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merge upstream af3 updates

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@sokrypton sokrypton released this 25 Jul 20:15
· 6 commits to main since this release
7518e11

Syncs 21 upstream commits from google-deepmind/alphafold3 into the fork (#2), keeping the OpenFold3 / ColabFold MSA additions intact.

Notable from upstream:

  • jax 0.10.2 + tokamax 0.0.12; jax[cuda12] is no longer pulled in on macOS
  • gs:// path support via etils.epath throughout
  • Lower memory use in OuterProductMean
  • Chain IDs in the summary confidence JSON
  • Example input JSONs under examples/

Fork-specific:

  • --jax_backend now defaults to auto, probing for a JAX GPU and falling back to CPU (setting --flash_attention_implementation=xla itself), so CPU-only and macOS runs still need no extra flags
  • Generated converter pickles are gitignored; rebuild with ccd_pickle_gen.py