[benjaminkramer510]

With duplicate variable names, seurat_v3 and seurat_v3_paper can select more than n_top_genes genes because .loc selects every occurrence of a selected name.

Select by position instead. The regression test checks that changing gene names leaves the selected genes and statistics unchanged, across both flavors, batching, inplace, and subset.

Validation: python -m pytest tests/test_highly_variable_genes.py -q — 237 passed, 1 xfailed, 280 subtests passed. The new test reproduced 39 selected genes instead of 30 before the fix; all 16 cases now pass. Repository hooks pass.

LLM usage

• LLM or coding agent used: OpenAI GPT-6 via Codex.

• If one was used, I, a human, have reviewed, understood and tested every changed line.

• Closes highly_variable_genes(flavor="seurat_v3") flags more than n_top_genes genes when var_names contain duplicates #4405

• Tests included.

A release note is included.