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bug(medcat): CU-869b07hr0 Add optional extra for embedding linker #209

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Merged
merged 3 commits into from
Nov 5, 2025
Merged

bug(medcat): CU-869b07hr0 Add optional extra for embedding linker #209

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24543a6
CU-869b07hr0: ADd explicit optional extras for embdedded linker.
mart-r Oct 30, 2025
949b6cd
CU-869b07hr0: Add check for optional extras to embedded linker
mart-r Oct 30, 2025
33866e0
CU-869b07hr0: Fix minor typo
mart-r Nov 5, 2025
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17 changes: 13 additions & 4 deletions medcat-v2/medcat/components/linking/embedding_linker.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,16 +5,25 @@
from medcat.tokenizing.tokenizers import BaseTokenizer
from typing import Optional, Iterator, Set
from medcat.vocab import Vocab
from torch import Tensor
from transformers import AutoTokenizer, AutoModel
from medcat.utils.postprocessing import create_main_ann
from tqdm import tqdm
from collections import defaultdict
import torch.nn.functional as F
import torch
import logging
import math

from medcat.utils.import_utils import ensure_optional_extras_installed
import medcat

# NOTE: the below needs to be before torch/transformers imports
_EXTRA_NAME = "embed-linker"
ensure_optional_extras_installed(medcat.__name__, _EXTRA_NAME)

# avoid linting issues due to above check
from torch import Tensor # noqa: E402
from transformers import AutoTokenizer, AutoModel # noqa: E402
import torch.nn.functional as F # noqa: E402
import torch # noqa: E402

logger = logging.getLogger(__name__)


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4 changes: 4 additions & 0 deletions medcat-v2/pyproject.toml
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Expand Up @@ -113,6 +113,10 @@ rel_cat = [
"scikit-learn>=1.1.3,<2.0",
"torch>=2.4.0,<3.0",
]
embed_linker = [
"transformers>=4.41.0,<5.0", # avoid major bump
"torch>=2.4.0,<3.0",
]
test = [] # TODO - list

[project.urls]
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