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🟡 Changes recommended
Unresolved defects break simulation reconstruction, violate requested trajectory rounding accuracy, and allow infinite precision to produce NaN coordinates.
3 open issues
What changed in this PR
Introduces delta-encoded storage for polymer conformations, targeting 2–4× smaller trajectory files while preserving transparent loading.
Changes:
- Adds integer-grid position encoding with anchors and automatic HDF5 decoding.
- Introduces
save_precision, defaults to a 0.04 grid step, and retains legacysave_decimalshandling. - Adds encoding tests, raises the h5py minimum, and updates the CI Python matrix.
| File | Description |
|---|---|
tests/test_pos_encoding.py |
Tests encoding accuracy, validation, warnings, and reporter round trips. |
tests/test_io.py |
Updates integration assertions for the new default precision. |
requirements.txt |
Raises minimum h5py version to 2.10. |
pyproject.toml |
Aligns the packaged h5py dependency minimum. |
polychrom/simulation.py |
Adds precision-based snapping and storage metadata. |
polychrom/hdf5_format.py |
Implements delta encoding, transparent decoding, and HDF5 v1.10 writes. |
.github/workflows/pythonapp.yml |
Updates tested Python versions to 3.11–3.14. |
Review effort: Balanced
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| if not precision > 0: | ||
| raise ValueError(f"pos_precision must be a positive number, got {precision}") |
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| precision = dataDict.get("pos_precision", False) | ||
| if "pos" in dataDict and precision is not False and precision is not None: | ||
| dataDict = dict(dataDict) # do not modify the caller's dict | ||
| encoded = encode_positions(dataDict.pop("pos"), precision) |
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| if "save_precision" in kwargs: | ||
| raise ValueError("Pass either save_precision or save_decimals, not both") |
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Description
Introduces new storage format to save 2x to 4x of space.
Bump of test versions.
PR Checklist
black .)isort .)flake8and try to resolve all the issues (work in progress!)