mypy-status mypy exited with status 1.

flair/data.py 12: error: Unused "type: ignore" comment [unused-ignore] 329: note: "add_label" of "DataPoint" defined here 529: error: Argument 2 of "add_label" is incompatible with supertype "DataPoint"; supertype defines the argument type as "Union[str, Label]" [override] 529: note: This violates the Liskov substitution principle 529: note: See https://mypy.readthedocs.io/en/stable/common_issues.html#incompatible-overrides 626: error: Argument 2 of "add_label" is incompatible with supertype "DataPoint"; supertype defines the argument type as "Union[str, Label]" [override] 626: note: This violates the Liskov substitution principle 626: note: See https://mypy.readthedocs.io/en/stable/common_issues.html#incompatible-overrides 632: error: Unexpected keyword argument "value" for "add_label" of "DataPoint" [call-arg] 329: note: "add_label" of "DataPoint" defined here 329: note: "add_label" of "DataPoint" defined here 329: note: "add_label" of "DataPoint" defined here 329: note: "add_label" of "DataPoint" defined here 329: note: "add_label" of "DataPoint" defined here

ruff pytest_ruff.RuffError: flair/data.py:9:52: F401 [*] `typing.Tuple` imported but unused | 7 | from operator import itemgetter 8 | from pathlib import Path 9 | from typing import Dict, Iterable, List, Optional, Tuple, Union, cast | ^^^^^ F401 10 | 11 | import torch | = help: Remove unused import: `typing.Tuple` flair/data.py:12:36: PGH003 Use specific rule codes when ignoring type issues | 11 | import torch 12 | from deprecated import deprecated # type: ignore | ^^^^^^^^^^^^^^ PGH003 13 | from torch.utils.data import Dataset, IterableDataset 14 | from torch.utils.data.dataset import ConcatDataset, Subset | flair/data.py:427:5: D415 [*] First line should end with a period, question mark, or exclamation point | 426 | class EntityLinkingCandidate: 427 | """Represent a single candidate returned by a CandidateGenerator""" | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ D415 428 | 429 | def __init__( | = help: Add closing punctuation flair/data.py:437:9: D205 1 blank line required between summary line and description | 435 | additional_ids: Optional[Union[List[str], str]] = None, 436 | ): 437 | """ | _________^ 438 | | :param concept_id: Identifier of the entity / concept from the knowledge base / ontology 439 | | :param concept_name: (Canonical) name of the entity / concept from the knowledge base / ontology 440 | | :param score: Matching score of the entity / concept according to the entity mention 441 | | :param additional_ids: List of additional identifiers for the concept / entity in the KB / ontology 442 | | :param database_name: Name of the knowlege base / ontology 443 | | """ | |___________^ D205 444 | self.concept_id = concept_id 445 | self.concept_name = concept_name | = help: Insert single blank line flair/data.py:437:9: D212 [*] Multi-line docstring summary should start at the first line | 435 | additional_ids: Optional[Union[List[str], str]] = None, 436 | ): 437 | """ | _________^ 438 | | :param concept_id: Identifier of the entity / concept from the knowledge base / ontology 439 | | :param concept_name: (Canonical) name of the entity / concept from the knowledge base / ontology 440 | | :param score: Matching score of the entity / concept according to the entity mention 441 | | :param additional_ids: List of additional identifiers for the concept / entity in the KB / ontology 442 | | :param database_name: Name of the knowlege base / ontology 443 | | """ | |___________^ D212 444 | self.concept_id = concept_id 445 | self.concept_name = concept_name | = help: Remove whitespace after opening quotes flair/data.py:461:5: D205 1 blank line required between summary line and description | 460 | class EntityLinkingLabel(Label): 461 | """ | _____^ 462 | | Label class models entity linking annotations. Each entity linking label has a data point it refers 463 | | to as well as the identifier and name of the concept / entity from a knowledge base or ontology. 464 | | Optionally, additional concepts identifier and the database name can be provided. 465 | | """ | |_______^ D205 466 | 467 | def __init__(self, data_point: DataPoint, candidates: List[EntityLinkingCandidate]): | = help: Insert single blank line flair/data.py:461:5: D212 [*] Multi-line docstring summary should start at the first line | 460 | class EntityLinkingLabel(Label): 461 | """ | _____^ 462 | | Label class models entity linking annotations. Each entity linking label has a data point it refers 463 | | to as well as the identifier and name of the concept / entity from a knowledge base or ontology. 464 | | Optionally, additional concepts identifier and the database name can be provided. 4

flair/datasets/biomedical.py 514: error: Incompatible default for argument "base_path" (default has type "None", argument has type "Union[str, Path]") [assignment] 514: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True 514: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase 600: error: Incompatible default for argument "base_path" (default has type "None", argument has type "Union[str, Path]") [assignment] 600: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True 600: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase 672: error: Incompatible default for argument "base_path" (default has type "None", argument has type "Union[str, Path]") [assignment] 672: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True 672: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase 742: error: Incompatible default for argument "base_path" (default has type "None", argument has type "Union[str, Path]") [assignment] 742: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True 742: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase 833: error: Incompatible default for argument "base_path" (default has type "None", argument has type "Union[str, Path]") [assignment] 833: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True 833: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase 2052: error: "Type[CHEMDNER]" has no attribute "default_dir" [attr-defined] 2096: error: Incompatible default for argument "tokenizer" (default has type "None", argument has type "Tokenizer") [assignment] 2096: note: PEP 484 prohibits implicit Optional. Accordingly, mypy has changed its default to no_implicit_optional=True 2096: note: Use https://github.com/hauntsaninja/no_implicit_optional to automatically upgrade your codebase

Black format check --- /home/runner/work/flair/flair/flair/datasets/biomedical.py 2023-07-12 16:11:43.298681 +0000 +++ /home/runner/work/flair/flair/flair/datasets/biomedical.py 2023-07-12 16:16:58.689536 +0000 @@ -2035,11 +2035,10 @@ conll_writer.write_to_conll(dev_data, dev_file) conll_writer.write_to_conll(test_data, test_file) super().__init__(data_folder, columns, in_memory=in_memory) - @staticmethod def download_dataset(data_dir: Path): data_url = "https://biocreative.bioinformatics.udel.edu/media/store/files/2014/chemdner_corpus.tar.gz" data_path = cached_path(data_url, data_dir) unpack_file(data_path, data_dir) @@ -4220,11 +4219,10 @@ conll_writer.write_to_conll(dev_data, dev_file) conll_writer.write_to_conll(test_data, test_file) super().__init__(data_folder, columns, in_memory=in_memory) - @staticmethod @AbstractMethod def download_corpus(data_folder: Path) -> Tuple[Path, Path, Path]: pass @@ -4393,11 +4391,10 @@ conll_writer.write_to_conll(dev_data, dev_file) conll_writer.write_to_conll(test_data, test_file) super().__init__(data_folder, columns, in_memory=in_memory) - @staticmethod @AbstractMethod def download_corpus(data_folder: Path): corpus_url = "http://nactem.ac.uk/anatomytagger/AnatEM-1.0.2.tar.gz" corpus_archive = cached_path(corpus_url, data_folder) @@ -4619,11 +4616,10 @@ BioBertHelper.convert_and_write(common_path / "JNLPBA", data_folder, tag_type=GENE_TAG) super().__init__(data_folder, columns, in_memory=in_memory) - class BIOBERT_CHEMICAL_BC5CDR(ColumnCorpus): """BC5CDR corpus with chemical annotations as used in the evaluation of BioBERT. For further details regarding BioBERT and it's evaluation, see Lee et al.: @@ -4651,11 +4647,10 @@ BioBertHelper.convert_and_write(common_path / "BC5CDR-chem", data_folder, tag_type=CHEMICAL_TAG) super().__init__(data_folder, columns, in_memory=in_memory) - class BIOBERT_DISEASE_BC5CDR(ColumnCorpus): """BC5CDR corpus with disease annotations as used in the evaluation of BioBERT. For further details regarding BioBERT and it's evaluation, see Lee et al.: @@ -4683,11 +4678,10 @@ BioBertHelper.convert_and_write(common_path / "BC5CDR-disease", data_folder, tag_type=DISEASE_TAG) super().__init__(data_folder, columns, in_memory=in_memory) - class BIOBERT_DISEASE_NCBI(ColumnCorpus): """NCBI disease corpus as used in the evaluation of BioBERT. For further details regarding BioBERT and it's evaluation, see Lee et al.: @@ -4715,11 +4709,10 @@ BioBertHelper.convert_and_write(common_path / "NCBI-disease", data_folder, tag_type=DISEASE_TAG) super().__init__(data_folder, columns, in_memory=in_memory) - class BIOBERT_SPECIES_LINNAEUS(ColumnCorpus): """Linneaeus corpus with species annotations as used in the evaluation of BioBERT. For further details regarding BioBERT and it's evaluation, see Lee et al.: @@ -4745,11 +4738,10 @@ if not (common_path / "linnaeus").exists(): BioBertHelper.download_corpora(common_path) BioBertHelper.convert_and_write(common_path / "linnaeus", data_folder, tag_type=SPECIES_TAG) super().__init__(data_folder, columns, in_memory=in_memory) - class BIOBERT_SPECIES_S800(ColumnCorpus): """S800 corpus with species annotations as used in the evaluation of BioBERT.

ruff pytest_ruff.RuffError: flair/datasets/biomedical.py:514:20: RUF013 [*] PEP 484 prohibits implicit `Optional` | 512 | def __init__( 513 | self, 514 | base_path: Union[str, Path] = None, | ^^^^^^^^^^^^^^^^ RUF013 515 | ): 516 | """:param base_path: Path to the corpus on your machine""" | = help: Convert to `Optional[T]` flair/datasets/biomedical.py:517:9: SIM108 [*] Use ternary operator `base_path = flair.cache_root / "datasets" if base_path is None else Path(base_path)` instead of `if`-`else`-block | 515 | ): 516 | """:param base_path: Path to the corpus on your machine""" 517 | if base_path is None: | _________^ 518 | | base_path = flair.cache_root / "datasets" 519 | | else: 520 | | base_path = Path(base_path) | |_______________________________________^ SIM108 521 | 522 | # this dataset name | = help: Replace `if`-`else`-block with `base_path = flair.cache_root / "datasets" if base_path is None else Path(base_path)` flair/datasets/biomedical.py:539:9: D415 [*] First line should end with a period, question mark, or exclamation point | 537 | @AbstractMethod 538 | def database_name(self) -> str: 539 | """Name of the database represented by the dictionary""" | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ D415 540 | 541 | @AbstractMethod | = help: Add closing punctuation flair/datasets/biomedical.py:543:9: D415 [*] First line should end with a period, question mark, or exclamation point | 541 | @AbstractMethod 542 | def download_dictionary(self, data_dir: Path) -> Path: 543 | """Download dictionary""" | ^^^^^^^^^^^^^^^^^^^^^^^^^ D415 544 | 545 | @AbstractMethod | = help: Add closing punctuation flair/datasets/biomedical.py:547:9: D415 [*] First line should end with a period, question mark, or exclamation point | 545 | @AbstractMethod 546 | def parse_dictionary(self, original_file: Path): 547 | """Parse data into HunFlair format""" | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ D415 548 | 549 | def stream(self) -> Iterator[Tuple[str, str]]: | = help: Add closing punctuation flair/datasets/biomedical.py:550:9: D202 [*] No blank lines allowed after function docstring (found 1) | 549 | def stream(self) -> Iterator[Tuple[str, str]]: 550 | """Stream preprocessed dictionary""" | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ D202 551 | 552 | with open(self.dataset_file) as fp: | = help: Remove blank line(s) after function docstring flair/datasets/biomedical.py:550:9: D415 [*] First line should end with a period, question mark, or exclamation point | 549 | def stream(self) -> Iterator[Tuple[str, str]]: 550 | """Stream preprocessed dictionary""" | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ D415 551 | 552 | with open(self.dataset_file) as fp: | = help: Add closing punctuation flair/datasets/biomedical.py:564:5: D205 1 blank line required between summary line and description | 563 | class ParsedBiomedicalEntityLinkingDictionary(AbstractBiomedicalEntityLinkingDictionary): 564 | """ | _____^ 565 | | Base dictionary with data already in preprocessed format, i.e. every line in the file must 566 | | be formatted as follows: 567 | | 568 | | concept_id||concept_name 569 | | 570 | | If multiple concept ids are associated to a given name they have to be separated by a `|`, e.g. 571 | | 572 | | 7157||TP53|tumor protein p53 573 | | """ | |_______^ D205 574 | 575 | def __init__(self, path: Path, database_name: str): | = help: Insert single blank line flair/datasets/biomedical.py:564:5: D212 [*] Multi-line docstring summary should start at the first line | 563 | class ParsedBiomedicalEntityLinkingDictionary(AbstractBiomedicalEntityLinkingDictionary): 564 | """ | _____^ 565 | |

ruff pytest_ruff.RuffError: flair/datasets/document_classification.py:1480:17: RUF012 Mutable class attributes should be annotated with `typing.ClassVar` | 1479 | class GLUE_SST2(CSVClassificationCorpus): 1480 | label_map = {0: "negative", 1: "positive"} | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ RUF012 1481 | 1482 | def __init__( |

ruff pytest_ruff.RuffError: flair/datasets/sequence_labeling.py:423:13: RUF012 Mutable class attributes should be annotated with `typing.ClassVar` | 421 | SPACE_AFTER_KEY = "space-after" 422 | # special key for feature columns 423 | FEATS = ["feats", "misc"] | ^^^^^^^^^^^^^^^^^ RUF012 424 | # special key for dependency head id 425 | HEAD = ["head", "head_id"] | flair/datasets/sequence_labeling.py:425:12: RUF012 Mutable class attributes should be annotated with `typing.ClassVar` | 423 | FEATS = ["feats", "misc"] 424 | # special key for dependency head id 425 | HEAD = ["head", "head_id"] | ^^^^^^^^^^^^^^^^^^^ RUF012 426 | 427 | def __init__( |

flair/datasets/text_text.py 414: error: Unexpected keyword argument "value" for "add_label" of "DataPoint" [call-arg]