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Sync OSS esm 3.4.2 - #426
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Co-Authored-By: Claude <noreply@anthropic.com>
Co-Authored-By: Claude <noreply@anthropic.com>
imathur1
approved these changes
Oct 28, 2026
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imathur1
approved these changes
Oct 28, 2026
scandido
approved these changes
Oct 29, 2026
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Syncs the internal tree to OSS ahead of the 3.4.2 PyPI release.
biotite<2. biotite 2.0 breaksProteinComplex.from_rcsbandannotate_sse(e.g.snippets/esm3.py,esmprotein.ipynb).client()/esmc_client()/esmfold2_client()now default to a 125s request timeout instead of waiting forever.guided_generateletsparallel_executorretry transient API errors instead of crashing on anAssertionError.snippets/esmc.pyon GPU machines, and drop theesm[gpu]extra from the docs (it no longer exists)./fold, a fix for ESMFold2: a ligand given as several CCD codes is returned as one residue #419, andtarget_structureremoved from the fold API.With the first four fixes, every cookbook recipe passed from a fresh 3.4.2 wheel install on H100s (except
binder_design, which needs Modal, and the Apple Silicon notebook). The ESMFold2 changes landed after that run, so the recipes haven't been rerun with them.🤖 Sent by a robot