[pre-commit.ci] pre-commit autoupdate (#1601)

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.7
+    rev: v0.6.1
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]

src/testing/anndata/_pytest.py

@@ -37,7 +37,7 @@ def _suppress_env_for_doctests(request: pytest.FixtureRequest) -> None:
         request.getfixturevalue("_doctest_env")
 
 
-@pytest.fixture()
+@pytest.fixture
 def _doctest_env(
     request: pytest.FixtureRequest, cache: pytest.Cache, tmp_path: Path
 ) -> Generator[None, None, None]:

tests/conftest.py

@@ -11,7 +11,7 @@
 from anndata.tests.helpers import subset_func  # noqa: F401
 
 
-@pytest.fixture()
+@pytest.fixture
 def backing_h5ad(tmp_path):
     return tmp_path / "test.h5ad"
 

tests/test_anncollection.py

@@ -11,7 +11,7 @@
 _dense = lambda a: a.toarray() if issparse(a) else a
 
 
-@pytest.fixture()
+@pytest.fixture
 def adatas(request):
     adata1 = ad.AnnData(X=request.param([[1, 2, 0], [4, 5, 0], [7, 8, 0]]))
     adata1.obs["a_test"] = ["a", "a", "b"]

tests/test_backed_dense.py

@@ -23,7 +23,7 @@ def diskfmt(request):
     return request.param
 
 
-@pytest.fixture()
+@pytest.fixture
 def file(tmp_path: Path, diskfmt: Literal["h5ad", "zarr"]) -> h5py.File | zarr.Group:
     path = tmp_path / f"test.{diskfmt}"
     if diskfmt == "zarr":

tests/test_backed_hdf5.py

@@ -28,7 +28,7 @@
 # -------------------------------------------------------------------------------
 
 
-@pytest.fixture()
+@pytest.fixture
 def adata():
     X_list = [
         [1, 2, 3],

tests/test_backed_sparse.py

@@ -40,7 +40,7 @@ def diskfmt(request):
 N = 50
 
 
-@pytest.fixture()
+@pytest.fixture
 def ondisk_equivalent_adata(
     tmp_path: Path, diskfmt: Literal["h5ad", "zarr"]
 ) -> tuple[AnnData, AnnData, AnnData, AnnData]:

tests/test_concatenate.py

@@ -292,7 +292,7 @@ def test_concatenate_layers(array_type, join_type):
     assert_equal(merged.X, merged.layers["a"])
 
 
-@pytest.fixture()
+@pytest.fixture
 def obsm_adatas():
     def gen_index(n):
         return [f"cell{i}" for i in range(n)]
@@ -1575,7 +1575,7 @@ def test_concat_duplicated_columns(join_type):
         concat([a, b], join=join_type)
 
 
-@pytest.mark.gpu()
+@pytest.mark.gpu
 def test_error_on_mixed_device():
     """https://github.com/scverse/anndata/issues/1083"""
     import cupy

tests/test_concatenate_disk.py

@@ -180,7 +180,7 @@ def test_concat_ordered_categoricals_retained(tmp_path, file_format):
     assert_eq_concat_on_disk(adatas, tmp_path, file_format)
 
 
-@pytest.fixture()
+@pytest.fixture
 def xxxm_adatas():
     def gen_index(n):
         return [f"cell{i}" for i in range(n)]

tests/test_dask.py

@@ -44,7 +44,7 @@ def diskfmt(request):
     return request.param
 
 
-@pytest.fixture()
+@pytest.fixture
 def adata(sizes):
     import dask.array as da
     import numpy as np

tests/test_dask_view_mem.py

@@ -38,7 +38,7 @@ def give_chunks(request):
 
 # Does some stuff so that dask can cache the
 # subclasscheck before the run.
-@pytest.fixture()
+@pytest.fixture
 def _alloc_cache():
     import dask.array as da
 

tests/test_deprecations.py

@@ -20,7 +20,7 @@
 from anndata.tests.helpers import assert_equal
 
 
-@pytest.fixture()
+@pytest.fixture
 def adata():
     adata = AnnData(
         X=sparse.csr_matrix([[0, 2, 3], [0, 5, 6]], dtype=np.float32),

tests/test_gpu.py

@@ -6,7 +6,7 @@
 from anndata import AnnData, Raw
 
 
-@pytest.mark.gpu()
+@pytest.mark.gpu
 def test_gpu():
     """
     For testing that the gpu mark works
@@ -16,7 +16,7 @@ def test_gpu():
     cupy.ones(1)
 
 
-@pytest.mark.gpu()
+@pytest.mark.gpu
 def test_adata_raw_gpu():
     import cupy as cp
     from cupyx.scipy import sparse as cupy_sparse
@@ -28,7 +28,7 @@ def test_adata_raw_gpu():
     assert isinstance(adata.raw.X, sparse.csr_matrix)
 
 
-@pytest.mark.gpu()
+@pytest.mark.gpu
 def test_raw_gpu():
     import cupy as cp
     from cupyx.scipy import sparse as cupy_sparse

tests/test_helpers.py

@@ -56,7 +56,7 @@
 #     assert tag in str(err.value)
 
 
-@pytest.fixture()
+@pytest.fixture
 def reusable_adata():
     """Reusable anndata for when tests shouldn’t mutate it"""
     return gen_adata((10, 10))
@@ -333,7 +333,7 @@ def test_as_dask_functions(input_type, as_dask_type, mem_type):
     "dask_matrix_type",
     DASK_MATRIX_PARAMS,
 )
-@pytest.mark.gpu()
+@pytest.mark.gpu
 def test_as_cupy_dask(dask_matrix_type):
     SHAPE = (100, 10)
     rng = np.random.default_rng(42)

tests/test_io_elementwise.py

@@ -186,7 +186,7 @@ def test_io_spec(store, value, encoding_type):
 
 
 # Can't instantiate cupy types at the top level, so converting them within the test
-@pytest.mark.gpu()
+@pytest.mark.gpu
 @pytest.mark.parametrize(
     ("value", "encoding_type"),
     [

tests/test_obsmvarm.py

@@ -11,7 +11,7 @@
 M, N = (100, 100)
 
 
-@pytest.fixture()
+@pytest.fixture
 def adata():
     X = np.zeros((M, N))
     obs = pd.DataFrame(

tests/test_obspvarp.py

@@ -16,7 +16,7 @@
 M, N = (200, 100)
 
 
-@pytest.fixture()
+@pytest.fixture
 def adata():
     X = np.zeros((M, N))
     obs = pd.DataFrame(

tests/test_raw.py

@@ -33,7 +33,7 @@
 )
 
 
-@pytest.fixture()
+@pytest.fixture
 def adata_raw() -> ad.AnnData:
     adata = ad.AnnData(
         np.array(data, dtype="int32"), obs=obs_dict, var=var_dict, uns=uns_dict

tests/test_readwrite.py

@@ -81,7 +81,7 @@ def diskfmt(request):
     return request.param
 
 
-@pytest.fixture()
+@pytest.fixture
 def rw(backing_h5ad):
     M, N = 100, 101
     orig = gen_adata((M, N))

tests/test_repr.py

@@ -12,7 +12,7 @@
 ADATA_ATTRS = ("obs", "var", "varm", "obsm", "layers", "obsp", "varp", "uns")
 
 
-@pytest.fixture()
+@pytest.fixture
 def adata():
     return ad.AnnData(
         np.zeros((20, 10)),

tests/test_settings.py

@@ -33,7 +33,7 @@ def validate_int_list(val) -> bool:
     return True
 
 
-@pytest.fixture()
+@pytest.fixture
 def settings() -> SettingsManager:
     settings = SettingsManager()
     settings.register(option, default_val, description, validate_bool)

tests/test_views.py

@@ -65,7 +65,7 @@ def view(self, dtype=None, typ=None):
         return self
 
 
-@pytest.fixture()
+@pytest.fixture
 def adata():
     adata = ad.AnnData(np.zeros((100, 100)))
     adata.obsm["o"] = np.zeros((100, 50))