tt-bio

# Changelog

All notable changes to TT-Bio are recorded here. Versioning is [SemVer](https://semver.org);
releases are cut from a commit that has passed the on-hardware test suite (see `RELEASING.md`).

## [Unreleased]

### Changed

- RFdiffusion3 ships both fused bias kernels on by default (`881704d2`). The sparse
  attention bias is built in one pass instead of a poke walk (5.83x at the op,
  `703d12a1`) and the whole score+bias chain is one kernel (4.42x at the op,
  `923a9396`); both learned multiplicity batching, worth 6.26x at batch 2
  (`fa7246da`). Every step is bit-exact: the fold A/B legs land byte-identical
  designs at +12.36 %, +5.10 %, +6.83 % and +4.65 % on ms/step (`583961c4`,
  `ee4a8980`, `64a14e68`, `599d81ff`). The published throughput table in
  `docs/rfd3-design.md` was regenerated with them on (`5123065e`).
- Triangle attention runs the q-split at or below 1024 padded tokens and gates it
  off above (`063f89db`).

### Fixed

- `--trace` with Protenix-v2 or OpenDDE silently returned wrong structures for every
  target after the first when one process folded several targets of the same size: the
  captured trace was keyed on shape alone and replayed the first target's conditioning.
  The trace is now re-captured when the conditioning changes. Regression gate:
  `scripts/trace_multitarget_parity.py` (two same-size targets, one process, trace on
  vs off, byte-identical CIFs required). Boltz-2 and BoltzGen were not affected: their
  predict path resets the trace cache between targets.
- Protenix-v2 crashed on targets between 385 and 506 residues: the h=1.5 normed pair
  tensor was held past its last use (`142e0109`). ESMFold2 hit the same class at large
  targets and now frees the pair-conditioning intermediates rather than row-tiling them
  (`08565983`). OpenDDE uploads `z_struct` as one allocation into an intact hole
  (`28a91107`) and frees the expander's row chunks after the loop (`d2ad024b`).
- A clean `pip install` was missing kernel sources: the wheel and sdist now ship every
  file under `tt_bio/kernels/` through recursive globs, so a new kernel directory cannot
  drop out again (`cb3ef828`, `baa6ad0a`).
- On a tt-metal built from source, tt-bio could not find the fabric mesh-graph
  descriptor (`ee73d9a4`) or the `generic_op` kernel sources (`e2fb610a`), so a lone
  Blackhole P300 chip would not open and the fused kernels would not build.
- A worker that died of an uncaught exception reported silence (`a5921d2d`), and a
  process holding a card could outlive whoever spawned it (`3bd84f04`, `26a8c085`).
- Protenix-v2 falls back to ttnn's own matmul planner when a tuned config clashes
  instead of failing the fold (`5a207fee`).

### Performance

- OpenFold3 at 512 residues: 51.19 -> 44.535 s on one Blackhole p150a, from running
  TriangleAttention's fp32-softmax tail height-sharded in L1 rather than
  DRAM-interleaved. Bit-exact — the same CIF digest (da9b4ed68f8c0405) and plDDT as the
  control arm, and it holds at 768