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7f9b7b3f0e
* initial commit * First draft that gets outputs without crashing! * Add all the ported openfold dependencies * testing * Restructure config files for ESMFold * Debugging to find output discrepancies * Mainly style * Make model runnable without extra deps * Remove utils and merge them to the modeling file * Use correct gelu and remove some debug prints * More cleanup * Update esm docs * Update conversion script to support ESMFold properly * Port some top-level changes from ESMFold repo * Expand EsmFold docstrings * Make attention_mask optional (default to all 1s) * Add inference test for ESMFold * Use config and not n kwargs * Add modeling output class * Remove einops * Remove chunking in ESM FFN * Update tests for ESMFold * Quality * REpo consistency * Remove tree dependency from ESMFold * make fixup * Add an error in case my structure map function breaks later * Remove needless code * Stop auto-casting the LM to float16 so CPU tests pass * Stop auto-casting the LM to float16 so CPU tests pass * Final test updates * Split test file * Copyright and quality * Unpin PyTorch to see built doc * Fix config file to_dict() method * Add some docstrings to the output * Skip TF checkpoint tests for ESM until we reupload those * make fixup * More docstrings * Unpin to get even with main * Flag example to write Co-authored-by: Sylvain Gugger <Sylvain.gugger@gmail.com> |
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