Clip floating point constants to bf16 range to avoid inf conversion

.github/workflows/check_runner_status.yml

@@ -35,7 +35,7 @@ jobs:
         if: ${{ always() }}
         run: |
           offline_runners=$(python3 -c 'fp = open("offline_runners.txt"); failed = fp.read(); fp.close(); print(failed)')
-          echo "::set-output name=offline_runners::$offline_runners"
+          echo "offline_runners=$offline_runners" >> $GITHUB_OUTPUT
 
   send_results:
     name: Send results to webhook

.github/workflows/self-nightly-scheduled.yml

@@ -83,7 +83,7 @@ jobs:
         name: Identify models to test
         working-directory: /transformers/tests
         run: |
-          echo "::set-output name=matrix::$(python3 -c 'import os; tests = os.getcwd(); model_tests = os.listdir(os.path.join(tests, "models")); d1 = sorted(list(filter(os.path.isdir, os.listdir(tests)))); d2 = sorted(list(filter(os.path.isdir, [f"models/{x}" for x in model_tests]))); d1.remove("models"); d = d2 + d1; print(d)')"
+          echo "matrix=$(python3 -c 'import os; tests = os.getcwd(); model_tests = os.listdir(os.path.join(tests, "models")); d1 = sorted(list(filter(os.path.isdir, os.listdir(tests)))); d2 = sorted(list(filter(os.path.isdir, [f"models/{x}" for x in model_tests]))); d1.remove("models"); d = d2 + d1; print(d)')" >> $GITHUB_OUTPUT
 
       - name: NVIDIA-SMI
         run: |

.github/workflows/self-past.yml

@@ -92,7 +92,7 @@ jobs:
         name: Identify models to test
         run: |
           cd tests
-          echo "::set-output name=matrix::$(python3 -c 'import os; tests = os.getcwd(); model_tests = os.listdir(os.path.join(tests, "models")); d1 = sorted(list(filter(os.path.isdir, os.listdir(tests)))); d2 = sorted(list(filter(os.path.isdir, [f"models/{x}" for x in model_tests]))); d1.remove("models"); d = d2 + d1; print(d)')"
+          echo "matrix=$(python3 -c 'import os; tests = os.getcwd(); model_tests = os.listdir(os.path.join(tests, "models")); d1 = sorted(list(filter(os.path.isdir, os.listdir(tests)))); d2 = sorted(list(filter(os.path.isdir, [f"models/{x}" for x in model_tests]))); d1.remove("models"); d = d2 + d1; print(d)')" >> $GITHUB_OUTPUT
 
   run_tests_single_gpu:
     name: Model tests

.github/workflows/self-push-caller.yml

@@ -32,7 +32,7 @@ jobs:
           run: |
             for file in ${{ steps.changed-files.outputs.all_changed_files }}; do
               if [ `basename "${file}"` = "setup.py" ]; then
-                echo ::set-output name=changed::"1"
+                echo "changed=1" >> $GITHUB_OUTPUT
               fi
             done
 

.github/workflows/self-push.yml

@@ -145,8 +145,8 @@ jobs:
           fi
           echo $keys
           echo $test_map
-          echo "::set-output name=matrix::$keys"
-          echo "::set-output name=test_map::$test_map"
+          echo "matrix=$keys" >> $GITHUB_OUTPUT
+          echo "test_map=$test_map" >> $GITHUB_OUTPUT
 
   run_tests_single_gpu:
     name: Model tests

.github/workflows/self-scheduled.yml

@@ -82,7 +82,7 @@ jobs:
         name: Identify models to test
         working-directory: /transformers/tests
         run: |
-          echo "::set-output name=matrix::$(python3 -c 'import os; tests = os.getcwd(); model_tests = os.listdir(os.path.join(tests, "models")); d1 = sorted(list(filter(os.path.isdir, os.listdir(tests)))); d2 = sorted(list(filter(os.path.isdir, [f"models/{x}" for x in model_tests]))); d1.remove("models"); d = d2 + d1; print(d)')"
+          echo "matrix=$(python3 -c 'import os; tests = os.getcwd(); model_tests = os.listdir(os.path.join(tests, "models")); d1 = sorted(list(filter(os.path.isdir, os.listdir(tests)))); d2 = sorted(list(filter(os.path.isdir, [f"models/{x}" for x in model_tests]))); d1.remove("models"); d = d2 + d1; print(d)')" >> $GITHUB_OUTPUT
 
       - name: NVIDIA-SMI
         run: |

README.md

@@ -272,6 +272,7 @@ Current number of checkpoints: ![](https://img.shields.io/endpoint?url=https://h
 1. **[BERTweet](https://huggingface.co/docs/transformers/model_doc/bertweet)** (from VinAI Research) released with the paper [BERTweet: A pre-trained language model for English Tweets](https://aclanthology.org/2020.emnlp-demos.2/) by Dat Quoc Nguyen, Thanh Vu and Anh Tuan Nguyen.
 1. **[BigBird-Pegasus](https://huggingface.co/docs/transformers/model_doc/bigbird_pegasus)** (from Google Research) released with the paper [Big Bird: Transformers for Longer Sequences](https://arxiv.org/abs/2007.14062) by Manzil Zaheer, Guru Guruganesh, Avinava Dubey, Joshua Ainslie, Chris Alberti, Santiago Ontanon, Philip Pham, Anirudh Ravula, Qifan Wang, Li Yang, Amr Ahmed.
 1. **[BigBird-RoBERTa](https://huggingface.co/docs/transformers/model_doc/big_bird)** (from Google Research) released with the paper [Big Bird: Transformers for Longer Sequences](https://arxiv.org/abs/2007.14062) by Manzil Zaheer, Guru Guruganesh, Avinava Dubey, Joshua Ainslie, Chris Alberti, Santiago Ontanon, Philip Pham, Anirudh Ravula, Qifan Wang, Li Yang, Amr Ahmed.
+1. **[BioGpt](https://huggingface.co/docs/transformers/main/model_doc/biogpt)** (from Microsoft Research AI4Science) released with the paper [BioGPT: generative pre-trained transformer for biomedical text generation and mining](https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbac409/6713511?guestAccessKey=a66d9b5d-4f83-4017-bb52-405815c907b9) by Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon and Tie-Yan Liu.
 1. **[Blenderbot](https://huggingface.co/docs/transformers/model_doc/blenderbot)** (from Facebook) released with the paper [Recipes for building an open-domain chatbot](https://arxiv.org/abs/2004.13637) by Stephen Roller, Emily Dinan, Naman Goyal, Da Ju, Mary Williamson, Yinhan Liu, Jing Xu, Myle Ott, Kurt Shuster, Eric M. Smith, Y-Lan Boureau, Jason Weston.
 1. **[BlenderbotSmall](https://huggingface.co/docs/transformers/model_doc/blenderbot-small)** (from Facebook) released with the paper [Recipes for building an open-domain chatbot](https://arxiv.org/abs/2004.13637) by Stephen Roller, Emily Dinan, Naman Goyal, Da Ju, Mary Williamson, Yinhan Liu, Jing Xu, Myle Ott, Kurt Shuster, Eric M. Smith, Y-Lan Boureau, Jason Weston.
 1. **[BLOOM](https://huggingface.co/docs/transformers/model_doc/bloom)** (from BigScience workshop) released by the [BigScience Workshop](https://bigscience.huggingface.co/).

README_es.md

@@ -272,6 +272,7 @@ Número actual de puntos de control: ![](https://img.shields.io/endpoint?url=htt
 1. **[BERTweet](https://huggingface.co/docs/transformers/model_doc/bertweet)** (from VinAI Research) released with the paper [BERTweet: A pre-trained language model for English Tweets](https://aclanthology.org/2020.emnlp-demos.2/) by Dat Quoc Nguyen, Thanh Vu and Anh Tuan Nguyen.
 1. **[BigBird-Pegasus](https://huggingface.co/docs/transformers/model_doc/bigbird_pegasus)** (from Google Research) released with the paper [Big Bird: Transformers for Longer Sequences](https://arxiv.org/abs/2007.14062) by Manzil Zaheer, Guru Guruganesh, Avinava Dubey, Joshua Ainslie, Chris Alberti, Santiago Ontanon, Philip Pham, Anirudh Ravula, Qifan Wang, Li Yang, Amr Ahmed.
 1. **[BigBird-RoBERTa](https://huggingface.co/docs/transformers/model_doc/big_bird)** (from Google Research) released with the paper [Big Bird: Transformers for Longer Sequences](https://arxiv.org/abs/2007.14062) by Manzil Zaheer, Guru Guruganesh, Avinava Dubey, Joshua Ainslie, Chris Alberti, Santiago Ontanon, Philip Pham, Anirudh Ravula, Qifan Wang, Li Yang, Amr Ahmed.
+1. **[BioGpt](https://huggingface.co/docs/transformers/main/model_doc/biogpt)** (from Microsoft Research AI4Science) released with the paper [BioGPT: generative pre-trained transformer for biomedical text generation and mining](https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbac409/6713511?guestAccessKey=a66d9b5d-4f83-4017-bb52-405815c907b9) by Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon and Tie-Yan Liu.
 1. **[Blenderbot](https://huggingface.co/docs/transformers/model_doc/blenderbot)** (from Facebook) released with the paper [Recipes for building an open-domain chatbot](https://arxiv.org/abs/2004.13637) by Stephen Roller, Emily Dinan, Naman Goyal, Da Ju, Mary Williamson, Yinhan Liu, Jing Xu, Myle Ott, Kurt Shuster, Eric M. Smith, Y-Lan Boureau, Jason Weston.
 1. **[BlenderbotSmall](https://huggingface.co/docs/transformers/model_doc/blenderbot-small)** (from Facebook) released with the paper [Recipes for building an open-domain chatbot](https://arxiv.org/abs/2004.13637) by Stephen Roller, Emily Dinan, Naman Goyal, Da Ju, Mary Williamson, Yinhan Liu, Jing Xu, Myle Ott, Kurt Shuster, Eric M. Smith, Y-Lan Boureau, Jason Weston.
 1. **[BLOOM](https://huggingface.co/docs/transformers/model_doc/bloom)** (from BigScience workshop) released by the [BigScience Workshop](https://bigscience.huggingface.co/).

README_ja.md

@@ -307,6 +307,7 @@ Flax、PyTorch、TensorFlowをcondaでインストールする方法は、それ
 1. **[BERTweet](https://huggingface.co/docs/transformers/model_doc/bertweet)** (from VinAI Research) released with the paper [BERTweet: A pre-trained language model for English Tweets](https://aclanthology.org/2020.emnlp-demos.2/) by Dat Quoc Nguyen, Thanh Vu and Anh Tuan Nguyen.
 1. **[BigBird-Pegasus](https://huggingface.co/docs/transformers/model_doc/bigbird_pegasus)** (from Google Research) released with the paper [Big Bird: Transformers for Longer Sequences](https://arxiv.org/abs/2007.14062) by Manzil Zaheer, Guru Guruganesh, Avinava Dubey, Joshua Ainslie, Chris Alberti, Santiago Ontanon, Philip Pham, Anirudh Ravula, Qifan Wang, Li Yang, Amr Ahmed.
 1. **[BigBird-RoBERTa](https://huggingface.co/docs/transformers/model_doc/big_bird)** (from Google Research) released with the paper [Big Bird: Transformers for Longer Sequences](https://arxiv.org/abs/2007.14062) by Manzil Zaheer, Guru Guruganesh, Avinava Dubey, Joshua Ainslie, Chris Alberti, Santiago Ontanon, Philip Pham, Anirudh Ravula, Qifan Wang, Li Yang, Amr Ahmed.
+1. **[BioGpt](https://huggingface.co/docs/transformers/main/model_doc/biogpt)** (from Microsoft Research AI4Science) released with the paper [BioGPT: generative pre-trained transformer for biomedical text generation and mining](https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbac409/6713511?guestAccessKey=a66d9b5d-4f83-4017-bb52-405815c907b9) by Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon and Tie-Yan Liu.
 1. **[Blenderbot](https://huggingface.co/docs/transformers/model_doc/blenderbot)** (from Facebook) released with the paper [Recipes for building an open-domain chatbot](https://arxiv.org/abs/2004.13637) by Stephen Roller, Emily Dinan, Naman Goyal, Da Ju, Mary Williamson, Yinhan Liu, Jing Xu, Myle Ott, Kurt Shuster, Eric M. Smith, Y-Lan Boureau, Jason Weston.
 1. **[BlenderbotSmall](https://huggingface.co/docs/transformers/model_doc/blenderbot-small)** (from Facebook) released with the paper [Recipes for building an open-domain chatbot](https://arxiv.org/abs/2004.13637) by Stephen Roller, Emily Dinan, Naman Goyal, Da Ju, Mary Williamson, Yinhan Liu, Jing Xu, Myle Ott, Kurt Shuster, Eric M. Smith, Y-Lan Boureau, Jason Weston.
 1. **[BLOOM](https://huggingface.co/docs/transformers/model_doc/bloom)** (from BigScience workshop) released by the [BigScience Workshop](https://bigscience.huggingface.co/).

README_ko.md

@@ -222,6 +222,7 @@ Flax, PyTorch, TensorFlow 설치 페이지에서 이들을 conda로 설치하는
 1. **[BERTweet](https://huggingface.co/docs/transformers/model_doc/bertweet)** (from VinAI Research) released with the paper [BERTweet: A pre-trained language model for English Tweets](https://aclanthology.org/2020.emnlp-demos.2/) by Dat Quoc Nguyen, Thanh Vu and Anh Tuan Nguyen.
 1. **[BigBird-Pegasus](https://huggingface.co/docs/transformers/model_doc/bigbird_pegasus)** (from Google Research) released with the paper [Big Bird: Transformers for Longer Sequences](https://arxiv.org/abs/2007.14062) by Manzil Zaheer, Guru Guruganesh, Avinava Dubey, Joshua Ainslie, Chris Alberti, Santiago Ontanon, Philip Pham, Anirudh Ravula, Qifan Wang, Li Yang, Amr Ahmed.
 1. **[BigBird-RoBERTa](https://huggingface.co/docs/transformers/model_doc/big_bird)** (from Google Research) released with the paper [Big Bird: Transformers for Longer Sequences](https://arxiv.org/abs/2007.14062) by Manzil Zaheer, Guru Guruganesh, Avinava Dubey, Joshua Ainslie, Chris Alberti, Santiago Ontanon, Philip Pham, Anirudh Ravula, Qifan Wang, Li Yang, Amr Ahmed.
+1. **[BioGpt](https://huggingface.co/docs/transformers/main/model_doc/biogpt)** (from Microsoft Research AI4Science) released with the paper [BioGPT: generative pre-trained transformer for biomedical text generation and mining](https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbac409/6713511?guestAccessKey=a66d9b5d-4f83-4017-bb52-405815c907b9) by Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon and Tie-Yan Liu.
 1. **[Blenderbot](https://huggingface.co/docs/transformers/model_doc/blenderbot)** (from Facebook) released with the paper [Recipes for building an open-domain chatbot](https://arxiv.org/abs/2004.13637) by Stephen Roller, Emily Dinan, Naman Goyal, Da Ju, Mary Williamson, Yinhan Liu, Jing Xu, Myle Ott, Kurt Shuster, Eric M. Smith, Y-Lan Boureau, Jason Weston.
 1. **[BlenderbotSmall](https://huggingface.co/docs/transformers/model_doc/blenderbot-small)** (from Facebook) released with the paper [Recipes for building an open-domain chatbot](https://arxiv.org/abs/2004.13637) by Stephen Roller, Emily Dinan, Naman Goyal, Da Ju, Mary Williamson, Yinhan Liu, Jing Xu, Myle Ott, Kurt Shuster, Eric M. Smith, Y-Lan Boureau, Jason Weston.
 1. **[BLOOM](https://huggingface.co/docs/transformers/model_doc/bloom)** (from BigScience workshop) released by the [BigScience Workshop](https://bigscience.huggingface.co/).

README_zh-hans.md

@@ -246,6 +246,7 @@ conda install -c huggingface transformers
 1. **[BERTweet](https://huggingface.co/docs/transformers/model_doc/bertweet)** (来自 VinAI Research) 伴随论文 [BERTweet: A pre-trained language model for English Tweets](https://aclanthology.org/2020.emnlp-demos.2/) 由 Dat Quoc Nguyen, Thanh Vu and Anh Tuan Nguyen 发布。
 1. **[BigBird-Pegasus](https://huggingface.co/docs/transformers/model_doc/bigbird_pegasus)** (来自 Google Research) 伴随论文 [Big Bird: Transformers for Longer Sequences](https://arxiv.org/abs/2007.14062) 由 Manzil Zaheer, Guru Guruganesh, Avinava Dubey, Joshua Ainslie, Chris Alberti, Santiago Ontanon, Philip Pham, Anirudh Ravula, Qifan Wang, Li Yang, Amr Ahmed 发布。
 1. **[BigBird-RoBERTa](https://huggingface.co/docs/transformers/model_doc/big_bird)** (来自 Google Research) 伴随论文 [Big Bird: Transformers for Longer Sequences](https://arxiv.org/abs/2007.14062) 由 Manzil Zaheer, Guru Guruganesh, Avinava Dubey, Joshua Ainslie, Chris Alberti, Santiago Ontanon, Philip Pham, Anirudh Ravula, Qifan Wang, Li Yang, Amr Ahmed 发布。
+1. **[BioGpt](https://huggingface.co/docs/transformers/main/model_doc/biogpt)** (来自 Microsoft Research AI4Science) 伴随论文 [BioGPT: generative pre-trained transformer for biomedical text generation and mining](https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbac409/6713511?guestAccessKey=a66d9b5d-4f83-4017-bb52-405815c907b9) 由 Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon and Tie-Yan Liu 发布。
 1. **[Blenderbot](https://huggingface.co/docs/transformers/model_doc/blenderbot)** (来自 Facebook) 伴随论文 [Recipes for building an open-domain chatbot](https://arxiv.org/abs/2004.13637) 由 Stephen Roller, Emily Dinan, Naman Goyal, Da Ju, Mary Williamson, Yinhan Liu, Jing Xu, Myle Ott, Kurt Shuster, Eric M. Smith, Y-Lan Boureau, Jason Weston 发布。
 1. **[BlenderbotSmall](https://huggingface.co/docs/transformers/model_doc/blenderbot-small)** (来自 Facebook) 伴随论文 [Recipes for building an open-domain chatbot](https://arxiv.org/abs/2004.13637) 由 Stephen Roller, Emily Dinan, Naman Goyal, Da Ju, Mary Williamson, Yinhan Liu, Jing Xu, Myle Ott, Kurt Shuster, Eric M. Smith, Y-Lan Boureau, Jason Weston 发布。
 1. **[BLOOM](https://huggingface.co/docs/transformers/model_doc/bloom)** (from BigScience workshop) released by the [BigScience Workshop](https://bigscience.huggingface.co/).

README_zh-hant.md

@@ -258,6 +258,7 @@ conda install -c huggingface transformers
 1. **[BERTweet](https://huggingface.co/docs/transformers/model_doc/bertweet)** (from VinAI Research) released with the paper [BERTweet: A pre-trained language model for English Tweets](https://aclanthology.org/2020.emnlp-demos.2/) by Dat Quoc Nguyen, Thanh Vu and Anh Tuan Nguyen.
 1. **[BigBird-Pegasus](https://huggingface.co/docs/transformers/model_doc/bigbird_pegasus)** (from Google Research) released with the paper [Big Bird: Transformers for Longer Sequences](https://arxiv.org/abs/2007.14062) by Manzil Zaheer, Guru Guruganesh, Avinava Dubey, Joshua Ainslie, Chris Alberti, Santiago Ontanon, Philip Pham, Anirudh Ravula, Qifan Wang, Li Yang, Amr Ahmed.
 1. **[BigBird-RoBERTa](https://huggingface.co/docs/transformers/model_doc/big_bird)** (from Google Research) released with the paper [Big Bird: Transformers for Longer Sequences](https://arxiv.org/abs/2007.14062) by Manzil Zaheer, Guru Guruganesh, Avinava Dubey, Joshua Ainslie, Chris Alberti, Santiago Ontanon, Philip Pham, Anirudh Ravula, Qifan Wang, Li Yang, Amr Ahmed.
+1. **[BioGpt](https://huggingface.co/docs/transformers/main/model_doc/biogpt)** (from Microsoft Research AI4Science) released with the paper [BioGPT: generative pre-trained transformer for biomedical text generation and mining](https://academic.oup.com/bib/advance-article/doi/10.1093/bib/bbac409/6713511?guestAccessKey=a66d9b5d-4f83-4017-bb52-405815c907b9) by Renqian Luo, Liai Sun, Yingce Xia, Tao Qin, Sheng Zhang, Hoifung Poon and Tie-Yan Liu.
 1. **[Blenderbot](https://huggingface.co/docs/transformers/model_doc/blenderbot)** (from Facebook) released with the paper [Recipes for building an open-domain chatbot](https://arxiv.org/abs/2004.13637) by Stephen Roller, Emily Dinan, Naman Goyal, Da Ju, Mary Williamson, Yinhan Liu, Jing Xu, Myle Ott, Kurt Shuster, Eric M. Smith, Y-Lan Boureau, Jason Weston.
 1. **[BlenderbotSmall](https://huggingface.co/docs/transformers/model_doc/blenderbot-small)** (from Facebook) released with the paper [Recipes for building an open-domain chatbot](https://arxiv.org/abs/2004.13637) by Stephen Roller, Emily Dinan, Naman Goyal, Da Ju, Mary Williamson, Yinhan Liu, Jing Xu, Myle Ott, Kurt Shuster, Eric M. Smith, Y-Lan Boureau, Jason Weston.
 1. **[BLOOM](https://huggingface.co/docs/transformers/model_doc/bloom)** (from BigScience workshop) released by the [BigScience Workshop](https://bigscience.huggingface.co/).

docker/transformers-all-latest-gpu/Dockerfile

@@ -56,6 +56,8 @@ RUN python3 -m pip install --no-cache-dir decord
 # For `dinat` model
 RUN python3 -m pip install --no-cache-dir natten
 
+RUN python3 -m pip install --no-cache-dir natten -f https://shi-labs.com/natten/wheels/$CUDA/
+
 # When installing in editable mode, `transformers` is not recognized as a package.
 # this line must be added in order for python to be aware of transformers.
 RUN cd transformers && python3 setup.py develop

docker/transformers-tensorflow-gpu/Dockerfile

@@ -18,6 +18,8 @@ RUN [ ${#TENSORFLOW} -gt 0 ] && VERSION='tensorflow=='$TENSORFLOW'.*' ||  VERSIO
 RUN python3 -m pip uninstall -y torch flax
 RUN python3 -m pip install -U "itsdangerous<2.1.0"
 
+RUN python3 -m pip install --no-cache-dir -U tensorflow_probability
+
 # When installing in editable mode, `transformers` is not recognized as a package.
 # this line must be added in order for python to be aware of transformers.
 RUN cd transformers && python3 setup.py develop

docs/source/en/_toctree.yml

@@ -209,6 +209,8 @@
         title: BigBird
       - local: model_doc/bigbird_pegasus
         title: BigBirdPegasus
+      - local: model_doc/biogpt
+        title: BioGpt
       - local: model_doc/blenderbot
         title: Blenderbot
       - local: model_doc/blenderbot-small