Backport PR #1419 on branch 0.10.x ([pre-commit.ci] pre-commit autoupdate)

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.2
+    rev: v0.3.2
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]

anndata/_core/merge.py

@@ -1,6 +1,7 @@
 """
 Code for merging/ concatenating AnnData objects.
 """
+
 from __future__ import annotations
 
 import typing

anndata/_types.py

@@ -1,6 +1,7 @@
 """
 Defines some useful types for this library. Should probably be cleaned up before thinking about exporting.
 """
+
 from __future__ import annotations
 
 from typing import Union

anndata/tests/test_annot.py

@@ -1,4 +1,5 @@
 """Test handling of values in `obs`/ `var`"""
+
 from __future__ import annotations
 
 import numpy as np

anndata/tests/test_awkward.py

@@ -1,4 +1,5 @@
 """Tests related to awkward arrays"""
+
 from __future__ import annotations
 
 import warnings

anndata/tests/test_concatenate.py

@@ -873,9 +873,9 @@ def test_nan_merge(axis, join_type, array_type):
     with warnings.catch_warnings():
         warnings.simplefilter("ignore", category=sparse.SparseEfficiencyWarning)
         for _ in range(10):
-            arr_nan[
-                np.random.choice(arr.shape[0]), np.random.choice(arr.shape[1])
-            ] = np.nan
+            arr_nan[np.random.choice(arr.shape[0]), np.random.choice(arr.shape[1])] = (
+                np.nan
+            )
 
     _data = {"X": sparse.csr_matrix(adata_shape), mapping_attr: {"arr": arr_nan}}
     orig1 = AnnData(**_data)

anndata/tests/test_dask.py

@@ -1,6 +1,7 @@
 """
 For tests using dask
 """
+
 from __future__ import annotations
 
 import pandas as pd
@@ -107,9 +108,10 @@ def test_dask_distributed_write(adata, tmp_path, diskfmt):
     pth = tmp_path / f"test_write.{diskfmt}"
     g = as_group(pth, mode="w")
 
-    with dd.LocalCluster(
-        n_workers=1, threads_per_worker=1, processes=False
-    ) as cluster, dd.Client(cluster):
+    with (
+        dd.LocalCluster(n_workers=1, threads_per_worker=1, processes=False) as cluster,
+        dd.Client(cluster),
+    ):
         M, N = adata.X.shape
         adata.obsm["a"] = da.random.random((M, 10))
         adata.obsm["b"] = da.random.random((M, 10))

anndata/tests/test_deprecations.py

@@ -3,6 +3,7 @@
 
 This includes correct behaviour as well as throwing warnings.
 """
+
 from __future__ import annotations
 
 import warnings

anndata/tests/test_io_conversion.py

@@ -1,6 +1,7 @@
 """\
 This file contains tests for conversion made during io.
 """
+
 from __future__ import annotations
 
 import h5py

anndata/tests/test_io_elementwise.py

@@ -1,6 +1,7 @@
 """
 Tests that each element in an anndata is written correctly
 """
+
 from __future__ import annotations
 
 import re

anndata/tests/test_x.py

@@ -1,4 +1,5 @@
 """Tests for the attribute .X"""
+
 from __future__ import annotations
 
 import numpy as np

benchmarks/benchmarks/readwrite.py

@@ -19,6 +19,7 @@
 * io for backed objects
 * Reading dense as sparse, writing sparse as dense
 """
+
 from __future__ import annotations
 
 import sys