GitLab

* Port core files + ESM (because ESM code is odd)

* Search-replace in modelling code

* Fix up transfo_xl as well

* Fix other core files + tests (still need to add correct import to tests)

* Fix cookiecutter

* make fixup, fix imports in some more core files

* Auto-add imports to tests

* Cleanup, add imports to sagemaker tests

* Use correct exception for importing tf_keras

* Fixes in modeling_tf_utils

* make fixup

* Correct version parsing code

* Ensure the pipeline tests correctly revert to float32 after each test

* Ensure the pipeline tests correctly revert to float32 after each test

* More tf.keras -> keras

* Add dtype cast

* Better imports of tf_keras

* Add a cast for tf.assign, just in case

* Fix callback imports

* hidden layers, huh, what are they good for (absolutely nothing)

* Some tests break with 1 hidden layer, use 2

* Use 1 hidden layer in a few slow models

* Use num_hidden_layers=2 everywhere

* Slightly higher tol for groupvit

* Slightly higher tol for groupvit

* Rework TF type hints to use | None instead of Optional[] for tf.Tensor

* Rework TF type hints to use | None instead of Optional[] for tf.Tensor

* Don't forget the imports

* Add the imports to tests too

* make fixup

* Refactor tests that depended on get_type_hints

* Better test refactor

* Fix an old hidden bug in the test_keras_fit input creation code

* Fix for the Deit tests

Fix weight tying in ESM

* Add PipelineTesterMixin

* remove class PipelineTestCaseMeta

* move validate_test_components

* Add for ViT

* Add to SPECIAL_MODULE_TO_TEST_MAP

* style and quality

* Add feature-extraction

* update

* raise instead of skip

* add tiny_model_summary.json

* more explicit

* skip tasks not in mapping

* add availability check

* Add Copyright

* A way to diable irrelevant tests

* update with main

* remove disable_irrelevant_tests

* skip tests

* better skip message

* better skip message

* Add all pipeline task tests

* revert

* Import PipelineTesterMixin

* subclass test classes with PipelineTesterMixin

* Add pipieline_model_mapping

* Fix import after adding pipieline_model_mapping

* Fix style and quality after adding pipieline_model_mapping

* Fix one more import after adding pipieline_model_mapping

* Fix style and quality after adding pipieline_model_mapping

* Fix test issues

* Fix import requirements

* Fix mapping for MobileViTModelTest

* Update

* Better skip message

* pipieline_model_mapping could not be None

* Remove some PipelineTesterMixin

* Fix typo

* revert tests_fetcher.py

* update

* rename

* revert

* Remove PipelineTestCaseMeta from ZeroShotAudioClassificationPipelineTests

* style and quality

* test fetcher for all pipeline/model tests

---------
Co-authored-by: ydshieh <ydshieh@users.noreply.github.com>

* Result of black 23.1

* Update target to Python 3.7

* Switch flake8 to ruff

* Configure isort

* Configure isort

* Apply isort with line limit

* Put the right black version

* adapt black in check copies

* Fix copies

* Re-enable TF ESM tests, make sure we use facebook checkpoints

* make fixup

* 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>