation warning for values >10 SD from mean
- Add infinity handling (converts to NaN)
- Add __all__ exports to calculator.py and reference.py
- Move imports to module top
- Complete README rewrite with:
  - Full methodology section with equations
  - Complete units table for all 45 nutrients
  - All 3 visualizations with images
  - Templates documentation
  - Enhanced validation section
  - API reference
- Enhanced validation notebook with side-by-side comparison
- Complete CHANGELOG with version history

Author: tclark-ufl

CHANGELOG.md

@@ -5,6 +5,121 @@ 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]
+
+## [1.0.13] - 2025-12-17
+
+### Added
+- **Scientific Precision Constants**: Explicit `FLOAT_DTYPE` (numpy.float64) and `VALIDATION_TOLERANCE` (1e-10) constants for reproducibility
+- **Bounds Validation**: New `validate_bounds` parameter warns about nutrient values >10 SD from global mean (catches unit errors like mg vs g)
+- **Infinity Handling**: Division edge cases now properly convert to NaN instead of inf
+- **Module Exports**: Added `__all__` to `calculator.py` and `reference.py` for explicit API definition
+- **Comprehensive README**: Complete rewrite with:
+  - Full methodology section with mathematical equations
+  - Complete units table for all 45 nutrients
+  - All three visualization examples with images
+  - Templates documentation
+  - Enhanced validation section with precision metrics
+  - API reference
+  - Proper academic citations
+
+### Changed
+- All internal calculations now explicitly use `numpy.float64` dtype
+- Improved warning messages for low nutrient coverage (<25%)
+- Enhanced docstrings with more examples and precision notes
+- Validation notebook now includes side-by-side comparison tables and statistical summaries
+
+### Fixed
+- Import statements moved to module top (was inside functions)
+- Type hints now use `Tuple` from typing for Python 3.9 compatibility
+
+### Documentation
+- Added complete units reference for all 45 DII nutrients
+- Enhanced CITATION.cff with full reference metadata
+- Added methodology section explaining z-score, centered percentile, and weighting
+
+## [1.0.12] - 2025-12-16
+
+### Fixed
+- PyPI badge caching issue resolved with cache-busting parameter
+- Combined GitHub Release and PyPI publish into single workflow
+
+## [1.0.11] - 2025-12-16
+
+### Fixed
+- GitHub Actions workflow for trusted PyPI publishing
+
+## [1.0.10] - 2025-12-16
+
+### Fixed
+- BumpVer configuration for CITATION.cff pattern matching
+
+## [1.0.9] - 2025-12-16
+
+### Added
+- Automated version synchronization with BumpVer across pyproject.toml, __init__.py, and CITATION.cff
+
+## [1.0.8] - 2025-12-16
+
+### Fixed
+- Version consistency across all package files
+
+## [1.0.7] - 2025-12-16
+
+### Changed
+- Updated minimum Python version to 3.10
+- Removed Python 3.8 and 3.9 from test matrix
+
+### Fixed
+- CI test failures on older Python versions
+
+## [1.0.6] - 2025-12-16
+
+### Added
+- Trusted publisher configuration for PyPI
+
+## [1.0.5] - 2025-12-15
+
+### Added
+- GitHub Actions workflows for automated testing and PyPI publishing
+- Input validation with TypeError for non-DataFrame inputs
+- Low nutrient coverage warning (<25% of DII nutrients)
+- Numeric coercion for string columns with warnings
+
+### Changed
+- Made matplotlib a required dependency (was optional)
+
+### Fixed
+- Visualization module simplified after matplotlib became required
+
+## [1.0.4] - 2025-12-15
+
+### Fixed
+- Fresh installation test verification
+- Package data inclusion in builds
+
+## [1.0.3] - 2025-12-15
+
+### Changed
+- README updates for PyPI display
+
+## [1.0.2] - 2025-12-15
+
+### Added
+- Visualization functions: `plot_dii_distribution`, `plot_nutrient_contributions`, `plot_dii_categories_pie`
+- Command-line interface (`dii` command)
+- Input templates in `templates/` folder
+
+## [1.0.1] - 2025-12-14
+
+### Added
+- CITATION.cff for proper academic citation
+- DATA_SOURCES.md documenting reference table provenance
+
+### Changed
+- Restructured to src/ layout
+- Added comprehensive docstrings
+
 ## [1.0.0] - 2025-06-01
 
 ### Added
@@ -24,3 +139,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Cross-validated with [dietaryindex R package](https://github.com/jamesjiadazhan/dietaryindex)
 - Tested with 13,580 NHANES participants - perfect match with original calculations
 
+[Unreleased]: https://github.com/strathlab-data/DII/compare/v1.0.13...HEAD
+[1.0.13]: https://github.com/strathlab-data/DII/compare/v1.0.12...v1.0.13
+[1.0.12]: https://github.com/strathlab-data/DII/compare/v1.0.11...v1.0.12
+[1.0.11]: https://github.com/strathlab-data/DII/compare/v1.0.10...v1.0.11
+[1.0.10]: https://github.com/strathlab-data/DII/compare/v1.0.9...v1.0.10
+[1.0.9]: https://github.com/strathlab-data/DII/compare/v1.0.8...v1.0.9
+[1.0.8]: https://github.com/strathlab-data/DII/compare/v1.0.7...v1.0.8
+[1.0.7]: https://github.com/strathlab-data/DII/compare/v1.0.6...v1.0.7
+[1.0.6]: https://github.com/strathlab-data/DII/compare/v1.0.5...v1.0.6
+[1.0.5]: https://github.com/strathlab-data/DII/compare/v1.0.4...v1.0.5
+[1.0.4]: https://github.com/strathlab-data/DII/compare/v1.0.3...v1.0.4
+[1.0.3]: https://github.com/strathlab-data/DII/compare/v1.0.2...v1.0.3
+[1.0.2]: https://github.com/strathlab-data/DII/compare/v1.0.1...v1.0.2
+[1.0.1]: https://github.com/strathlab-data/DII/compare/v1.0.0...v1.0.1
+[1.0.0]: https://github.com/strathlab-data/DII/releases/tag/v1.0.0