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

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

Author: pre-commit-ci[bot]

benchmarks/benchmarks/preprocessing.py

@@ -16,7 +16,9 @@ class PreprocessingSuite:
     param_names = ["input_data"]
 
     def setup(self, input_data: str):
-        self.adata = rsc.get.anndata_to_GPU(self._data_dict[input_data].copy(), copy=True)
+        self.adata = rsc.get.anndata_to_GPU(
+            self._data_dict[input_data].copy(), copy=True
+        )
 
     def time_calculate_qc_metrics(self, *_):
         self.adata.var["mt"] = self.adata.var_names.str.startswith("MT-")

benchmarks/benchmarks/readwrite.py

@@ -38,12 +38,14 @@
 
 sc.settings.datasetdir = pathlib.Path(__file__).parent.resolve() / "data"
 
+
 @dataclass
 class Dataset:
     path: Path
     get: Callable[[], anndata.AnnData]
 
-path="/p/project/training2406/team_scverse/gold2/rapids_singlecell/benchmarks/data/pbmc3k_raw.h5ad"
+
+path = "/p/project/training2406/team_scverse/gold2/rapids_singlecell/benchmarks/data/pbmc3k_raw.h5ad"
 
 
 class ToGPUSuite:

benchmarks/benchmarks/squidpy.py

@@ -11,17 +11,20 @@
 
 import rapids_singlecell as rsc
 
-import pathlib
 
 class ToolsSuite:
     _data_dict = dict(
-        visium_sge=ad.read_h5ad("/p/project/training2406/team_scverse/gold2/rapids_singlecell/benchmarks/data/paul15.h5ad"),
+        visium_sge=ad.read_h5ad(
+            "/p/project/training2406/team_scverse/gold2/rapids_singlecell/benchmarks/data/paul15.h5ad"
+        ),
     )
     params = _data_dict.keys()
     param_names = ["input_data"]
 
     def setup(self, input_data):
-        self.adata = rsc.get.anndata_to_GPU(self._data_dict[input_data].copy(), copy=True)
+        self.adata = rsc.get.anndata_to_GPU(
+            self._data_dict[input_data].copy(), copy=True
+        )
 
     def time_ligrec(self, *_):
         gene_ids = self.adata.var.index

benchmarks/benchmarks/tools.py

@@ -9,8 +9,6 @@
 
 import rapids_singlecell as rsc
 
-import pathlib
-
 
 class ToolsSuite:
     _data_dict = dict(
@@ -20,7 +18,9 @@ class ToolsSuite:
     param_names = ["input_data"]
 
     def setup(self, input_data):
-        self.adata = rsc.get.anndata_to_GPU(self._data_dict[input_data].copy(), copy=True)
+        self.adata = rsc.get.anndata_to_GPU(
+            self._data_dict[input_data].copy(), copy=True
+        )
         assert "X_pca" in self.adata.obsm
 
     def time_umap(self, *_):