Add test and actually fix

scverse · Jan 9, 2025 · 1f6e318 · 1f6e318
1 parent 4ed89bc
commit 1f6e318
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Showing 2 changed files with 8 additions and 1 deletion.
diff --git a/src/scanpy/tools/_rank_genes_groups.py b/src/scanpy/tools/_rank_genes_groups.py
@@ -70,7 +70,7 @@ def _ranks(
         get_chunk = lambda X, left, right: adapt(X[:, left:right])
 
     # Calculate chunk frames
-    max_chunk = min(_CONST_MAX_SIZE // n_cells, 1)
+    max_chunk = max(_CONST_MAX_SIZE // n_cells, 1)
 
     for left in range(0, n_genes, max_chunk):
         right = min(left + max_chunk, n_genes)

diff --git a/tests/test_rank_genes_groups.py b/tests/test_rank_genes_groups.py
@@ -307,6 +307,13 @@ def test_wilcoxon_tie_correction(reference):
     np.testing.assert_allclose(test_obj.stats[groups[0]]["pvals"], pvals)
 
 
+def test_wilcoxon_huge_data(monkeypatch):
+    max_size = 300
+    adata = pbmc68k_reduced()
+    monkeypatch.setattr(sc.tl._rank_genes_groups, "_CONST_MAX_SIZE", max_size)
+    rank_genes_groups(adata, groupby="bulk_labels", method="wilcoxon")
+
+
 @pytest.mark.parametrize(
     ("n_genes_add", "n_genes_out_add"),
     [pytest.param(0, 0, id="equal"), pytest.param(2, 1, id="more")],