Changelog

0.2.0 — 2026-04

• Renamed package from nucbox to uchrom / u-chrom.

• New core container ChromData with HDF5 persistence (.h5cd) and format versioning (see Concepts — on-disk format).

• uchrom.io.save_particles / extended read_particles — all reconstruction modules now write .h5cd by default.

• Bulk MDS reconstruction (uchrom.recon.bulk.mds) — PyTorch SMACOF with inter-chromosomal whole-genome support.

• Browser updates:

  • Trace-aware rendering (per (chrom, trace_id) polymer).

  • “Per Trace” colour mode.

  • Unified Chromosome / Region / Trace Management tab.

  • Trace Statistics panel (Distance Matrix / Contact Map / Rg Histogram / Split by Trace).

  • Click-to-identify trace overlay.

  • Draggable Layers / Properties divider.

  • macOS Dock icon + startup logo.

• ArcFISH-style axis-wise F-test loop caller (uchrom.strc.loop.call_loops_axiswise_f) — GPU-accelerated via PyTorch, CLI under python -m uchrom.strc.loop.

• New population-aggregate modules:

  • uchrom.fea.distance (median distance matrix, contact frequency, radius of gyration)

  • uchrom.fea.arc (axis variance cube, LOWESS filter+normalise, axis weights)

  • uchrom.pl.trace_stats (matplotlib helpers)

  • uchrom.utils.stats (Cauchy combination test, log-log LOWESS)

• Version stamp on .h5cd files with MAJOR/MINOR semantics and legacy-file handling.