Complete Package Restructuring to Modern Python Standards#1
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- Update project metadata (keywords, classifiers for PyPI) - Reorganize sections in canonical PEP 621 order - Update version to 1.0.0 - Add comprehensive package metadata
- Move all Ruff settings from ruff.toml to pyproject.toml - Delete ruff.toml file - Add C901 complexity rule to ignore list
- Add strict MyPy configuration to pyproject.toml - Configure module-level overrides for gradual migration - Enable disallow_untyped_defs with override exceptions - Add mypy to dev dependencies
- Move all code to src/taxembed/ package - Create logical modules: models, training, data, visualization, analysis, validation, builders, cli - Add proper __init__.py files for clean imports - Organize code into maintainable structure
- Delete train_small.py, train_hierarchical.py - Remove analyze_hierarchy*.py files - Clean up build_transitive_closure.py and other root scripts - All functionality now in src/taxembed/ package
- Remove docs/archive/ directory (30+ redundant files) - Remove obsolete documentation files - Keep README.md, CONTRIBUTING.md, docs/user-guide.md, docs/theory.md - Consolidate scattered docs into clean structure
- Preserve original poincare-embeddings code for reference - Add _vendor/README.md explaining provenance
- Train command uses python -m taxembed.cli.train - Visualize command uses python -m taxembed.visualization.umap_viz - Remove non-existent script path references - All CLI commands now properly use package structure Note: Changes included in previous structure commit
- Fix path resolution to find project root (3 levels up) - Add auto-extraction of .dmp files via ensure_taxdump() - Remove wrong data directory path calculation - Ensure visualization finds taxonomy files Note: Changes included in previous structure commit
- Add Development section to README.md with tool quickstart - Expand CONTRIBUTING.md with detailed Ruff, MyPy, Pytest guides - Add Development section to docs/user-guide.md - Add docs/theory.md with mathematical background - Include code quality workflow examples
- Add .mypy_cache/ for MyPy type checker - Use /data/ to ignore only root directory, not src/taxembed/data/ - Remove obsolete entries (wordnet, tox, old venv names) - Simplify and organize ignore patterns
- Delete Makefile in favor of pyproject.toml scripts - Remove requirements.txt (using pyproject.toml) - Remove QUICKSTART.md (info now in README.md) - Clean up remaining hype/ Cython files - Remove scripts/cleanup and regenerate scripts - All commands now via uv and pyproject.toml
- Add examples/ directory with demonstration scripts - Add comprehensive test suite (conftest, test_models, test_training, test_data, test_validation) - Add CODE_OF_CONDUCT.md - Update uv.lock with latest dependencies - Complete package restructuring
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Complete Package Restructuring to Modern Python Standards
🎯 Overview
Transform
taxembedfrom a research codebase with scattered scripts into a production-ready Python package following modern best practices (PEP 517, 518, 621).🚀 Key Changes
Package Structure
src/taxembed/with logical module organization_vendor/for referenceConfiguration & Tooling
pyproject.tomlwith all settings (Ruff, MyPy, Pytest)Makefile,ruff.toml,requirements.txtBug Fixes
Documentation
Cleanup
.gitignorewith proper exclusions✅ Quality Assurance
All quality checks passing:
🔄 Migration Impact
BREAKING CHANGE: Complete restructure - no backwards compatibility.
Before: 40+ scattered scripts in root
After: Clean
src/taxembed/package structureCLI interface unchanged - all commands work the same way:
Note: Project was not in production use.
📦 What This Enables
Result: A production-ready, professionally structured Python package ready for future development.