v0.2.2

[0.2.2] - 2026-07-09

Turns MSA on by default for Boltz-2 / Protenix-v2 (the fix for the misleading no-MSA
accuracy result) and ships the ESMC multi-card embedding fanout. No model numerics changed
vs 0.2.1 — the MSA compute path was already hardware-gated; this only flips its default and
adds a local-DB→online fallback with a privacy notice, plus a --single_sequence opt-out.
Ground-truth gate on the default path (examples/prot.yaml): Boltz-2 CA-RMSD 2.49 Å / TM
0.78, Protenix-v2 3.47 Å / TM 0.75.

Added

• Multi-card fanout for tt-bio embed — --devices 0,1,2,3 (CLI) / devices=[...] (tt_bio.esmc.embed) shards a sequence set across several TT cards, one pinned worker per card, and reassembles the embeddings in input order. Data-parallel and lossless: each shard's output is bit-exact to the single-card path (verified on-hardware, Δ=0 per-residue/pooled/logits).
• --single_sequence flag for predict — deliberately fold Boltz-2/Protenix-v2 without an MSA (skips both the local-DB lookup and the online fallback), for batch-screening orphan sequences.

Changed

• Boltz-2 and Protenix-v2 use an MSA by default — these MSA-dependent models no longer silently fold single-sequence (the cause of the alarming "~10 Å Protenix-v2" result; see docs/protenix-accuracy-investigation.md). With no MSA flags, predict uses a local ColabFold DB (~/.boltz/msa_db) if present, else falls back to the online ColabFold server and prints a one-line notice naming the server the sequences are sent to (they leave the machine). Pass --msa_db_path for a private offline DB, or --single_sequence to skip the MSA. ESMFold2 / ESMFold2-Fast are unchanged (single-sequence by design). Ground-truth gate on the default path (examples/prot.yaml): Boltz-2 CA-RMSD 2.49 Å / TM 0.78, Protenix-v2 3.47 Å / TM 0.75.