Add ESMFold (#19977)

* 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>

utils/check_inits.py

@@ -268,6 +268,7 @@ def get_transformers_submodules():
 IGNORE_SUBMODULES = [
     "convert_pytorch_checkpoint_to_tf2",
     "modeling_flax_pytorch_utils",
+    "models.esm.openfold_utils",
 ]
 
 

utils/check_repo.py

@@ -140,6 +140,7 @@ TEST_FILES_WITH_NO_COMMON_TESTS = [
 # should **not** be the rule.
 IGNORE_NON_AUTO_CONFIGURED = PRIVATE_MODELS.copy() + [
     # models to ignore for model xxx mapping
+    "EsmForProteinFolding",
     "TimeSeriesTransformerForPrediction",
     "PegasusXEncoder",
     "PegasusXDecoder",