From 86828f90ae9436e4a00d4756879a474757e19f2e Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Tue, 31 Mar 2026 15:01:58 +0100 Subject: [PATCH 1/4] CU-869cqbd24: Allow transformers 5 in core lib --- medcat-v2/pyproject.toml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/medcat-v2/pyproject.toml b/medcat-v2/pyproject.toml index 26179a9b6..c8a802f62 100644 --- a/medcat-v2/pyproject.toml +++ b/medcat-v2/pyproject.toml @@ -91,7 +91,7 @@ spacy = [ "spacy", ] meta_cat = [ - "transformers>=4.41.0,<5.0", # avoid major bump + "transformers>=4.41.0,<6.0", # avoid major bump "peft>0.8.2,<1.0", "torch>=2.4.0,<3.0", "scikit-learn>=1.1.3,<2.0", @@ -104,7 +104,7 @@ dict_ner = [ ] deid = [ "datasets>=2.2.2,<3.0.0", - "transformers>=4.41.0,<5.0", # avoid major bump + "transformers>=4.41.0,<6.0", # avoid major bump "scikit-learn>=1.1.3,<2.0", "torch>=2.4.0,<3.0", # since 3.13 we need to use later version of scipy for it @@ -112,7 +112,7 @@ deid = [ "scipy>=1.14; python_version >= '3.13'", ] rel_cat = [ - "transformers>=4.41.0,<5.0", # avoid major bump + "transformers>=4.41.0,<6.0", # avoid major bump "scikit-learn>=1.1.3,<2.0", "torch>=2.4.0,<3.0", ] From 81a6c68de3d7ec8a578526012a9e28d0069d1cb0 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Tue, 31 Mar 2026 15:02:18 +0100 Subject: [PATCH 2/4] CU-869cqbd24: Allow transformers 5 in medcat-service --- medcat-service/requirements.txt | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/medcat-service/requirements.txt b/medcat-service/requirements.txt index a6369294d..92d36980c 100644 --- a/medcat-service/requirements.txt +++ b/medcat-service/requirements.txt @@ -4,7 +4,7 @@ simplejson==3.19.3 setuptools-rust==1.11.0 medcat[meta-cat,spacy,deid]~=2.6.0 # pinned because of issues with de-id models and past models (it will not do any de-id) -transformers>=4.34.0,<5.0.0 +transformers>=4.34.0,<6.0.0 requests==2.32.4 fastapi[standard]==0.128.0 pydantic>=2.11.10,<2.12.5 @@ -17,4 +17,4 @@ opentelemetry-resource-detector-containerid==0.60b0 opentelemetry-instrumentation-fastapi==0.60b0 opentelemetry-instrumentation-requests==0.60b0 opentelemetry-instrumentation-threading==0.60b0 -opentelemetry-instrumentation-httpx==0.60b0 \ No newline at end of file +opentelemetry-instrumentation-httpx==0.60b0 From 241c072127e90106965a08b73c07681729e8ca33 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Tue, 31 Mar 2026 16:05:50 +0100 Subject: [PATCH 3/4] CU-869cqbd24: Use shorthand imports for transformers stuff --- .../components/addons/meta_cat/mctokenizers/bert_tokenizer.py | 4 ++-- .../components/addons/relation_extraction/bert/model.py | 2 +- .../components/addons/relation_extraction/bert/tokenizer.py | 2 +- .../components/addons/relation_extraction/llama/model.py | 2 +- .../addons/relation_extraction/modernbert/config.py | 2 +- .../components/addons/relation_extraction/modernbert/model.py | 2 +- .../medcat/components/addons/relation_extraction/tokenizer.py | 2 +- 7 files changed, 8 insertions(+), 8 deletions(-) diff --git a/medcat-v2/medcat/components/addons/meta_cat/mctokenizers/bert_tokenizer.py b/medcat-v2/medcat/components/addons/meta_cat/mctokenizers/bert_tokenizer.py index 4661285d1..dccd39672 100644 --- a/medcat-v2/medcat/components/addons/meta_cat/mctokenizers/bert_tokenizer.py +++ b/medcat-v2/medcat/components/addons/meta_cat/mctokenizers/bert_tokenizer.py @@ -1,7 +1,7 @@ import logging import os from typing import Optional, Union, overload -from transformers.models.bert.tokenization_bert_fast import BertTokenizerFast +from transformers import BertTokenizerFast from medcat.components.addons.meta_cat.mctokenizers.tokenizers import ( TokenizerWrapperBase) @@ -15,7 +15,7 @@ class TokenizerWrapperBERT(TokenizerWrapperBase): MetaCAT models. Args: - transformers.models.bert.tokenization_bert_fast.BertTokenizerFast: + transformers.BertTokenizerFast: A huggingface Fast BERT. """ name = 'bert-tokenizer' diff --git a/medcat-v2/medcat/components/addons/relation_extraction/bert/model.py b/medcat-v2/medcat/components/addons/relation_extraction/bert/model.py index 09549474f..ac297d8fb 100644 --- a/medcat-v2/medcat/components/addons/relation_extraction/bert/model.py +++ b/medcat-v2/medcat/components/addons/relation_extraction/bert/model.py @@ -3,7 +3,7 @@ import torch from torch import nn -from transformers.models.bert.modeling_bert import BertModel +from transformers import BertModel from medcat.config.config_rel_cat import ConfigRelCAT from medcat.components.addons.relation_extraction.ml_utils import ( diff --git a/medcat-v2/medcat/components/addons/relation_extraction/bert/tokenizer.py b/medcat-v2/medcat/components/addons/relation_extraction/bert/tokenizer.py index ac0140c09..07d8d2f40 100644 --- a/medcat-v2/medcat/components/addons/relation_extraction/bert/tokenizer.py +++ b/medcat-v2/medcat/components/addons/relation_extraction/bert/tokenizer.py @@ -1,7 +1,7 @@ import os import logging -from transformers.models.bert.tokenization_bert_fast import BertTokenizerFast +from transformers import BertTokenizerFast from medcat.config.config_rel_cat import ConfigRelCAT from medcat.components.addons.relation_extraction.tokenizer import ( diff --git a/medcat-v2/medcat/components/addons/relation_extraction/llama/model.py b/medcat-v2/medcat/components/addons/relation_extraction/llama/model.py index 2a9f35b87..c939df38f 100644 --- a/medcat-v2/medcat/components/addons/relation_extraction/llama/model.py +++ b/medcat-v2/medcat/components/addons/relation_extraction/llama/model.py @@ -4,7 +4,7 @@ import torch from torch import nn -from transformers.models.llama import LlamaModel +from transformers import LlamaModel from medcat.config.config_rel_cat import ConfigRelCAT from medcat.components.addons.relation_extraction.llama.config import ( diff --git a/medcat-v2/medcat/components/addons/relation_extraction/modernbert/config.py b/medcat-v2/medcat/components/addons/relation_extraction/modernbert/config.py index 274c17d6a..0c80724aa 100644 --- a/medcat-v2/medcat/components/addons/relation_extraction/modernbert/config.py +++ b/medcat-v2/medcat/components/addons/relation_extraction/modernbert/config.py @@ -2,7 +2,7 @@ import os from typing import cast -from transformers.models.modernbert import ModernBertConfig +from transformers import ModernBertConfig from medcat.config.config_rel_cat import ConfigRelCAT from medcat.components.addons.relation_extraction.config import ( diff --git a/medcat-v2/medcat/components/addons/relation_extraction/modernbert/model.py b/medcat-v2/medcat/components/addons/relation_extraction/modernbert/model.py index 8236fbda8..31a158454 100644 --- a/medcat-v2/medcat/components/addons/relation_extraction/modernbert/model.py +++ b/medcat-v2/medcat/components/addons/relation_extraction/modernbert/model.py @@ -3,7 +3,7 @@ import os from torch import nn -from transformers.models.modernbert import ModernBertModel +from transformers import ModernBertModel from medcat.config.config_rel_cat import ConfigRelCAT from medcat.components.addons.relation_extraction.ml_utils import ( diff --git a/medcat-v2/medcat/components/addons/relation_extraction/tokenizer.py b/medcat-v2/medcat/components/addons/relation_extraction/tokenizer.py index cc0dc454f..8d0bc519d 100644 --- a/medcat-v2/medcat/components/addons/relation_extraction/tokenizer.py +++ b/medcat-v2/medcat/components/addons/relation_extraction/tokenizer.py @@ -1,6 +1,6 @@ import os from typing import Optional -from transformers.models.bert.tokenization_bert_fast import BertTokenizerFast +from transformers import BertTokenizerFast from transformers import PreTrainedTokenizerFast import logging From 709cedd8d7d4d75ef5d4314ffc2da23df2918e2e Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Tue, 31 Mar 2026 16:30:26 +0100 Subject: [PATCH 4/4] CU-869cqbd24: Change where a type hint is defined to fix data class issue --- .../components/addons/relation_extraction/bert/config.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/medcat-v2/medcat/components/addons/relation_extraction/bert/config.py b/medcat-v2/medcat/components/addons/relation_extraction/bert/config.py index d53c6b30d..22c67887a 100644 --- a/medcat-v2/medcat/components/addons/relation_extraction/bert/config.py +++ b/medcat-v2/medcat/components/addons/relation_extraction/bert/config.py @@ -17,7 +17,10 @@ class RelExtrBertConfig(RelExtrBaseConfig): name = 'bert-config' pretrained_model_name_or_path = "bert-base-uncased" - hf_model_config: BertConfig + + def __init__(self, *args, **kwargs): + super().__init__(*args, **kwargs) + self.hf_model_config: BertConfig @classmethod def load(cls, pretrained_model_name_or_path: str,