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scverse · May 13, 2024 · 69f9781 · 69f9781
1 parent 055f79b
commit 69f9781
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Showing 4 changed files with 13 additions and 8 deletions.
diff --git a/benchmarks/benchmarks/utils.py → benchmarks/benchmarks/_utils.py b/benchmarks/benchmarks/utils.py → benchmarks/benchmarks/_utils.py
diff --git a/benchmarks/benchmarks/preprocessing_counts.py b/benchmarks/benchmarks/preprocessing_counts.py
@@ -9,13 +9,14 @@
 
 import scanpy as sc
 
-from .utils import get_count_dataset
+from ._utils import get_count_dataset
 
 if TYPE_CHECKING:
     from anndata import AnnData
 
-    from .utils import Dataset
+    from ._utils import Dataset
 
+# setup variables
 
 adata: AnnData
 batch_key: str | None
@@ -28,7 +29,7 @@ def setup(dataset: Dataset, *_):
     assert "log1p" not in adata.uns
 
 
-# The actual test suite begins here
+# ASV suite
 
 params: list[Dataset] = ["pbmc68k_reduced", "pbmc3k"]
 param_names = ["dataset"]
@@ -81,7 +82,8 @@ def peakmem_normalize_total(*_):
 
 
 def time_log1p(*_):
-    assert "log1p" not in adata.uns, "ASV bug?"
+    # TODO: This would fail: assert "log1p" not in adata.uns, "ASV bug?"
+    # https://github.com/scverse/scanpy/issues/3052
     sc.pp.log1p(adata)
 
 

diff --git a/benchmarks/benchmarks/preprocessing_log.py b/benchmarks/benchmarks/preprocessing_log.py
@@ -12,12 +12,14 @@
 import scanpy as sc
 from scanpy.preprocessing._utils import _get_mean_var
 
-from .utils import get_dataset
+from ._utils import get_dataset
 
 if TYPE_CHECKING:
     from anndata import AnnData
 
-    from .utils import Dataset
+    from ._utils import Dataset
+
+# setup variables
 
 
 adata: AnnData
@@ -30,7 +32,7 @@ def setup(dataset: Dataset, *_):
     adata, batch_key = get_dataset(dataset)
 
 
-# The actual test suite begins here
+# ASV suite
 
 params: list[Dataset] = ["pbmc68k_reduced", "pbmc3k"]
 param_names = ["dataset"]

diff --git a/benchmarks/benchmarks/tools.py b/benchmarks/benchmarks/tools.py
@@ -9,11 +9,12 @@
 
 import scanpy as sc
 
-from .utils import pbmc68k_reduced
+from ._utils import pbmc68k_reduced
 
 if TYPE_CHECKING:
     from anndata import AnnData
 
+# setup variables
 
 adata: AnnData