feat: presets

[flying-sheep]

• Closes Add Seurat compatibility preset #3609
• Tests included or not required because:

• Release notes not necessary because:

Self-documenting presets work!

E.g.:

• code:

  scanpy/src/scanpy/_settings.py

  Lines 90 to 96 in 3bae7ae

  	@_preset_property("flavor")
  	def highly_variable_genes() -> Mapping[Preset, HVGFlavor]:
  	"""Flavor for :func:`~scanpy.pp.highly_variable_genes`."""
  	return {
  	Preset.ScanpyV1: "seurat",
  	Preset.SeuratV5: "seurat_v3",
  	}

• docs: https://icb-scanpy--3653.com.readthedocs.build/en/3653/generated/scanpy.Preset.highly_variable_genes.html

TODO

• actually add everything to SeuratV5 flavor

[codecov]

❌ 1 Tests Failed:

Tests completed	Failed	Passed	Skipped
2294	1	2293	458

View the top 1 failed test(s) by shortest run time

tests/test_highly_variable_genes.py::test_compare_to_upstream[dask_array_sparse-1d_chunked-csr_matrix-seurat-fgd]

Stack Traces | 0.137s run time

#x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[33m"#x1B[39;49;00m#x1B[33mfunc#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, [#x1B[33m"#x1B[39;49;00m#x1B[33mhvg#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mfgd#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
    #x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[90m#x1B[39;49;00m
        (#x1B[33m"#x1B[39;49;00m#x1B[33mflavor#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mparams#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mref_path#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
        [#x1B[90m#x1B[39;49;00m
            pytest.param(#x1B[90m#x1B[39;49;00m
                #x1B[33m"#x1B[39;49;00m#x1B[33mseurat#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[96mdict#x1B[39;49;00m(min_mean=#x1B[94m0.0125#x1B[39;49;00m, max_mean=#x1B[94m3#x1B[39;49;00m, min_disp=#x1B[94m0.5#x1B[39;49;00m), FILE, #x1B[96mid#x1B[39;49;00m=#x1B[33m"#x1B[39;49;00m#x1B[33mseurat#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            ),#x1B[90m#x1B[39;49;00m
            pytest.param(#x1B[90m#x1B[39;49;00m
                #x1B[33m"#x1B[39;49;00m#x1B[33mcell_ranger#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[96mdict#x1B[39;49;00m(n_top_genes=#x1B[94m100#x1B[39;49;00m), FILE_CELL_RANGER, #x1B[96mid#x1B[39;49;00m=#x1B[33m"#x1B[39;49;00m#x1B[33mcell_ranger#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            ),#x1B[90m#x1B[39;49;00m
        ],#x1B[90m#x1B[39;49;00m
    )#x1B[90m#x1B[39;49;00m
    #x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[33m"#x1B[39;49;00m#x1B[33marray_type#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, ARRAY_TYPES)#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_compare_to_upstream#x1B[39;49;00m(#x1B[90m#x1B[39;49;00m
        *,#x1B[90m#x1B[39;49;00m
        request: pytest.FixtureRequest,#x1B[90m#x1B[39;49;00m
        func: Literal[#x1B[33m"#x1B[39;49;00m#x1B[33mhvg#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mfgd#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
        flavor: Literal[#x1B[33m"#x1B[39;49;00m#x1B[33mseurat#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mcell_ranger#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
        params: #x1B[96mdict#x1B[39;49;00m[#x1B[96mstr#x1B[39;49;00m, #x1B[96mfloat#x1B[39;49;00m | #x1B[96mint#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
        ref_path: Path,#x1B[90m#x1B[39;49;00m
        array_type: Callable,#x1B[90m#x1B[39;49;00m
    ):#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m func == #x1B[33m"#x1B[39;49;00m#x1B[33mfgd#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m #x1B[95mand#x1B[39;49;00m flavor == #x1B[33m"#x1B[39;49;00m#x1B[33mcell_ranger#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            reason = #x1B[33m"#x1B[39;49;00m#x1B[33mThe deprecated filter_genes_dispersion behaves differently with cell_ranger#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            request.applymarker(pytest.mark.xfail(reason=reason))#x1B[90m#x1B[39;49;00m
        hvg_info = pd.read_csv(ref_path)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        pbmc = pbmc68k_reduced()#x1B[90m#x1B[39;49;00m
        pbmc.X = pbmc.raw.X#x1B[90m#x1B[39;49;00m
        pbmc.X = array_type(pbmc.X)#x1B[90m#x1B[39;49;00m
        pbmc.var_names_make_unique()#x1B[90m#x1B[39;49;00m
        sc.pp.filter_cells(pbmc, min_counts=#x1B[94m1#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        sc.pp.normalize_total(pbmc, target_sum=#x1B[94m1e4#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m func == #x1B[33m"#x1B[39;49;00m#x1B[33mhvg#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            sc.pp.log1p(pbmc)#x1B[90m#x1B[39;49;00m
            sc.pp.highly_variable_genes(pbmc, flavor=flavor, **params, inplace=#x1B[94mTrue#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        #x1B[94melif#x1B[39;49;00m func == #x1B[33m"#x1B[39;49;00m#x1B[33mfgd#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94mwith#x1B[39;49;00m pytest.warns(#x1B[96mFutureWarning#x1B[39;49;00m, match=#x1B[33mr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33msc#x1B[39;49;00m#x1B[33m\#x1B[39;49;00m#x1B[33m.pp#x1B[39;49;00m#x1B[33m\#x1B[39;49;00m#x1B[33m.highly_variable_genes#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m):  #x1B[90m# noqa: PT031#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                #x1B[90m# https://github..../pandas/issues/61928#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                warnings.filterwarnings(#x1B[90m#x1B[39;49;00m
                    #x1B[33m"#x1B[39;49;00m#x1B[33mignore#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33mr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33minvalid value encountered in cast#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[96mRuntimeWarning#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                )#x1B[90m#x1B[39;49;00m
                sc.pp.filter_genes_dispersion(#x1B[90m#x1B[39;49;00m
                    pbmc, flavor=flavor, **params, log=#x1B[94mTrue#x1B[39;49;00m, subset=#x1B[94mFalse#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
                )#x1B[90m#x1B[39;49;00m
        #x1B[94melse#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            pytest.fail(#x1B[33mf#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33mUnknown func #x1B[39;49;00m#x1B[33m{#x1B[39;49;00mfunc#x1B[33m}#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        np.testing.assert_array_equal(#x1B[90m#x1B[39;49;00m
            hvg_info[#x1B[33m"#x1B[39;49;00m#x1B[33mhighly_variable#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m], pbmc.var[#x1B[33m"#x1B[39;49;00m#x1B[33mhighly_variable#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# (still) Not equal to tolerance rtol=2e-05, atol=2e-05#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# np.testing.assert_allclose(4, 3.9999, rtol=2e-05, atol=2e-05)#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
>       np.testing.assert_allclose(#x1B[90m#x1B[39;49;00m
            hvg_info[#x1B[33m"#x1B[39;49;00m#x1B[33mmeans#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
            pbmc.var[#x1B[33m"#x1B[39;49;00m#x1B[33mmeans#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
            rtol=#x1B[94m2e-05#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
            atol=#x1B[94m2e-05#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31mtests/test_highly_variable_genes.py#x1B[0m:426: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

args = (<function assert_allclose.<locals>.compare at 0x7f02e46dafc0>, array([1.88077032, 0.86220696, 2.78955474, 3.51562963,...6, 2.32597827, 1.59182085, 3.16090039, 3.48005717,
       2.51568575, 3.51163705, 1.30307758, 2.53377802, 2.18815013]))
kwds = {'equal_nan': True, 'err_msg': '', 'header': 'Not equal to tolerance rtol=2e-05, atol=2e-05', 'strict': False, ...}

    #x1B[0m#x1B[37m@wraps#x1B[39;49;00m(func)#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92minner#x1B[39;49;00m(*args, **kwds):#x1B[90m#x1B[39;49;00m
        #x1B[94mwith#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._recreate_cm():#x1B[90m#x1B[39;49;00m
>           #x1B[94mreturn#x1B[39;49;00m func(*args, **kwds)#x1B[90m#x1B[39;49;00m
                   ^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE           AssertionError: #x1B[0m
#x1B[1m#x1B[31mE           Not equal to tolerance rtol=2e-05, atol=2e-05#x1B[0m
#x1B[1m#x1B[31mE           #x1B[0m
#x1B[1m#x1B[31mE           Mismatched elements: 134 / 765 (17.5%)#x1B[0m
#x1B[1m#x1B[31mE           Max absolute difference among violations: 0.01282391#x1B[0m
#x1B[1m#x1B[31mE           Max relative difference among violations: 0.00696457#x1B[0m
#x1B[1m#x1B[31mE            ACTUAL: array([1.88077 , 0.862207, 2.789555, 3.51563 , 0.779662, 2.495507,#x1B[0m
#x1B[1m#x1B[31mE                  2.051983, 2.200089, 2.121406, 2.272991, 2.340023, 2.030907,#x1B[0m
#x1B[1m#x1B[31mE                  2.267801, 1.565244, 2.465999, 0.676449, 2.246484, 3.938324,...#x1B[0m
#x1B[1m#x1B[31mE            DESIRED: array([1.88077 , 0.862207, 2.789555, 3.515629, 0.779662, 2.495507,#x1B[0m
#x1B[1m#x1B[31mE                  2.051983, 2.200089, 2.121406, 2.272991, 2.340023, 2.030907,#x1B[0m
#x1B[1m#x1B[31mE                  2.267801, 1.565244, 2.465999, 0.676449, 2.246485, 3.938324,...#x1B[0m

#x1B[1m#x1B[.../usr/lib/python3.12/contextlib.py#x1B[0m:81: AssertionError

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[flying-sheep]

TODO: add jaccard to seurat preset #3828