lint: ruff fixes

Author: pidoux7

docs/scripts/autorefs/plugin.py

@@ -84,9 +84,7 @@ def handleMatch(self, m, data) -> Union[Element, EvalIDType]:  # type: ignore[ov
 
         return self.makeTag(identifier, text), m.start(0), end
 
-    def evalId(
-        self, data: str, index: int, text: str
-    ) -> EvalIDType:  # noqa: N802 (parent's casing)
+    def evalId(self, data: str, index: int, text: str) -> EvalIDType:  # noqa: N802 (parent's casing)
         """Evaluate the id portion of `[ref][id]`.
 
         If `[ref][]` use `[ref]`.
@@ -157,9 +155,7 @@ def relative_url(url_a: str, url_b: str) -> str:
     return f"{relative}#{anchor}"
 
 
-def fix_ref(
-    url_mapper: Callable[[str], str], unmapped: List[str]
-) -> Callable:  # noqa: WPS212,WPS231
+def fix_ref(url_mapper: Callable[[str], str], unmapped: List[str]) -> Callable:  # noqa: WPS212,WPS231
     """Return a `repl` function for [`re.sub`](https://docs.python.org/3/library/re.html#re.sub).
 
     In our context, we match Markdown references and replace them with HTML links.
@@ -225,9 +221,7 @@ def fix_refs(html: str, url_mapper: Callable[[str], str]) -> Tuple[str, List[str
 class AutorefsExtension(Extension):
     """Extension that inserts auto-references in Markdown."""
 
-    def extendMarkdown(
-        self, md: Markdown
-    ) -> None:  # noqa: N802 (casing: parent method's name)
+    def extendMarkdown(self, md: Markdown) -> None:  # noqa: N802 (casing: parent method's name)
         """Register the extension.
 
         Add an instance of our [`AutoRefInlineProcessor`][mkdocs_autorefs.references.AutoRefInlineProcessor] to the Markdown parser.
@@ -268,9 +262,7 @@ def __init__(self) -> None:
         super().__init__()
         self._url_map: Dict[str, str] = {}
         self._abs_url_map: Dict[str, str] = {}
-        self.get_fallback_anchor: Optional[
-            Callable[[str], Optional[str]]
-        ] = None  # noqa: WPS234
+        self.get_fallback_anchor: Optional[Callable[[str], Optional[str]]] = None  # noqa: WPS234
         self._priority_patterns = None
 
     @property
@@ -355,9 +347,7 @@ def get_item_url(  # noqa: WPS234
         """
         return self._get_item_url(identifier, fallback)
 
-    def on_config(
-        self, config: Config, **kwargs
-    ) -> Config:  # noqa: W0613,R0201 (unused arguments, cannot be static)
+    def on_config(self, config: Config, **kwargs) -> Config:  # noqa: W0613,R0201 (unused arguments, cannot be static)
         """Instantiate our Markdown extension.
 
         Hook for the [`on_config` event](https://www.mkdocs.org/user-guide/plugins/#on_config).
@@ -375,9 +365,7 @@ def on_config(
         config["markdown_extensions"].append(AutorefsExtension())
         return config
 
-    def on_page_markdown(
-        self, markdown: str, page: Page, **kwargs
-    ) -> str:  # noqa: W0613 (unused arguments)
+    def on_page_markdown(self, markdown: str, page: Page, **kwargs) -> str:  # noqa: W0613 (unused arguments)
         """Remember which page is the current one.
 
         Arguments:
@@ -391,9 +379,7 @@ def on_page_markdown(
         self.current_page = page.url  # noqa: WPS601
         return markdown
 
-    def on_page_content(
-        self, html: str, page: Page, **kwargs
-    ) -> str:  # noqa: W0613 (unused arguments)
+    def on_page_content(self, html: str, page: Page, **kwargs) -> str:  # noqa: W0613 (unused arguments)
         """Map anchors to URLs.
 
         Hook for the [`on_page_content` event](https://www.mkdocs.org/user-guide/plugins/#on_page_content).
@@ -431,9 +417,7 @@ def map_urls(self, page: Page, anchor: AnchorLink) -> None:
         for child in anchor.children:
             self.map_urls(page, child)
 
-    def on_post_page(
-        self, output: str, page: Page, **kwargs
-    ) -> str:  # noqa: W0613 (unused arguments)
+    def on_post_page(self, output: str, page: Page, **kwargs) -> str:  # noqa: W0613 (unused arguments)
         """Fix cross-references.
 
         Hook for the [`on_post_page` event](https://www.mkdocs.org/user-guide/plugins/#on_post_page).

scripts/adicap.py

@@ -35,7 +35,6 @@ def parse_each_dict(df, dictionaryCode: str):
 def get_decode_dict(df, dict_keys=["D1", "D2", "D3", "D4", "D5", "D6", "D7"]):
     decode_dict = {}
     for key in dict_keys:
-
         decode_dict[key] = parse_each_dict(df, dictionaryCode=key)
 
     return decode_dict

scripts/conjugate_verbs.py

@@ -15,7 +15,7 @@
 def conjugate_verbs(
     output_path: Path = typer.Argument(
         "edsnlp/resources/verbs.csv.gz", help="Path to the output CSV table."
-    )
+    ),
 ) -> None:
     """
     Convenience script to automatically conjugate a set of verbs,

scripts/serve.py

@@ -32,7 +32,6 @@
 
 
 class Entity(BaseModel):  # (2)
-
     # OMOP-style attributes
     start: int
     end: int
@@ -56,7 +55,6 @@ class Document(BaseModel):  # (1)
 async def process(
     notes: List[str],  # (2)
 ):
-
     documents = []
 
     for doc in nlp.pipe(notes):

tests/connectors/test_labeltool.py

@@ -9,7 +9,6 @@
 
 
 def test_docs2labeltool(nlp):
-
     modifiers = ["negated", "hypothesis", "reported_speech"]
 
     docs = list(nlp.pipe(texts))

tests/connectors/test_omop.py

@@ -25,7 +25,6 @@ def random_text():
 
 
 def random_note_nlp(text):
-
     ents = []
 
     for match in re.finditer(r"\w+", text):
@@ -44,7 +43,6 @@ def random_note_nlp(text):
 
 @pytest.fixture
 def note():
-
     df = pd.DataFrame(dict(note_text=[random_text() for _ in range(10)]))
     df["note_id"] = range(len(df))
     df["note_datetime"] = "2021-10-19"
@@ -54,7 +52,6 @@ def note():
 
 @pytest.fixture
 def note_nlp(note):
-
     df = note.copy()
     df["ents"] = df.note_text.apply(random_note_nlp)
     df = df.explode("ents")
@@ -77,7 +74,6 @@ def docs(omop: OmopConnector, note, note_nlp):
 
 
 def test_omop2docs(docs, note, note_nlp):
-
     lexical_variants = note_nlp.groupby("note_id")["lexical_variant"].agg(list)
 
     for doc, text, lvs in zip(docs, note.note_text, lexical_variants):

tests/matchers/test_phrase.py

@@ -21,7 +21,6 @@ def test_eds_phrase_matcher(doc, nlp):
 
 
 def test_offset(blank_nlp):
-
     text = "Ceci est un test de matching"
 
     doc = blank_nlp(text)
@@ -45,7 +44,6 @@ def test_offset(blank_nlp):
 
 
 def test_remove(blank_nlp):
-
     pattern = blank_nlp("matching")
     pattern2 = blank_nlp("Ceci")
 

tests/pipelines/core/test_contextual_matcher.py

@@ -156,7 +156,6 @@
 
 @pytest.mark.parametrize("params,example", list(zip(ALL_PARAMS, EXAMPLES)))
 def test_contextual(blank_nlp, params, example):
-
     include_assigned, replace_entity, reduce_mode_stage, reduce_mode_metastase = params
 
     blank_nlp.add_pipe(
@@ -225,9 +224,7 @@ def test_contextual(blank_nlp, params, example):
     assert len(doc.ents) == len(entities)
 
     for entity, ent in zip(entities, doc.ents):
-
         for modifier in entity.modifiers:
-
             assert (
                 rgetattr(ent, modifier.key) == modifier.value
             ), f"{modifier.key} labels don't match."

tests/pipelines/core/test_normalisation.py

@@ -25,7 +25,6 @@ def test_full_normalization(doc):
 @fixture
 def nlp_factory(blank_nlp):
     def f(a=False, lc=False, q=False, p=False):
-
         if a:
             a = dict(accents=accents)
         if q:
@@ -48,7 +47,6 @@ def f(a=False, lc=False, q=False, p=False):
 
 
 def test_normalization_accents(nlp_factory, text):
-
     nlp = nlp_factory(a=True)
     doc = nlp(text)
 
@@ -58,7 +56,6 @@ def test_normalization_accents(nlp_factory, text):
 
 
 def test_normalization_spaces(nlp_factory, text):
-
     nlp = nlp_factory(a=True)
     doc = nlp("Phrase    avec des espaces \n et un retour à la ligne")
 
@@ -67,7 +64,6 @@ def test_normalization_spaces(nlp_factory, text):
 
 
 def test_normalization_quotes(nlp_factory, text):
-
     nlp = nlp_factory(q=True)
     doc = nlp(text)
 
@@ -79,7 +75,6 @@ def test_normalization_quotes(nlp_factory, text):
 
 
 def test_normalization_lowercase(nlp_factory, text):
-
     nlp = nlp_factory(lc=True)
     doc = nlp(text)
 
@@ -89,7 +84,6 @@ def test_normalization_lowercase(nlp_factory, text):
 
 
 def test_normalization_pollution(nlp_factory, text):
-
     nlp = nlp_factory(p=True)
     doc = nlp(text)
 

tests/pipelines/misc/test_consultation_date.py

@@ -53,7 +53,6 @@
 @pytest.mark.parametrize("date_pipeline", [True, False])
 @pytest.mark.parametrize("example", [cons, cons_town, cons_town_doc])
 def test_cons_dates(date_pipeline, example, blank_nlp):
-
     blank_nlp.add_pipe(
         "eds.normalizer",
         config=dict(lowercase=True, accents=True, quotes=True, pollution=False),