v1.6.0; refer to changelog.md

Merged
AM
3d ago
+10119-7254

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.py becomes spectral.py; fft_descriptors and dct_descriptors are deprecated aliases of spectral_descriptors.
  • Several v1.5.0 heuristics (e.g. linguistic_complexity, disorder_propensity) are deprecated and warn; they are removed in 2.0.
  • all_descriptors drops from 10,757 to 1,402 columns, and the classic/extended/all descriptor sets are reorganized.
  • conjoint_triad values are normalized by default; pass normalize=False for raw counts.
  • Removed the varname dependency.

Bug fixes

  • instability_index uses the correct DIWV table (25 of 400 entries were wrong), and quasi_sequence_order composition terms are now fractions that sum to 1.
  • kappa scores single-sign sequences instead of returning NaN and is ~100× faster; ctd_distribution clamps quantile indices and assigns window scores to the centre residue.
  • charge_fractions now reports NCPR, and APAAC, motif-composition, and aggregation edge cases are fixed; the Eisenberg scale is split into eisenberg_arb1984 and eisenberg_jmb1984.