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

* CU-869b07hr0: ADd explicit optional extras for embdedded linker.

* CU-869b07hr0: Add check for optional extras to embedded linker

* CU-869b07hr0: Fix minor typo

Author: mart-r

medcat-v2/medcat/components/linking/embedding_linker.py

@@ -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__)
 
 

medcat-v2/pyproject.toml

@@ -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]