ci: fix benchmarks

benchmarks/benchmarks/preprocessing_counts.py

@@ -25,7 +25,6 @@
 
 
 def cache_adata(dataset: Dataset, layer: KeyCount) -> None:
-    """Without this caching, asv was running several processes which meant the data was repeatedly downloaded."""
     adata, batch_key = get_count_dataset(dataset, layer=layer)
     assert "lop1p" not in adata.uns
     adata.uns["batch_key"] = batch_key
@@ -40,6 +39,7 @@ class PreprocessingCountsSuite:  # noqa: D101
     param_names = ("dataset", "layer")
 
     def setup_cache(self) -> None:
+        """Without this caching, asv was running several processes which meant the data was repeatedly downloaded."""
         for dataset, layer in product(*self.params):
             cache_adata(dataset, layer)
 

benchmarks/benchmarks/tools.py

@@ -5,6 +5,8 @@
 
 from __future__ import annotations
 
+from pathlib import Path
+
 import anndata as ad
 
 import scanpy as sc
@@ -13,42 +15,44 @@
 
 
 class ToolsSuite:  # noqa: D101
-    def setup_cache(self) -> None:
+    def setup_cache(self) -> Path:
         adata = pbmc68k_reduced()
         assert "X_pca" in adata.obsm
-        adata.write_h5ad("adata.h5ad")
+        adata.write_h5ad(path := Path("adata.h5ad"))
+        # we need to have a parameter, else asv doesn’t run `setup_cache` before `setup`
+        return path
 
-    def setup(self) -> None:
-        self.adata = ad.read_h5ad("adata.h5ad")
+    def setup(self, path: Path) -> None:
+        self.adata = ad.read_h5ad(path)
 
-    def time_umap(self) -> None:
+    def time_umap(self, *_) -> None:
         sc.tl.umap(self.adata, rng=None)
 
-    def peakmem_umap(self) -> None:
+    def peakmem_umap(self, *_) -> None:
         sc.tl.umap(self.adata, rng=None)
 
-    def time_diffmap(self) -> None:
+    def time_diffmap(self, *_) -> None:
         sc.tl.diffmap(self.adata)
 
-    def peakmem_diffmap(self) -> None:
+    def peakmem_diffmap(self, *_) -> None:
         sc.tl.diffmap(self.adata)
 
-    def time_leiden(self) -> None:
+    def time_leiden(self, *_) -> None:
         sc.tl.leiden(self.adata, flavor="igraph")
 
-    def peakmem_leiden(self) -> None:
+    def peakmem_leiden(self, *_) -> None:
         sc.tl.leiden(self.adata, flavor="igraph")
 
-    def time_rank_genes_groups(self) -> None:
+    def time_rank_genes_groups(self, *_) -> None:
         sc.tl.rank_genes_groups(self.adata, "bulk_labels", method="wilcoxon")
 
-    def peakmem_rank_genes_groups(self) -> None:
+    def peakmem_rank_genes_groups(self, *_) -> None:
         sc.tl.rank_genes_groups(self.adata, "bulk_labels", method="wilcoxon")
 
-    def time_combat(self) -> None:
+    def time_combat(self, *_) -> None:
         sc.pp.combat(self.adata, key="bulk_labels")
 
-    def peakmem_combat(self) -> None:
+    def peakmem_combat(self, *_) -> None:
         sc.pp.combat(self.adata, key="bulk_labels")