tests: remove_zero_variance_vars and remove_contaminants#25
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tests: remove_zero_variance_vars and remove_contaminants#25
remove_zero_variance_vars and remove_contaminants#25Conversation
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| with pytest.warns(UserWarning, match=r"at least one group"): | ||
| filtered = remove_zero_variance_vars( | ||
| adata, group_by="group", inplace=False, | ||
| ) |
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Need to check for remaining vars
idf-io
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| adata, group_by="group", inplace=False, | ||
| ) | ||
| assert "peptide_id" in filtered.var.columns | ||
| assert "protein_id" in filtered.var.columns |
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| # ── G. Data type variants ────────────────────────────────────── | ||
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| def test_float32_matrix(self): |
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Can you explain the reason behind this test? @leventetn
Remember, you are responsible for every line of code you write.
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| protein_key="uniprot_id", | ||
| inplace=False, | ||
| ) | ||
| assert list(filtered.var_names) == ["protein_0", "protein_3", "protein_4"] |
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For a more robust test you need to use "uniprot_id"s that don't match the adata.var_names in both name and order. In the current version of the test could have the bug that if the function remove_contaminants uses the adata.var_names even if an alternative protein_key is supplied, the test would still pass.
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