GitLab

* Fix link to table transformer detection microsoft model

* Fix doc styles

* rembert onnx config

* formatting
Co-authored-by: Ho <erincho@bcd0745f972b.ant.amazon.com>

* add type annotations for esm chunk_utils

use isinstance builtin instead of 'type(x) is y'; add assertions to aid in type inferencing; use bools instead of ints in _get_minimal_slice_set for improved type clarity; refactor to avoid re-assigning to the same variable with a different type

* add type annotations for esm data_transforms

refactor to avoid re-assigning to the same variable with a different type

* add type annotations for esm feats utils

refactor to avoid re-assigning to the same variable with a different type

* add type annotations for esm loss utils

* add/fix type annotations for esm rigit_utils

refactor to avoid re-assigning to the same variable with a different type; fix Callable, Tuple type hints; match conditional structure to other methods; fix return type on Rotation.cat and Rotation.unsqueeze

* add type annotations for esm tensor_utils

overload for tree_map; use insinstance builtin instead of 'type(x) is y'; export dict_multimap, flatten_final_dims, permute_final_dims in openfold_utils

* add type annotations for esm protein utils

add FIXME for attempted string mutation; add missing None check in get_pdb_headers; fix potentially unbound variable 'chain_tag' in to_pdb; modify get_pdb_headers return type

* add type annotations for esm residue constants

hints on collection constants; remove magic trailing comma to reduce number of lines; change list -> tuple for rigid_group_atom_positions for improved hinting

* code style fixup
Co-authored-by: Matt <rocketknight1@gmail.com>

* Make convert_to_onnx runable as script again

Fix `convert_graph_to_onnx.py` relative import so it can be run as a script again.

* Trigger CI

* add support for `from_pt`

* add tf_flax utility file

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

* remove flax related modifications

* add test

* remove FLAX related commits

* fixup

* remove safetensor todos

* revert deletion
Co-authored-by: Sylvain Gugger <35901082+sgugger@users.noreply.github.com>

* Expected output for the test changed

* fix failing asr test

* biogpt initial commit

* updated init

* fix faster decoding with use_cache

* 1. fix input_ids and input_embeds with correct device
2. added _keys_to_ignore_on_load_missing
3. updated prepare_inputs_for_generation

* add activation_dropout and scale_embedding

* replace fsmt attention with bart attention

* added test

* run make fix-copies

* doc init and fix build

* updated README with proper information

* 1. added tips to docs
2. updated BioGptTokenizer func

* 1. added tokenizer test
2. refactor tokenizer

* make fixup

* add biogpt fairseq to hf converter

* updated layer names more
similar to original checkpoints

* config update doc string and set defaults

* added "#copied" from bart model and
updated doc strings

* enable model_input_names in tokenizer

* 1.  positionalembedding depending on attention_mask
2. added attention mask to prepare for generation

* added test to verify past and generation

* BioGptLMHeadModel -> BioGptForCausalLM

* fix typo

* tokenization and test
Copyright and updated assertion

* updated Copyright and
one func at time in line

* Copyright updates and
minor doc fix

* replace assertion with ValueError

* rm extra space

* added code syntax

* revert cmnt position change

* add tokenizer to auto

* updated doc string

* tokenizer doc string update

* biogpt hub model update to microsoft/biogpt

* make fixup

* rm cmnt to fix flake8 5.0.4 vs 6 error

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

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

* Remove is_encoder_decoder from some vision models

* cleanup more

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

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

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

* fix small nit

* add last file

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

* Draft addition of new head

* Finish adding contact heads + tests for ESM

* Add TF contact prediction head

* make fixup

* Minor fix to convert_esm.py

* Clean up function names and comments

* init timesformer

* apply fix-copies

* reformat style

* revert back some incoorect style updates

* init timesformer

* apply fix-copies

* reformat style

* revert back some incoorect style updates

* update timseformer doc

* add some functions and classes

* add new config params

* implement multiple classes

* update TimeSformerLayer

* update TimeSformerModel, TimeSformerPreTrainedModel, TimeSformerEncoder

* several fixes

* reformat

* temporary update

* fix some typos

* fix weight converter

* more fixes

* fix a typo

* fix typo

* remove redundant params

* fix for latest hf-hub

* merge fix

* fix some checks

* video classification works with einops

* add paper info to docs

* merge fix

* remove redundant line

* remove redundant docstring

* update config

* fix some typos

* fix converter

* update some test constants

* refactor einops functions

* reformat

* fix a comment

* remove redundat imports

* reformat

* fix a typo

* remove comment

* remove unused imports

* remove redundant doc line

* reformat

* add missing line

* fix docs

* fix timesformer auto feat ext

* add unittests

* reformat

* fix docs

* some fixes and updates

* fix readme

* fix modeling

* fix readme

* update index

* revert _toctree.yml changes

* update timseformer.mdx

* update drop_path_prob to drop_path_rate

* add dosctring for drop_path_rate

* update TimeSformerPatchEmbed naming

* remove to_2tuple

* explicit use of nn.functional

* reformat

* many updates from review comments

* fix a typo

* reformat

* remove assert, better variable name

* make variable names more explicit

* add some adapted from

* more explicit variable names

* remove redundant docstring

* fix initilaization

* move permute inside embedding

* update class names

* remove unused imports

* add test for video classification

* update PretrainedModel with PreTrainedModel

* remove double permute

* update based on sylvain's review

* aply auto fix

* update image_processing_auto for timesformer

* update hub urls

* reformat

* remove duplicate import

* update doc link

* fix cuda OOM by using single Prior

* only send to device when used

* use custom model

* fix link in pipeline device map

* oops this is the correct link

* make style

Co-authored-by: Niels Rogge <nielsrogge@Nielss-MacBook-Pro.local>

* Update ZeroShotObjectDetectionPipeline expect output

* Update src/transformers/pipelines/zero_shot_object_detection.py
Co-authored-by: Nicolas Patry <patry.nicolas@protonmail.com>
Co-authored-by: ydshieh <ydshieh@users.noreply.github.com>
Co-authored-by: Nicolas Patry <patry.nicolas@protonmail.com>

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

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

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

* Fix Data2VecTextForCasualLM example code documentation

* Change RobertaTokenizer to AutoTokenizer in data2vectext example code

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

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