GitLab

* 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>

* Partial TF port for ESM model

* Add ESM-TF tests

* Add the various imports for TF-ESM

* TF weight conversion almost ready

* Stop ignoring the decoder weights in PT

* Add tests and lots of fixes

* fix-copies

* Fix imports, add model docs

* Add get_vocab() to tokenizer

* Fix vocab links for pretrained files

* Allow multiple inputs with a sep

* Use EOS as SEP token because ESM vocab lacks SEP

* Correctly return special tokens mask from ESM tokenizer

* make fixup

* Stop testing unsupported embedding resizing

* Handle TF bias correctly

* Skip all models with slow tokenizers in the token classification test

* Fixing the batch/unbatcher of pipelines to accomodate the `None` being

passed around.

* Fixing pipeline bug caused by slow tokenizer  being different.

* Update src/transformers/models/esm/modeling_tf_esm.py
Co-authored-by: Joao Gante <joaofranciscocardosogante@gmail.com>

* Update src/transformers/models/esm/modeling_tf_esm.py
Co-authored-by: Joao Gante <joaofranciscocardosogante@gmail.com>

* Update src/transformers/models/esm/modeling_tf_esm.py
Co-authored-by: Joao Gante <joaofranciscocardosogante@gmail.com>

* Update set_input_embeddings and the copyright notices
Co-authored-by: Your Name <you@example.com>
Co-authored-by: Nicolas Patry <patry.nicolas@protonmail.com>
Co-authored-by: Joao Gante <joaofranciscocardosogante@gmail.com>