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release: AtomWorks 3.0.1 with SASA fixes and HF reads - #119
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* fix: remove retained hydrogens from Dimorphite products * fix: configure existing Dimorphite hydrogen removal
Co-authored-by: jiechen7 <jiechen7@uw.edu>
BREAKING CHANGE: replace atom_filter with occlusion_mask for environment filtering; use sasa_mask to select scored atoms without removing their occluders.
* feat: stream indexed blob records from pinned Hugging Face datasets * ci: test HF streaming and build its guide on GitHub runners * test: trim HF transport cases and explain dataset repository access * fix: avoid read-ahead for weighted HF blob reads * chore: trim HF reader CI and clarify shard caching * chore: keep HF reader PR focused on core code
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AtomWorks 3.0.1 fixes SASA scoring versus occlusion masks, removes retained Dimorphite hydrogens, and preserves standard annotation aliases during protonation. It adds revision-pinned Hugging Face dataset reads through the optional
hfextra. Indexed metadata uses the Hub cache; blob records use exact ranged reads. Long-running training should download shards locally or use colocated object storage.The release also repairs versioned documentation navigation and removes links to the deleted 3.0 release branch.
Validation: four targeted scientific regressions passed, nine release/documentation helper tests passed, Ruff passed across the repository, and the 3.0.1 wheel and sdist built locally. The public PR workflow will run the complete scientific, wheel, build, and documentation checks before merge.