GitLab

* Allow non-special tokens to be added

* Add test, fix token adding code

* Revert changes to id_to_token and token_to_id

* Update the ESM tokenizer to be a bit more standardized

* Update src/transformers/models/esm/tokenization_esm.py
Co-authored-by: Arthur <48595927+ArthurZucker@users.noreply.github.com>

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Co-authored-by: Arthur <48595927+ArthurZucker@users.noreply.github.com>

* try to stylify using ruff

* might need to remove these changes?

* use ruf format andruff check

* use isinstance instead of type comparision

* use # fmt: skip

* use # fmt: skip

* nits

* soem styling changes

* update ci job

* nits isinstance

* more files update

* nits

* more nits

* small nits

* check and format

* revert wrong changes

* actually use formatter instead of checker

* nits

* well docbuilder is overwriting this commit

* revert notebook changes

* try to nuke docbuilder

* style

* fix feature exrtaction test

* remve `indent-width = 4`

* fixup

* more nits

* update the ruff version that we use

* style

* nuke docbuilder styling

* leve the print for detected changes

* nits

* Remove file I/O
Co-authored-by: charliermarsh <charlie.r.marsh@gmail.com>

* style

* nits

* revert notebook changes

* Add # fmt skip when possible

* Add # fmt skip when possible

* Fix

* More `  # fmt: skip` usage

* More `  # fmt: skip` usage

* More `  # fmt: skip` usage

* NIts

* more fixes

* fix tapas

* Another way to skip

* Recommended way

* Fix two more fiels

* Remove asynch
Remove asynch

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Co-authored-by: charliermarsh <charlie.r.marsh@gmail.com>

* Rebase ESM PR and update all file formats

* Fix test relative imports

* Add __init__.py to the test dir

* Disable gradient checkpointing

* Remove references to TFESM... FOR NOW >:|

* Remove completed TODOs from tests

* Convert docstrings to mdx, fix-copies from BERT

* fix-copies for the README and index

* Update ESM's __init__.py to the modern format

* Add to _toctree.yml

* Ensure we correctly copy the pad_token_id from the original ESM model

* Ensure we correctly copy the pad_token_id from the original ESM model

* Tiny grammar nitpicks

* Make the layer norm after embeddings an optional flag

* Make the layer norm after embeddings an optional flag

* Update the conversion script to handle other model classes

* Remove token_type_ids entirely, fix attention_masking and add checks to convert_esm.py

* Break the copied from link from BertModel.forward to remove token_type_ids

* Remove debug array saves

* Begin ESM-2 porting

* Add a hacky workaround for the precision issue in original repo

* Code cleanup

* Remove unused checkpoint conversion code

* Remove unused checkpoint conversion code

* Fix copyright notices

* Get rid of all references to the TF weights conversion

* Remove token_type_ids from the tests

* Fix test code

* Update src/transformers/__init__.py
Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>

* Update src/transformers/__init__.py
Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>

* Update README.md
Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>

* Add credit

* Remove _ args and __ kwargs in rotary embedding

* Assertively remove asserts

* Replace einsum with torch.outer()

* Fix docstring formatting

* Remove assertions in tokenization

* Add paper citation to ESMModel docstring

* Move vocab list to single line

* Remove ESMLayer from init

* Add Facebook copyrights

* Clean up RotaryEmbedding docstring

* Fix docstring formatting

* Fix docstring for config object

* Add explanation for new config methods

* make fix-copies

* Rename all the ESM- classes to Esm-

* Update conversion script to allow pushing to hub

* Update tests to point at my repo for now

* Set config properly for tests

* Remove the gross hack that forced loss of precision in inv_freq and instead copy the data from the model being converted

* make fixup

* Update expected values for slow tests

* make fixup

* Remove EsmForCausalLM for now

* Remove EsmForCausalLM for now

* Fix padding idx test

* Updated README and docs with ESM-1b and ESM-2 separately (#19221)

* Updated README and docs with ESM-1b and ESM-2 separately

* Update READMEs, longer entry with 3 citations

* make fix-copies
Co-authored-by: Your Name <you@example.com>
Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>
Co-authored-by: Tom Sercu <tsercu@fb.com>
Co-authored-by: Your Name <you@example.com>