[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

docs/extensions/function_images.py

@@ -2,6 +2,7 @@
 
 Adapted from scanpy (c) Philipp Angerer
 """
+
 import re
 from pathlib import Path
 from typing import Any

src/scirpy/io/_convert_anndata.py

@@ -1,4 +1,5 @@
 """Convert IrCells to AnnData and vice-versa"""
+
 from collections.abc import Iterable
 from importlib.metadata import version
 from typing import cast

src/scirpy/ir_dist/__init__.py

@@ -1,4 +1,5 @@
 """Compute distances between immune receptor sequences"""
+
 import itertools
 from collections.abc import Sequence
 from typing import Literal, Optional, Union

src/scirpy/pl/_vdj_usage.py

@@ -106,9 +106,7 @@ def vdj_usage(
     )
     df = get_airr(params, airr_variables, chains).assign(
         # make sure this also works with mudata columns:
-        cell_weights=_normalize_counts(tmp_obs, normalize_to)
-        if isinstance(normalize_to, (bool, str))
-        else normalize_to
+        cell_weights=_normalize_counts(tmp_obs, normalize_to) if isinstance(normalize_to, (bool, str)) else normalize_to
     )
     for col in df.columns:
         if col.startswith("VJ") or col.startswith("VDJ"):

src/scirpy/pl/base.py

@@ -1,4 +1,5 @@
 """Base plotting functions"""
+
 import itertools
 from collections.abc import Sequence
 from typing import Literal, Optional, Union

src/scirpy/tests/test_workflow.py

@@ -8,6 +8,7 @@
 The tests need to be quick in order not to overload the bioconda CI,
 but AIRR-compliance mandates to have these tests.
 """
+
 import pandas as pd
 import pandas.testing as pdt
 import pytest

src/scirpy/util/__init__.py

@@ -59,13 +59,11 @@ class DataHandler:
 
     @overload
     @staticmethod
-    def default(data: None) -> None:
-        ...
+    def default(data: None) -> None: ...
 
     @overload
     @staticmethod
-    def default(data: "DataHandler.TYPE") -> "DataHandler":
-        ...
+    def default(data: "DataHandler.TYPE") -> "DataHandler": ...
 
     @staticmethod
     def default(data):
@@ -119,12 +117,10 @@ def _check_chain_indices(self):
             index_chains(self.adata, airr_key=self._airr_key, key_added=self._chain_idx_key)
 
     @overload
-    def get_obs(self, columns: str) -> pd.Series:
-        ...
+    def get_obs(self, columns: str) -> pd.Series: ...
 
     @overload
-    def get_obs(self, columns: Sequence[str]) -> pd.DataFrame:
-        ...
+    def get_obs(self, columns: Sequence[str]) -> pd.DataFrame: ...
 
     def get_obs(self, columns):
         """\