mypy-status mypy exited with status 1.

ruff pytest_ruff.RuffError: flair/models/__init__.py:1:1: I001 [*] Import block is un-sorted or un-formatted | 1 | / from .clustering import ClusteringModel 2 | | from .entity_mention_linking import EntityMentionLinker 3 | | from .entity_linker_model import SpanClassifier 4 | | from .language_model import LanguageModel 5 | | from .lemmatizer_model import Lemmatizer 6 | | from .multitask_model import MultitaskModel 7 | | from .pairwise_classification_model import TextPairClassifier 8 | | from .pairwise_regression_model import TextPairRegressor 9 | | from .regexp_tagger import RegexpTagger 10 | | from .relation_classifier_model import RelationClassifier 11 | | from .relation_extractor_model import RelationExtractor 12 | | from .sequence_tagger_model import SequenceTagger 13 | | from .tars_model import FewshotClassifier, TARSClassifier, TARSTagger 14 | | from .text_classification_model import TextClassifier 15 | | from .text_regression_model import TextRegressor 16 | | from .word_tagger_model import TokenClassifier, WordTagger 17 | | 18 | | __all__ = [ | |_^ I001 19 | "EntityMentionLinker", 20 | "SpanClassifier", | = help: Organize imports

ruff pytest_ruff.RuffError: flair/models/entity_mention_linking.py:831:9: D200 One-line docstring should fit on one line | 829 | dataset_name: Optional[str] = None, 830 | ) -> "EntityMentionLinker": 831 | """Loads a model for biomedical named entity normalization. | _________^ 832 | | 833 | | """ | |___________^ D200 834 | if not isinstance(model_name_or_path, str): 835 | raise ValueError(f"String matching model name has to be an string (and not {type(model_name_or_path)}") | = help: Reformat to one line

flair/models/entity_mention_linking.py 672: error: List comprehension has incompatible type List[Embeddings[Any]]; expected List[DocumentEmbeddings] [misc]

Black format check --- /home/runner/work/flair/flair/flair/models/entity_mention_linking.py 2023-12-24 13:37:14.924253+00:00 +++ /home/runner/work/flair/flair/flair/models/entity_mention_linking.py 2023-12-24 13:40:03.664110+00:00 @@ -90,11 +90,10 @@ MODEL_NAME_TO_DICTIONARY = { "dmis-lab/biosyn-sapbert-bc5cdr-disease": "ctd-disease", "dmis-lab/biosyn-sapbert-ncbi-disease": "ctd-disease", "dmis-lab/biosyn-sapbert-bc5cdr-chemical": "ctd-chemical", "dmis-lab/biosyn-sapbert-bc2gn": "ncbi-gene", - "dmis-lab/biosyn-biobert-bc5cdr-disease": "ctd-chemical", "dmis-lab/biosyn-biobert-ncbi-disease": "ctd-disease", "dmis-lab/biosyn-biobert-bc5cdr-chemical": "ctd-chemical", "dmis-lab/biosyn-biobert-bc2gn": "ncbi-gene", } @@ -788,11 +787,10 @@ if model_name in hf_model_map: model_name = hf_model_map[model_name] return hf_download(model_name) - @classmethod def _init_model_with_state_dict(cls, state: Dict[str, Any], **kwargs) -> "EntityMentionLinker": candidate_generator = CandidateSearchIndex._from_state(state["candidate_search_index"]) preprocessor = EntityPreprocessor._from_state(state["entity_preprocessor"]) entity_label_type = state["entity_label_type"] @@ -826,13 +824,11 @@ sparse_weight: float = DEFAULT_SPARSE_WEIGHT, entity_type: Optional[str] = None, dictionary: Optional[EntityLinkingDictionary] = None, dataset_name: Optional[str] = None, ) -> "EntityMentionLinker": - """Loads a model for biomedical named entity normalization. - - """ + """Loads a model for biomedical named entity normalization.""" if not isinstance(model_name_or_path, str): raise ValueError(f"String matching model name has to be an string (and not {type(model_name_or_path)}") model_name_or_path = cast(str, model_name_or_path) if dictionary is None:

ruff pytest_ruff.RuffError: flair/models/sequence_tagger_model.py:1:1: I001 [*] Import block is un-sorted or un-formatted | 1 | / import logging 2 | | import tempfile 3 | | from pathlib import Path 4 | | from typing import Any, Dict, List, Optional, Tuple, Union, cast 5 | | from urllib.error import HTTPError 6 | | 7 | | import torch 8 | | import torch.nn 9 | | import torch.nn.functional as F 10 | | from torch.nn.utils.rnn import pack_padded_sequence, pad_packed_sequence 11 | | from tqdm import tqdm 12 | | 13 | | import flair.nn 14 | | from flair.data import Dictionary, Label, Sentence, Span, get_spans_from_bio 15 | | from flair.datasets import DataLoader, FlairDatapointDataset 16 | | from flair.embeddings import TokenEmbeddings 17 | | from flair.file_utils import cached_path, unzip_file, hf_download 18 | | from flair.models.sequence_tagger_utils.crf import CRF 19 | | from flair.models.sequence_tagger_utils.viterbi import ViterbiDecoder, ViterbiLoss 20 | | from flair.training_utils import store_embeddings 21 | | 22 | | log = logging.getLogger("flair") | |_^ I001 | = help: Organize imports flair/models/sequence_tagger_model.py:5:26: F401 [*] `urllib.error.HTTPError` imported but unused | 3 | from pathlib import Path 4 | from typing import Any, Dict, List, Optional, Tuple, Union, cast 5 | from urllib.error import HTTPError | ^^^^^^^^^ F401 6 | 7 | import torch | = help: Remove unused import: `urllib.error.HTTPError` flair/models/sequence_tagger_model.py:767:9: F841 Local variable `get_from_model_hub` is assigned to but never used | 765 | cache_dir = Path("models") 766 | 767 | get_from_model_hub = False | ^^^^^^^^^^^^^^^^^^ F841 768 | 769 | # check if model name is a valid local file | = help: Remove assignment to unused variable `get_from_model_hub`

test_biomedical_entity_linking[False] OSError: [Errno 39] Directory not empty: 'cache/flair/models/bio-genes'