v3.1.5 - cp313 wheels for Colab's Python 3.13

Colab upgraded its default runtime to Python 3.13 on 2026-08-25 (colabtools#6081). The v3.1.4 release shipped only a cp312 wheel, so installing it on a current Colab runtime failed with:

ERROR: alphafold3_open-3.1.4-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl
is not a supported wheel on this platform.

This release ships both cp312 and cp313 manylinux_2_28 x86_64 wheels, so it installs on Colab's 3.13 runtime and on 3.12 environments alike.

No functional changes to AlphaFold 3 / OpenFold3 inference — packaging only (#5).

v3.1.4 - alphabet fix in diffusion

Merge pull request #4 from sokrypton/fix-of3-feature-layouts

Fix diffusion conditioning feature layout; add OF3 conversion tests and verification harness

v3.1.3 - alphabet bugfix

bugfix

merge upstream af3 updates

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

fixing ccd code issues

v3.1.1

ccd codes cleanup

add support for openfold3 and colabfold msa server

v3.1.0

Update build_data.py