[pre-commit.ci] pre-commit autoupdate (#3210)

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/scanpy/_pytest/fixtures/__init__.py

@@ -37,7 +37,7 @@ def float_dtype(request):
     return request.param
 
 
-@pytest.fixture()
+@pytest.fixture
 def _doctest_env(cache: pytest.Cache, tmp_path: Path) -> Generator[None, None, None]:
     from scanpy._compat import chdir
 

src/testing/scanpy/_pytest/fixtures/data.py

@@ -50,12 +50,12 @@ def pbmc3ks_parametrized_session(request) -> dict[bool, AnnData]:
     }
 
 
-@pytest.fixture()
+@pytest.fixture
 def pbmc3k_parametrized(pbmc3ks_parametrized_session) -> Callable[[], AnnData]:
     return pbmc3ks_parametrized_session[False].copy
 
 
-@pytest.fixture()
+@pytest.fixture
 def pbmc3k_parametrized_small(pbmc3ks_parametrized_session) -> Callable[[], AnnData]:
     return pbmc3ks_parametrized_session[True].copy
 

tests/conftest.py

@@ -56,7 +56,7 @@ def _caplog_adapter(caplog: pytest.LogCaptureFixture) -> Generator[None, None, N
     sc.settings._root_logger.removeHandler(caplog.handler)
 
 
-@pytest.fixture()
+@pytest.fixture
 def imported_modules():
     return IMPORTED
 
@@ -69,7 +69,7 @@ class CompareResult(TypedDict):
     tol: int
 
 
-@pytest.fixture()
+@pytest.fixture
 def check_same_image(add_nunit_attachment):
     from urllib.parse import quote
 
@@ -117,7 +117,7 @@ def fmt_descr(descr):
     return check_same_image
 
 
-@pytest.fixture()
+@pytest.fixture
 def image_comparer(check_same_image):
     from matplotlib import pyplot as plt
 
@@ -139,7 +139,7 @@ def save_and_compare(*path_parts: Path | os.PathLike, tol: int):
     return save_and_compare
 
 
-@pytest.fixture()
+@pytest.fixture
 def plt():
     from matplotlib import pyplot as plt
 

tests/test_aggregated.py

@@ -22,13 +22,13 @@ def metric(request: pytest.FixtureRequest) -> AggType:
     return request.param
 
 
-@pytest.fixture()
+@pytest.fixture
 def df_base():
     ax_base = ["A", "B"]
     return pd.DataFrame(index=ax_base)
 
 
-@pytest.fixture()
+@pytest.fixture
 def df_groupby():
     ax_groupby = [
         *["v0", "v1", "v2"],
@@ -49,7 +49,7 @@ def df_groupby():
     return df_groupby
 
 
-@pytest.fixture()
+@pytest.fixture
 def X():
     data = [
         *[[0, -2], [1, 13], [2, 1]],  # v

tests/test_binary.py

@@ -19,7 +19,7 @@
 HERE = Path(__file__).parent
 
 
-@pytest.fixture()
+@pytest.fixture
 def _set_path(monkeypatch: MonkeyPatch) -> None:
     monkeypatch.setenv("PATH", str(HERE / "_scripts"), prepend=os.pathsep)
 

tests/test_clustering.py

@@ -8,7 +8,7 @@
 from testing.scanpy._pytest.marks import needs
 
 
-@pytest.fixture()
+@pytest.fixture
 def adata_neighbors():
     return pbmc68k_reduced()
 

tests/test_datasets.py

@@ -33,15 +33,15 @@ def _tmp_dataset_dir(tmp_path: Path) -> None:
     sc.settings.datasetdir = tmp_path / "scanpy_data"
 
 
-@pytest.mark.internet()
+@pytest.mark.internet
 def test_burczynski06():
     with pytest.warns(UserWarning, match=r"Variable names are not unique"):
         adata = sc.datasets.burczynski06()
     assert adata.shape == (127, 22283)
     assert not (adata.X == 0).any()
 
 
-@pytest.mark.internet()
+@pytest.mark.internet
 @needs.openpyxl
 def test_moignard15():
     with warnings.catch_warnings():
@@ -56,19 +56,19 @@ def test_moignard15():
     assert adata.shape == (3934, 42)
 
 
-@pytest.mark.internet()
+@pytest.mark.internet
 def test_paul15():
     sc.datasets.paul15()
 
 
-@pytest.mark.internet()
+@pytest.mark.internet
 def test_pbmc3k():
     adata = sc.datasets.pbmc3k()
     assert adata.shape == (2700, 32738)
     assert "CD8A" in adata.var_names
 
 
-@pytest.mark.internet()
+@pytest.mark.internet
 def test_pbmc3k_processed():
     with warnings.catch_warnings(record=True) as records:
         adata = sc.datasets.pbmc3k_processed()
@@ -78,7 +78,7 @@ def test_pbmc3k_processed():
     assert len(records) == 0
 
 
-@pytest.mark.internet()
+@pytest.mark.internet
 def test_ebi_expression_atlas():
     adata = sc.datasets.ebi_expression_atlas("E-MTAB-4888")
     # The shape changes sometimes
@@ -111,7 +111,7 @@ def test_pbmc68k_reduced():
         sc.datasets.pbmc68k_reduced()
 
 
-@pytest.mark.internet()
+@pytest.mark.internet
 def test_visium_datasets():
     """Tests that reading/ downloading works and is does not have global effects."""
     with pytest.warns(UserWarning, match=r"Variable names are not unique"):
@@ -121,7 +121,7 @@ def test_visium_datasets():
     assert_adata_equal(hheart, hheart_again)
 
 
-@pytest.mark.internet()
+@pytest.mark.internet
 def test_visium_datasets_dir_change(tmp_path: Path):
     """Test that changing the dataset dir doesn't break reading."""
     with pytest.warns(UserWarning, match=r"Variable names are not unique"):
@@ -132,7 +132,7 @@ def test_visium_datasets_dir_change(tmp_path: Path):
     assert_adata_equal(mbrain, mbrain_again)
 
 
-@pytest.mark.internet()
+@pytest.mark.internet
 def test_visium_datasets_images():
     """Test that image download works and is does not have global effects."""
 

tests/test_embedding_plots.py

@@ -85,7 +85,7 @@ def adata():
     return adata
 
 
-@pytest.fixture()
+@pytest.fixture
 def fixture_request(request):
     """Returns a Request object.
 

tests/test_get.py

@@ -33,7 +33,7 @@ def transpose_adata(adata: AnnData, *, expect_duplicates: bool = False) -> AnnDa
 )
 
 
-@pytest.fixture()
+@pytest.fixture
 def adata():
     """
     adata.X is np.ones((2, 2))

tests/test_highly_variable_genes.py

@@ -36,7 +36,7 @@ def adata_sess() -> AnnData:
     return adata
 
 
-@pytest.fixture()
+@pytest.fixture
 def adata(adata_sess: AnnData) -> AnnData:
     return adata_sess.copy()
 

tests/test_ingest.py

@@ -26,7 +26,7 @@
 T = np.array([[2.0, 3.5, 4.0, 1.0, 4.7], [3.2, 2.0, 5.0, 5.0, 8.0]], dtype=np.float32)
 
 
-@pytest.fixture()
+@pytest.fixture
 def adatas():
     pbmc = pbmc68k_reduced()
     n_split = 500

tests/test_neighbors.py

@@ -119,7 +119,7 @@ def get_neighbors() -> Neighbors:
     return Neighbors(anndata_v0_8_constructor_compat(np.array(X)))
 
 
-@pytest.fixture()
+@pytest.fixture
 def neigh() -> Neighbors:
     return get_neighbors()
 

tests/test_neighbors_key_added.py

@@ -11,7 +11,7 @@
 key = "test"
 
 
-@pytest.fixture()
+@pytest.fixture
 def adata():
     return sc.AnnData(pbmc68k_reduced().X)
 

tests/test_package_structure.py

@@ -53,7 +53,7 @@
 ]
 
 
-@pytest.fixture()
+@pytest.fixture
 def in_project_dir():
     wd_orig = Path.cwd()
     os.chdir(proj_dir)

tests/test_paga.py

@@ -27,7 +27,7 @@ def pbmc_session():
     return pbmc
 
 
-@pytest.fixture()
+@pytest.fixture
 def pbmc(pbmc_session):
     return pbmc_session.copy()
 

tests/test_pca.py

@@ -110,7 +110,7 @@ def zero_center(request: pytest.FixtureRequest):
     return request.param
 
 
-@pytest.fixture()
+@pytest.fixture
 def pca_params(
     array_type, svd_solver_type: Literal[None, "valid", "invalid"], zero_center
 ):

tests/test_plotting.py

@@ -849,7 +849,7 @@ def gene_symbols_adatas_session() -> tuple[AnnData, AnnData]:
     return a, b
 
 
-@pytest.fixture()
+@pytest.fixture
 def gene_symbols_adatas(gene_symbols_adatas_session) -> tuple[AnnData, AnnData]:
     a, b = gene_symbols_adatas_session
     return a.copy(), b.copy()
@@ -993,7 +993,7 @@ def pbmc_scatterplots_session() -> AnnData:
     return pbmc
 
 
-@pytest.fixture()
+@pytest.fixture
 def pbmc_scatterplots(pbmc_scatterplots_session) -> AnnData:
     return pbmc_scatterplots_session.copy()
 
@@ -1352,7 +1352,7 @@ def test_scatter_no_basis_per_var(image_comparer):
     save_and_compare_images("scatter_AAAGCCTGGCTAAC-1_vs_AAATTCGATGCACA-1")
 
 
-@pytest.fixture()
+@pytest.fixture
 def pbmc_filtered() -> Callable[[], AnnData]:
     pbmc = pbmc68k_reduced()
     sc.pp.filter_genes(pbmc, min_cells=10)

tests/test_preprocessing_distributed.py

@@ -31,7 +31,7 @@
 pytestmark = [needs.zarr]
 
 
-@pytest.fixture()
+@pytest.fixture
 @filter_oldformatwarning
 def adata() -> AnnData:
     a = read_zarr(input_file)

tests/test_qc_metrics.py

@@ -15,7 +15,7 @@
 )
 
 
-@pytest.fixture()
+@pytest.fixture
 def anndata():
     a = np.random.binomial(100, 0.005, (1000, 1000))
     adata = AnnData(

tests/test_queries.py

@@ -8,7 +8,7 @@
 from testing.scanpy._pytest.marks import needs
 
 
-@pytest.mark.internet()
+@pytest.mark.internet
 @needs.gprofiler
 def test_enrich():
     pbmc = pbmc68k_reduced()
@@ -33,7 +33,7 @@ def test_enrich():
     assert "set2" in enrich_list["query"].unique()
 
 
-@pytest.mark.internet()
+@pytest.mark.internet
 @needs.pybiomart
 def test_mito_genes():
     pbmc = pbmc68k_reduced()

tests/test_scrublet.py

@@ -176,7 +176,7 @@ def scrub_small_sess() -> AnnData:
     return adata
 
 
-@pytest.fixture()
+@pytest.fixture
 def scrub_small(scrub_small_sess: AnnData):
     return scrub_small_sess.copy()