Settings docs overhaul by flying-sheep · Pull Request #3672 · scverse/scanpy

flying-sheep · 2025-06-06T10:04:54Z

Preparation PR for presets

Compare:

Old	New
Settings	Settings (click here to see a diff)
`scanpy._settings.ScanpyConfig`	`scanpy.settings`
`set_figure_params` on both `sc` and `sc.settings`	`sc.settings.set_figure_params` deprecated in favor of `sc.set_figure_params`
`scanpy._settings.ScanpyConfig.verbosity`	`scanpy.settings.verbosity` and `scanpy.Verbosity`
`scanpy.logging.print_versions` deprecated	`scanpy.logging.print_versions` deprecated and moved to “Deprecated Functions”

TODO

make inherited-members skipping work
extract into own PR

codecov · 2025-06-06T11:17:33Z

❌ 1 Tests Failed:

Tests completed	Failed	Passed	Skipped
2119	1	2118	105

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

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

Stack Traces | 0.066s 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
            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
            #x1B[94mraise#x1B[39;49;00m #x1B[96mAssertionError#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[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: 100 / 765 (13.1%)#x1B[0m
#x1B[1m#x1B[31mE       Max absolute difference among violations: 0.01983668#x1B[0m
#x1B[1m#x1B[31mE       Max relative difference among violations: 0.01231257#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[31mtests/test_highly_variable_genes.py#x1B[0m:406: AssertionError

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Co-authored-by: Ilan Gold <ilanbassgold@gmail.com>

ilan-gold

Just a suggestion

Co-authored-by: Ilan Gold <ilanbassgold@gmail.com>

flying-sheep added 17 commits May 28, 2025 09:34

WIP presets

5eb83a4

Merge branch 'main' into pa/presets

fd59bea

notebooks

df3c3a6

introduce singleton code

db4c0d3

works, except for role

af89ce5

just use attr link

513c417

skip inherited members

b7d5a17

skip inherited stuff

736c752

fix organization

368ea84

fix verbosity documentation

5c260d4

more docs

b630891

more verbosity docs

5028415

document all intended settings attrs

dcd783a

more links

8a626c2

document defaults

c9a06dd

improve other side

3bae7ae

undo presets

b158545

flying-sheep changed the base branch from pa/presets to main June 6, 2025 10:05

Merge branch 'main' into pa/settings-overhaul

70d48f3

flying-sheep added this to the 1.11.3 milestone Jun 6, 2025

flying-sheep requested a review from ilan-gold June 6, 2025 10:08

flying-sheep changed the title ~~Settings overhaul~~ Settings docs overhaul Jun 6, 2025

fix broken test

28a5ea3

make into decorator

8335ff9

flying-sheep added the Area - Documentation 📒 label Jun 6, 2025

flying-sheep added 2 commits June 6, 2025 14:29

Merge branch 'main' into pa/settings-overhaul

78fc7c0

relnote

4942123

flying-sheep mentioned this pull request Jun 6, 2025

new settings link scverse/scanpy-tutorials#175

Merged

ilan-gold reviewed Jun 6, 2025

View reviewed changes

Comment thread docs/extensions/autosummary_skip_inherited.py

Comment thread src/scanpy/_singleton.py Outdated

Comment thread src/scanpy/_singleton.py Outdated

flying-sheep added 3 commits June 10, 2025 11:03

comment on stack magic

3a7d95a

simplify documenting()

12f7807

simpler skipping

c8a023c

flying-sheep requested a review from ilan-gold June 10, 2025 09:31

Merge branch 'main' into pa/settings-overhaul

04f96e1

ilan-gold reviewed Jun 10, 2025

View reviewed changes

Comment thread docs/extensions/autosummary_skip_inherited.py Outdated

Comment thread docs/extensions/autosummary_skip_inherited.py

comment inherited impl

f9228c6

Co-authored-by: Ilan Gold <ilanbassgold@gmail.com>

ilan-gold approved these changes Jun 10, 2025

View reviewed changes

Comment thread docs/extensions/autosummary_skip_inherited.py

flying-sheep and others added 2 commits June 10, 2025 13:32

metaclass docs

36d28d2

Co-authored-by: Ilan Gold <ilanbassgold@gmail.com>

Merge branch 'main' into pa/settings-overhaul

3767c65

flying-sheep enabled auto-merge (squash) June 10, 2025 12:08

flying-sheep disabled auto-merge June 10, 2025 12:13

merged version of notebooks

22ed905

flying-sheep enabled auto-merge (squash) June 10, 2025 12:15

flying-sheep merged commit e095c46 into main Jun 10, 2025

flying-sheep deleted the pa/settings-overhaul branch June 10, 2025 12:23

lumberbot-app Bot added the Still Needs Manual Backport label Jun 10, 2025

flying-sheep added a commit that referenced this pull request Jun 10, 2025

Backport PR #3672: Settings docs overhaul

4c4af0e

flying-sheep mentioned this pull request Jun 10, 2025

Backport PR #3672 on branch 1.11.x (Settings docs overhaul) #3680

Merged

flying-sheep removed the Still Needs Manual Backport label Jun 10, 2025

scverse deleted a comment from lumberbot-app Bot Jun 10, 2025

flying-sheep self-assigned this Jun 10, 2025

flying-sheep added a commit that referenced this pull request Jun 10, 2025

Backport PR #3672 on branch 1.11.x (Settings docs overhaul) (#3680)

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Settings docs overhaul - #3672

Settings docs overhaul#3672
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flying-sheep commented Jun 6, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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TODO

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❌ 1 Tests Failed:

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flying-sheep commented Jun 6, 2025 •

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