Xibin Bayes Zhou 45c7bfb157 Add evolla rebase main (#36232) ...

* add evolla

* adding protein encoder part

* add initial processing test

* save processor

* add docstring

* add evolla processor

* add two test

* change vision to protein

* change resampler to sequence_compressor

* change vision to protein

* initial update for llama

* add initial update for llamaForCausalLM

* add `test_processor`, `test_saprot_output`, `test_protein_encoder_output`

* change evolla, but still working on it

* add test_single_forward

* pass test_attention_outputs

* pass test_hidden_states_output

* pass test_save_load and test_from_pretrained_no_checkpoint

* pass test_cpu_offload

* skip some tests

* update new progress

* skip test_model_is_small

* pass test_model_weights_reload_no_missing_tied_weights

* pass test_model_get_set_embeddings

* pass test_cpu_offload

* skip test_resize_embeddings

* add pipeline_model_mapping

* remote old setUp

* pass processor save_pretrained and load_pretrained

* remove pooling layer

* pass test_inputs_embeds_matches_input_ids

* pass test_model_is_small

* pass test_attention_outputs

* pass test_initialization

* pass test_model_get_set_embeddings

* pass test_single_forward

* skip test_disk_offload_bin and test_disk_offload_safetensors

* fix most tests

* pass test_protein_encoder_output

* remove useless code

* add EvollaForProteinText2Text

* pass test_saprot_output

* pass all EvollaModelTest test and remove processor test

* add processor test to its own file

* skip is_training since esm skipped it and the saprot code causes error when setting is_training True

* pass processor tests

* solve all except config

* pass most cases

* change init

* add doc to `configuration_evolla.py`

* remove image_processing test

* remove extra processor test

* remove extra modules

* remove extra modules

* change all configs into one config

* pass all evolla test

* pass `make fixup`

* update short summary

* update Evolla-10B-hf

* pass check_dummies.py and check_code_quality

* fix  `tests/models/auto/test_tokenization_auto.py::AutoTokenizerTest::test_model_name_edge_cases_in_mappings`

* remove dummy codes

* change format

* fix llava issue

* update format

* update to solve llama3 access issue

* update to make forward right

* solve processor save load problem from instructblip solution

* remove unexpected file

* skip `test_generation_tester_mixin_inheritance`

* add `test_single_forward_correct` and `test_inference_natural_language_protein_reasoning`

* add `modular_evolla.py`

* solved issue #36362

* run `make fixup`

* update modular

* solve float32 training

* add fix

* solve `utils/check_docstrings.py`

* update

* update

* update

* remove other files and replace sequential and einsum

* add use case in document

* update the models

* update model

* change some wrong code

* Update src/transformers/models/evolla/modular_evolla.py

Co-authored-by: Cyril Vallez <cyril.vallez@gmail.com>

* Update src/transformers/models/evolla/modular_evolla.py

Co-authored-by: Cyril Vallez <cyril.vallez@gmail.com>

* Update src/transformers/models/evolla/modular_evolla.py

Co-authored-by: Cyril Vallez <cyril.vallez@gmail.com>

* Update src/transformers/models/evolla/modular_evolla.py

Co-authored-by: Cyril Vallez <cyril.vallez@gmail.com>

* fix issues mentioned in PR

* update style and rearrange the placement

* fix return_dict argument issue

* solve SaProtConfig issue

* Solve EvollaSaProtRotaryEmbedding issue

* solve attention_mask issue

* solve almosst all issues

* make style

* update config

* remove unrelated pickle file

* delete pickle files

* fix config

* simplify a lot

* remove past k-v from encoder

* continue work

* style

* skip it from init

* fix init

* fix init

* simplify more

* fill in docstrings

* change test for generation

* skip test

* fix style

---------

Co-authored-by: Chenchen Han <13980209828@163.com>
Co-authored-by: Cyril Vallez <cyril.vallez@huggingface.co>
Co-authored-by: Cyril Vallez <cyril.vallez@gmail.com>

2025-07-25 19:11:57 +02:00

..

internal

[cache refactor] Move all the caching logic to a per-layer approach (#39106)

2025-07-22 16:10:25 +02:00

main_classes

FP-Quant support (#38696)

2025-07-23 11:41:10 +02:00

model_doc

Add evolla rebase main (#36232)

2025-07-25 19:11:57 +02:00

quantization

FP-Quant support (#38696)

2025-07-23 11:41:10 +02:00

reference

Enhance Model Loading By Providing Parallelism, Uses Optional Env Flag (#36835)

2025-05-23 16:39:47 +00:00

tasks

Rename huggingface_cli to hf (#39630)

2025-07-25 14:10:04 +02:00

_config.py

Add optimized PixtralImageProcessorFast (#34836)

2024-11-28 16:04:05 +01:00

_redirects.yml

Docs / Quantization: Redirect deleted page (#31063)

2024-05-28 18:29:22 +02:00

_toctree.yml

Add evolla rebase main (#36232)

2025-07-25 19:11:57 +02:00

accelerate.md

change fsdp_strategy to fsdp in TrainingArguments in accelerate doc (#38807)

2025-06-13 15:32:40 +00:00

accelerator_selection.md

[docs] add xpu environment variable for gpu selection (#38194)

2025-05-30 16:05:07 +00:00

add_new_model.md

[docs] Model contribution (#38995)

2025-06-26 12:25:14 -07:00

add_new_pipeline.md

[docs] Redesign (#31757)

2025-03-03 10:33:46 -08:00

agents.md

[serve] Cursor support, move docs into separate page, add more examples (#39133)

2025-07-03 17:04:16 +01:00

attention_interface.md

[docs] update attention implementation and cache docs (#39547)

2025-07-22 15:06:43 +02:00

auto_docstring.md

Improve @auto_docstring doc and rename args_doc.py to auto_docstring.py (#39439)

2025-07-18 18:00:34 +00:00

backbones.md

[docs] Redesign (#31757)

2025-03-03 10:33:46 -08:00

cache_explanation.md

[cache refactor] Move all the caching logic to a per-layer approach (#39106)

2025-07-22 16:10:25 +02:00

chat_extras.md

Update chat_extras.md with content correction (#36599)

2025-03-07 13:09:02 +00:00

chat_templating_multimodal.md

Enable XPU doc (#38929)

2025-06-30 07:56:55 -07:00

chat_templating_writing.md

[docs] Redesign (#31757)

2025-03-03 10:33:46 -08:00

chat_templating.md

[docs] Redesign (#31757)

2025-03-03 10:33:46 -08:00

community.md

Fixed Majority of the Typos in transformers[en] Documentation (#33350)

2024-09-09 10:47:24 +02:00

contributing.md

…

conversations.md

[serve] Cursor support, move docs into separate page, add more examples (#39133)

2025-07-03 17:04:16 +01:00

custom_models.md

Rename huggingface_cli to hf (#39630)

2025-07-25 14:10:04 +02:00

debugging.md

[docs] Redesign (#31757)

2025-03-03 10:33:46 -08:00

deepspeed.md

chore: Fix typos in docs and examples (#36524)

2025-03-04 13:47:41 +00:00

executorch.md

[docs] Redesign (#31757)

2025-03-03 10:33:46 -08:00

fast_tokenizers.md

[docs] Redesign (#31757)

2025-03-03 10:33:46 -08:00

feature_extractors.md

Enable XPU doc (#38929)

2025-06-30 07:56:55 -07:00

fsdp.md

[docs] Redesign (#31757)

2025-03-03 10:33:46 -08:00

generation_features.md

chore: Fix typos in docs and examples (#36524)

2025-03-04 13:47:41 +00:00

generation_strategies.md

Fix custom generate from local directory (#38916)

2025-06-20 17:36:57 +01:00

gguf.md

Fix gguf docs (#36601)

2025-03-11 15:29:14 +01:00

glossary.md

Use HF papers (#38184)

2025-06-13 11:07:09 +00:00

how_to_hack_models.md

[doc] fix bugs in how_to_hack_models.md (#38198)

2025-05-19 10:37:54 -07:00

hpo_train.md

[Nit] Add Note on SigOpt being in Public Archive Mode (#38610)

2025-06-05 14:07:23 -07:00

image_processors.md

🔴 Video processors as a separate class (#35206)

2025-05-12 11:55:51 +02:00

index.md

[docs] Update docs moved to the course (#38800)

2025-06-13 12:02:27 -07:00

installation.md

byebye torch 2.0 (#37277)

2025-04-07 15:19:47 +02:00

kv_cache.md

[cache refactor] Move all the caching logic to a per-layer approach (#39106)

2025-07-22 16:10:25 +02:00

llm_optims.md

[docs] update attention implementation and cache docs (#39547)

2025-07-22 15:06:43 +02:00

llm_tutorial_optimization.md

Use HF papers (#38184)

2025-06-13 11:07:09 +00:00

llm_tutorial.md

No more Tuple, List, Dict (#38797)

2025-06-17 19:37:18 +01:00

model_memory_anatomy.md

Use HF papers (#38184)

2025-06-13 11:07:09 +00:00

model_sharing.md

Rename huggingface_cli to hf (#39630)

2025-07-25 14:10:04 +02:00

models.md

Fix grammatical error in models documentation (#39019)

2025-06-25 14:55:22 +00:00

modular_transformers.md

Fix typos and grammar issues in documentation and code (#39598)

2025-07-23 12:43:11 +00:00

notebooks.md

…

optimizers.md

Add StableAdamW Optimizer (#39446)

2025-07-16 13:35:53 +02:00

pad_truncation.md

Fixed Majority of the Typos in transformers[en] Documentation (#33350)

2024-09-09 10:47:24 +02:00

peft.md

[docs] Redesign (#31757)

2025-03-03 10:33:46 -08:00

perf_hardware.md

Improve grammar and clarity in perf_hardware.md (#39428)

2025-07-16 12:15:15 -07:00

perf_infer_cpu.md

remove ipex_optimize_model usage (#38632)

2025-06-06 20:04:44 +02:00

perf_infer_gpu_multi.md

switch default xpu tp backend to pytorch built-in XCCL from pytorch 2.8 (#39024)

2025-06-30 08:54:05 -07:00

perf_infer_gpu_one.md

[docs] update attention implementation and cache docs (#39547)

2025-07-22 15:06:43 +02:00

perf_torch_compile.md

[docs] Redesign (#31757)

2025-03-03 10:33:46 -08:00

perf_train_cpu_many.md

remove ipex_optimize_model usage (#38632)

2025-06-06 20:04:44 +02:00

perf_train_cpu.md

remove ipex_optimize_model usage (#38632)

2025-06-06 20:04:44 +02:00

perf_train_gaudi.md

Add Intel Gaudi doc (#37855)

2025-04-29 13:28:06 -07:00

perf_train_gpu_many.md

[docs] Tensor parallelism (#38241)

2025-06-26 14:40:45 -07:00

perf_train_gpu_one.md

[docs] Typos - Single GPU efficient training features (#38964)

2025-06-23 12:33:10 -07:00

perf_train_special.md

[docs] Redesign (#31757)

2025-03-03 10:33:46 -08:00

perplexity.md

[docs] use device-agnostic API instead of cuda (#34913)

2024-11-26 09:23:34 -08:00

philosophy.md

[docs] fixed links with 404 (#27327)

2023-11-06 19:45:03 +00:00

pipeline_gradio.md

[docs] Redesign (#31757)

2025-03-03 10:33:46 -08:00

pipeline_tutorial.md

chore: Fix typos in docs and examples (#36524)

2025-03-04 13:47:41 +00:00

pipeline_webserver.md

fix and enhance pipeline_webserver.md (#36992)

2025-04-15 08:35:05 -07:00

pr_checks.md

Fixed Majority of the Typos in transformers[en] Documentation (#33350)

2024-09-09 10:47:24 +02:00

processors.md

[docs] add Audio import (#38195)

2025-05-19 13:16:35 +00:00

quicktour.md

Rename huggingface_cli to hf (#39630)

2025-07-25 14:10:04 +02:00

run_scripts.md

Remove research projects (#36645)

2025-03-11 13:47:38 +00:00

serialization.md

[docs] Redesign (#31757)

2025-03-03 10:33:46 -08:00

serving.md

[docs] Create page on inference servers with transformers backend (#39550)

2025-07-22 15:31:10 +02:00

testing.md

[tests] remove TF tests (uses of require_tf) (#38944)

2025-06-25 17:29:10 +00:00

tflite.md

[docs] Redesign (#31757)

2025-03-03 10:33:46 -08:00

tokenizer_summary.md

Use HF papers (#38184)

2025-06-13 11:07:09 +00:00

tools.md

[serve] Cursor support, move docs into separate page, add more examples (#39133)

2025-07-03 17:04:16 +01:00

torchscript.md

Fix wording in torchscript.md (#38004)

2025-05-08 16:47:45 +01:00

trainer.md

[Docs] Fix typo in CustomTrainer compute_loss method and adjust loss reduction logic (#39391)

2025-07-14 09:25:06 -07:00

training.md

Fix typos and grammar issues in documentation and code (#39598)

2025-07-23 12:43:11 +00:00

transformers_as_backend.md

Fix link in "Inference server backends" doc (#39589)

2025-07-22 16:44:08 +00:00

troubleshooting.md

Update all references to canonical models (#29001)

2024-02-16 08:16:58 +01:00

video_processors.md

🔴 Video processors as a separate class (#35206)

2025-05-12 11:55:51 +02:00