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chore!: remove use_highly_variable#4039

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chore!: remove use_highly_variable#4039
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@flying-sheep flying-sheep commented Apr 7, 2026

  • Closes #
  • Tests included or not required because:

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codecov bot commented Apr 7, 2026

❌ 2 Tests Failed:

Tests completed Failed Passed Skipped
1832 2 1830 908
View the top 2 failed test(s) by shortest run time 
tests/test_pca.py::test_obsm_mask_error[array]
Stack Traces | 0.004s run time 
mask_type = 'array'

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[33m"#x1B[39;49;00m#x1B[33mmask_type#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, [#x1B[33m"#x1B[39;49;00m#x1B[33mhighly_variable#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33marray#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_obsm_mask_error#x1B[39;49;00m(mask_type: Literal[#x1B[33m"#x1B[39;49;00m#x1B[33mhighly_variable#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33marray#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]) -> #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Check that trying to use mask_var with obsm raises an error."""#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        adata = AnnData(A_list)#x1B[90m#x1B[39;49;00m
        mask_var = (#x1B[90m#x1B[39;49;00m
            _helpers.random_mask(adata.shape[#x1B[94m1#x1B[39;49;00m]) #x1B[94mif#x1B[39;49;00m mask_type == #x1B[33m"#x1B[39;49;00m#x1B[33marray#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m #x1B[94melse#x1B[39;49;00m mask_type#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
        #x1B[94mwith#x1B[39;49;00m pytest.raises(#x1B[90m#x1B[39;49;00m
            #x1B[96mValueError#x1B[39;49;00m, match=#x1B[33mr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mArgument `mask_var` is incompatible with `obsm`.#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        ):#x1B[90m#x1B[39;49;00m
>           sc.pp.pca(adata, mask_var=mask_var, obsm=#x1B[33m"#x1B[39;49;00m#x1B[33mX_pca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, copy=#x1B[94mTrue#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/test_pca.py#x1B[0m:436: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[.../scanpy/_utils/random.py#x1B[0m:201: in wrapper
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m func(*args, **kwargs)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../preprocessing/_pca/__init__.py#x1B[0m:239: in pca
    #x1B[0mx = _get_obs_rep(adata_comp, layer=layer, obsm=obsm)#x1B[90m#x1B[39;49;00m
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/get/get.py#x1B[0m:434: in _get_obs_rep
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m adata.obsm[obsm]#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.few-extras/lib/python3.14.../anndata/_core/aligned_mapping.py#x1B[0m:164: in __getitem__
    #x1B[0m_subset(#x1B[96mself#x1B[39;49;00m.parent_mapping[key], #x1B[96mself#x1B[39;49;00m.subset_idx),#x1B[90m#x1B[39;49;00m
            ^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = AxisArrays with keys: , key = 'X_pca'

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92m__getitem__#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m, key: #x1B[96mstr#x1B[39;49;00m) -> Value:#x1B[90m#x1B[39;49;00m
>       #x1B[94mreturn#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._data[key]#x1B[90m#x1B[39;49;00m
               ^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       KeyError: 'X_pca'#x1B[0m

#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.few-extras/lib/python3.14.../anndata/_core/aligned_mapping.py#x1B[0m:215: KeyError
tests/test_pca.py::test_obsm_mask_error[highly_variable]
Stack Traces | 0.004s run time 
mask_type = 'highly_variable'

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[33m"#x1B[39;49;00m#x1B[33mmask_type#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, [#x1B[33m"#x1B[39;49;00m#x1B[33mhighly_variable#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33marray#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_obsm_mask_error#x1B[39;49;00m(mask_type: Literal[#x1B[33m"#x1B[39;49;00m#x1B[33mhighly_variable#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33marray#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]) -> #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Check that trying to use mask_var with obsm raises an error."""#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        adata = AnnData(A_list)#x1B[90m#x1B[39;49;00m
        mask_var = (#x1B[90m#x1B[39;49;00m
            _helpers.random_mask(adata.shape[#x1B[94m1#x1B[39;49;00m]) #x1B[94mif#x1B[39;49;00m mask_type == #x1B[33m"#x1B[39;49;00m#x1B[33marray#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m #x1B[94melse#x1B[39;49;00m mask_type#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
        #x1B[94mwith#x1B[39;49;00m pytest.raises(#x1B[90m#x1B[39;49;00m
            #x1B[96mValueError#x1B[39;49;00m, match=#x1B[33mr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mArgument `mask_var` is incompatible with `obsm`.#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        ):#x1B[90m#x1B[39;49;00m
>           sc.pp.pca(adata, mask_var=mask_var, obsm=#x1B[33m"#x1B[39;49;00m#x1B[33mX_pca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, copy=#x1B[94mTrue#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/test_pca.py#x1B[0m:436: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[.../scanpy/_utils/random.py#x1B[0m:201: in wrapper
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m func(*args, **kwargs)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../preprocessing/_pca/__init__.py#x1B[0m:230: in pca
    #x1B[0mmask_var_param, mask_var = mask_var, _check_mask(adata, mask_var, #x1B[33m"#x1B[39;49;00m#x1B[33mvar#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
                                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

data = AnnData object with n_obs × n_vars = 6 × 5, mask = 'highly_variable'
dim = 'var'

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92m_check_mask#x1B[39;49;00m[M: NDArray[np.bool] | NDArray[np.floating] | pd.Series | #x1B[94mNone#x1B[39;49;00m](#x1B[90m#x1B[39;49;00m
        data: AnnData | np.ndarray | CSBase | DaskArray,#x1B[90m#x1B[39;49;00m
        mask: #x1B[96mstr#x1B[39;49;00m | M,#x1B[90m#x1B[39;49;00m
        dim: Literal[#x1B[33m"#x1B[39;49;00m#x1B[33mobs#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mvar#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
        *,#x1B[90m#x1B[39;49;00m
        allow_probabilities: #x1B[96mbool#x1B[39;49;00m = #x1B[94mFalse#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
    ) -> M:  #x1B[90m# Could also be a series, but should be one or the other#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Validate mask argument.#x1B[39;49;00m
    #x1B[33m#x1B[39;49;00m
    #x1B[33m    Params#x1B[39;49;00m
    #x1B[33m    ------#x1B[39;49;00m
    #x1B[33m    data#x1B[39;49;00m
    #x1B[33m        Annotated data matrix or numpy array.#x1B[39;49;00m
    #x1B[33m    mask#x1B[39;49;00m
    #x1B[33m        Mask (or probabilities if `allow_probabilities=True`).#x1B[39;49;00m
    #x1B[33m        Either an appropriatley sized array, or name of a column.#x1B[39;49;00m
    #x1B[33m    dim#x1B[39;49;00m
    #x1B[33m        The dimension being masked.#x1B[39;49;00m
    #x1B[33m    allow_probabilities#x1B[39;49;00m
    #x1B[33m        Whether to allow probabilities as `mask`#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m mask #x1B[95mis#x1B[39;49;00m #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94mreturn#x1B[39;49;00m mask#x1B[90m#x1B[39;49;00m
        desc = #x1B[33m"#x1B[39;49;00m#x1B[33mmask/probabilities#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m #x1B[94mif#x1B[39;49;00m allow_probabilities #x1B[94melse#x1B[39;49;00m #x1B[33m"#x1B[39;49;00m#x1B[33mmask#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m #x1B[96misinstance#x1B[39;49;00m(mask, #x1B[96mstr#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m #x1B[96misinstance#x1B[39;49;00m(data, AnnData):#x1B[90m#x1B[39;49;00m
                msg = #x1B[33mf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mCannot refer to #x1B[39;49;00m#x1B[33m{#x1B[39;49;00mdesc#x1B[33m}#x1B[39;49;00m#x1B[33m with string without providing anndata object as argument#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[94mraise#x1B[39;49;00m #x1B[96mValueError#x1B[39;49;00m(msg)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
            annot: pd.DataFrame = #x1B[96mgetattr#x1B[39;49;00m(data, dim)#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m mask #x1B[95mnot#x1B[39;49;00m #x1B[95min#x1B[39;49;00m annot.columns:#x1B[90m#x1B[39;49;00m
                msg = (#x1B[90m#x1B[39;49;00m
                    #x1B[33mf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mDid not find `adata.#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mdim#x1B[33m}#x1B[39;49;00m#x1B[33m[#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mmask#x1B[33m!r}#x1B[39;49;00m#x1B[33m]`. #x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                    #x1B[33mf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mEither add the #x1B[39;49;00m#x1B[33m{#x1B[39;49;00mdesc#x1B[33m}#x1B[39;49;00m#x1B[33m first to `adata.#x1B[39;49;00m#x1B[33m{#x1B[39;49;00mdim#x1B[33m}#x1B[39;49;00m#x1B[33m`#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                    #x1B[33mf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mor consider using the #x1B[39;49;00m#x1B[33m{#x1B[39;49;00mdesc#x1B[33m}#x1B[39;49;00m#x1B[33m argument with an array.#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                )#x1B[90m#x1B[39;49;00m
>               #x1B[94mraise#x1B[39;49;00m #x1B[96mValueError#x1B[39;49;00m(msg)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE               ValueError: Did not find `adata.var['highly_variable']`. Either add the mask first to `adata.var`or consider using the mask argument with an array.#x1B[0m

#x1B[1m#x1B[.../scanpy/get/get.py#x1B[0m:515: ValueError

#x1B[33mDuring handling of the above exception, another exception occurred:#x1B[0m

mask_type = 'highly_variable'

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[33m"#x1B[39;49;00m#x1B[33mmask_type#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, [#x1B[33m"#x1B[39;49;00m#x1B[33mhighly_variable#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33marray#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_obsm_mask_error#x1B[39;49;00m(mask_type: Literal[#x1B[33m"#x1B[39;49;00m#x1B[33mhighly_variable#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33marray#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]) -> #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Check that trying to use mask_var with obsm raises an error."""#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        adata = AnnData(A_list)#x1B[90m#x1B[39;49;00m
        mask_var = (#x1B[90m#x1B[39;49;00m
            _helpers.random_mask(adata.shape[#x1B[94m1#x1B[39;49;00m]) #x1B[94mif#x1B[39;49;00m mask_type == #x1B[33m"#x1B[39;49;00m#x1B[33marray#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m #x1B[94melse#x1B[39;49;00m mask_type#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
>       #x1B[94mwith#x1B[39;49;00m pytest.raises(#x1B[90m#x1B[39;49;00m
            #x1B[96mValueError#x1B[39;49;00m, match=#x1B[33mr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mArgument `mask_var` is incompatible with `obsm`.#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        ):#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       AssertionError: Regex pattern did not match.#x1B[0m
#x1B[1m#x1B[31mE         Expected regex: 'Argument `mask_var` is incompatible with `obsm`.'#x1B[0m
#x1B[1m#x1B[31mE         Actual message: "Did not find `adata.var['highly_variable']`. Either add the mask first to `adata.var`or consider using the mask argument with an array."#x1B[0m

#x1B[1m#x1B[31mtests/test_pca.py#x1B[0m:433: AssertionError

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@flying-sheep