v0.1.6

[0.1.6] - 2026-08-30

Fixed

• Negative-dominant D_offset now detected in physics validators. The
  D_offset/D0 overfitting checks only compared ratio > 0.5, missing the
  symmetric case where a large-magnitude negative offset dominates D0
  (e.g. D_offset_ref/D0_ref = -0.503 in a real C045 two_component fit,
  implying a negative diffusion coefficient at early times). Both checks now
  compare abs(ratio) > 0.5 (#75).
• Resolved mypy hard-gate failures on main (CI run 33300386957): explicit
  type annotations for union-typed locals in fallback_chain.py,
  recovery.py, and validation.py, plus a new AngleGroup TypedDict in
  chunking.py replacing an overly-loose dict[str, Any] (#73).
• Duplicate HeterodyneModel class name. Two unrelated classes shared
  the name — core/heterodyne_model.py's PhysicsModelBase adapter and
  core/heterodyne_model_stateful.py's public stateful model — so
  from xpcsjax.core.heterodyne_model import HeterodyneModel and
  from xpcsjax.core import HeterodyneModel silently returned different
  classes. Renamed the adapter to HeterodynePhysicsAdapter across every
  real call site; the public xpcsjax.core.HeterodyneModel export is
  unaffected (#71).
• Stratified-LS (>=1M point) diagonal-exclusion mask compared indices
  into two independently-built np.unique() arrays instead of the actual
  t1/t2 values, wrongly zeroing real off-diagonal points and keeping
  true diagonal ones (#71).
• Hybrid-streaming per_angle_mode="constant" fallback index
  misalignment. In the quantile-estimation-failure fallback, L3's
  regularization group indices and L4's gradient-collapse-monitor watched
  indices were resolved via the literal per_angle_mode_actual string
  instead of the real 2-param [contrast_mean, offset_mean, *physical]
  layout the fallback actually uses, watching the scaling head as if it
  were physics (#71).
• coerce_finite_float no longer silently coerces a stray YAML boolean
  (e.g. a typo'd max: true) to 1.0/0.0 at the shared bounds/values
  validation boundary (#71).
• Degenerate 1-frame Siegert-ceiling check no longer reads the excluded
  tau=0 diagonal spike. The matrix.shape[1] <= 1 fallback branch in
  data/filtering_utils.py and data/validation.py read diagonal[0]
  into the check instead of skipping it, reintroducing the anti-pattern the
  surrounding code otherwise avoids (#71).
• 19 correctness gaps closed in the NLSQ fitting workflow and 6 more across
  config/core/viz, found via independent step-by-step audits that traced the
  NLSQ workflow and docs/diagrams/architecture.md against the real code.

Removed

• ~7800 lines of confirmed-dead code removed repo-wide (ponytail-audit).

Documentation

• Config examples across the documentation now match the shipped YAML
  templates exactly — bounds format, key nesting, and the heterodyne
  physics/scaling parameter layout — instead of several invented shapes
  that a reader could not actually load (#70).
• Theory prose terminology and notation cleaned up: dropped the "diffusion
  integral" label for D(t1,t2) (referred to by symbol only, alongside
  J(t)), and aligned Sphinx theory notation with the README (#69, #70).

Dependencies

• nlsq bumped 0.7.1 → 0.7.4 and evosax bumped 0.2.0 → 0.3.1 in
  uv.lock and the conda recipe (conda-recipe/xpcsjax/meta.yaml); host
  setuptools floor raised to >=77 to match evosax 0.3.1's build
  requirement (#74).