feat(jump_smiles): migrate to uv and add idempotency testing #93
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- Convert pyproject.toml from Poetry to PEP 621 standard format - Switch build backend from poetry-core to hatchling - Add explicit Python version constraint (>=3.11,<3.13) for RDKit compatibility - Add CLI entry point via [project.scripts] - Create main() function for proper Fire CLI integration - Add comprehensive class docstrings for standardization methods - Suppress RDKit 2023.9.5 deprecation warnings in pytest.ini - Update README with uv installation and usage patterns - Add uv.lock for reproducible dependency resolution - Format code with ruff - Bump version to 0.0.2 Maintains strict RDKit 2023.9.5 pinning for JUMP dataset reproducibility. 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
Add comprehensive idempotency testing infrastructure to verify that standardizing already-standardized SMILES produces identical results. This ensures the standardization process is deterministic and stable. Changes: - Add test/test_idempotency.py with parameterized tests for 100-sample and full dataset - Add scripts/download_jump_compounds.py for refreshing test data (sandboxed with uv) - Include compressed JUMP compounds test data (~1.7MB with only SMILES column) - Update pytest.ini with slow/very_slow markers for test organization - Update README.md and CLAUDE.md with testing instructions The test data contains ~115k real JUMP compounds and tests can run in two modes: - Fast mode: 100 randomly sampled compounds (~11 seconds) - Full mode: All ~115k compounds (marked as very_slow) 🤖 Generated with [Claude Code](https://claude.ai/code) Co-Authored-By: Claude <[email protected]>
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Summary
Changes
test/test_idempotency.pywith configurable dataset sizes (sample/full)Test plan
uv sync🤖 Generated with Claude Code
Co-Authored-By: Claude [email protected]