v1.6.0; refer to changelog.md
Merged
AM
3d ago+10119+10119+01234567890123456789012345678901234567890123456789-7254-7254-0123456789012345678901234567890123456789
Summary by cubic
v1.6.0 is a descriptor audit release that corrects several descriptor formulas, data tables, and API structure. Descriptor outputs change in this release; pin protpy<1.6 to reproduce older results.
Breaking changes
- Descriptor values are no longer rounded; the golden-file baseline is regenerated for v1.6.0 and tests compare with a tolerance.
signal.pybecomesspectral.py;fft_descriptorsanddct_descriptorsare deprecated aliases ofspectral_descriptors.- Several v1.5.0 heuristics (e.g.
linguistic_complexity,disorder_propensity) are deprecated and warn; they are removed in 2.0. all_descriptorsdrops from 10,757 to 1,402 columns, and the classic/extended/all descriptor sets are reorganized.conjoint_triadvalues are normalized by default; passnormalize=Falsefor raw counts.- Removed the
varnamedependency.
Bug fixes
instability_indexuses the correct DIWV table (25 of 400 entries were wrong), andquasi_sequence_ordercomposition terms are now fractions that sum to 1.kappascores single-sign sequences instead of returning NaN and is ~100× faster;ctd_distributionclamps quantile indices and assigns window scores to the centre residue.charge_fractionsnow reports NCPR, and APAAC, motif-composition, and aggregation edge cases are fixed; the Eisenberg scale is split intoeisenberg_arb1984andeisenberg_jmb1984.