Merge branch 'main' into fix-497

.pre-commit-config.yaml

@@ -7,12 +7,12 @@ default_stages:
 minimum_pre_commit_version: 2.16.0
 repos:
   - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v3.0.3
+    rev: v4.0.0-alpha.8
     hooks:
       - id: prettier
         exclude: '^\.conda'
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.14
+    rev: v0.3.3
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]

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/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):
         """\

src/scirpy/util/graph/_fr_size_aware_layout.py

@@ -117,9 +117,7 @@ def layout_fr_size_aware(
         dimensionality_node_positions = np.array(list(node_positions.values())).shape[1]
         assert (
             dimensionality_node_positions == dimensionality
-        ), "The dimensionality of values of `node_positions` (d={}) must match the dimensionality of `origin`/ `scale` (d={})!".format(
-            dimensionality_node_positions, dimensionality
-        )
+        ), f"The dimensionality of values of `node_positions` (d={dimensionality_node_positions}) must match the dimensionality of `origin`/ `scale` (d={dimensionality})!"
 
         is_valid = _is_within_bbox(list(node_positions.values()), origin=origin, scale=scale)
         if not np.all(is_valid):