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feat: accept --fast_kernels for the AlphaFold 3 backend - #59
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Restore the AF2 README entry's explanation (quoted values, ~2x on compute capability 8.0+), add the AF3 entry, correct the common.smk comment that still called the flag AlphaFold2-only, and align the flag test's name and AlphaLink case with its neighbours. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Summary
Accept AlphaPulldown's
--fast_kernelsflag for the AlphaFold 3 backend too (KosinskiLab/AlphaPulldown#646). AlphaFold 2 already accepts it (#58).fast_kernelsjoins the AF3 inference flags inworkflow/rules/common.smk. AlphaLink still rejects it, and the comment says so.--fast_kernels: "off"with the same quoting note.The released AlphaFold 3 images (≤ 2.9.1) reject
--fast_kernels. The next release bumps the default container tags inconfig/config.yaml; a follow-up test PR adds a check that fails until it does.Validation
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