Backport PR #4096 on branch 1.12.x (chore: use scverse-misc’s `@deprecated`) by flying-sheep · Pull Request #4109 · scverse/scanpy

flying-sheep · 2026-05-07T16:09:39Z

Backport PR #4096

codecov · 2026-05-07T16:11:26Z

❌ 5 Tests Failed:

Tests completed	Failed	Passed	Skipped
1816	5	1811	935

View the top 3 failed test(s) by shortest run time

tests/test_preprocessing.py::test_normalize_per_cell

Stack Traces | 0.006s run time

#x1B[1m#x1B[31mE   Failed: DID NOT WARN. No warnings of type (<class 'FutureWarning'>,) matching the regex were emitted.#x1B[0m
#x1B[1m#x1B[31m     Regex: sc\.pp\.normalize_total#x1B[0m
#x1B[1m#x1B[31m     Emitted warnings: [ FutureWarning("The function normalize_per_cell is deprecated and will be removed in the future. Use :func:`~scanpy.pp.normalize_total` instead.\nThe new function is equivalent to the present\nfunction, except that\n\n* the new function doesn't filter cells based on `min_counts`,\n    use :func:`~scanpy.pp.filter_cells` if filtering is needed.\n* some arguments were renamed\n* `copy` is replaced by `inplace`"),#x1B[0m
#x1B[1m#x1B[31m      FutureWarning("The function normalize_per_cell is deprecated and will be removed in the future. Use :func:`~scanpy.pp.normalize_total` instead.\nThe new function is equivalent to the present\nfunction, except that\n\n* the new function doesn't filter cells based on `min_counts`,\n    use :func:`~scanpy.pp.filter_cells` if filtering is needed.\n* some arguments were renamed\n* `copy` is replaced by `inplace`")].#x1B[0m
All traceback entries are hidden. Pass `--full-trace` to see hidden and internal frames.

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

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_normalize_per_cell#x1B[39;49;00m() -> #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
        x = np.array([[#x1B[94m1#x1B[39;49;00m, #x1B[94m0#x1B[39;49;00m], [#x1B[94m3#x1B[39;49;00m, #x1B[94m0#x1B[39;49;00m], [#x1B[94m5#x1B[39;49;00m, #x1B[94m6#x1B[39;49;00m]], dtype=np.float32)#x1B[90m#x1B[39;49;00m
        adata = AnnData(x.copy())#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.normalize_total#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       FutureWarning: The function normalize_per_cell is deprecated and will be removed in the future. Use :func:`~scanpy.pp.normalize_total` instead.#x1B[0m
#x1B[1m#x1B[31mE       The new function is equivalent to the present#x1B[0m
#x1B[1m#x1B[31mE       function, except that#x1B[0m
#x1B[1m#x1B[31mE       #x1B[0m
#x1B[1m#x1B[31mE       * the new function doesn't filter cells based on `min_counts`,#x1B[0m
#x1B[1m#x1B[31mE           use :func:`~scanpy.pp.filter_cells` if filtering is needed.#x1B[0m
#x1B[1m#x1B[31mE       * some arguments were renamed#x1B[0m
#x1B[1m#x1B[31mE       * `copy` is replaced by `inplace`#x1B[0m

#x1B[1m#x1B[31mtests/test_preprocessing.py#x1B[0m:105: FutureWarning

src/scanpy/preprocessing/_simple.py::scanpy.preprocessing._simple.normalize_per_cell

Stack Traces | 0.007s run time

516 `adata.X` : :class:`numpy.ndarray` | :class:`scipy.sparse.csr_matrix` (dtype `float`)
517     Normalized count data matrix.
518 
519 Examples
520 --------
521 >>> import scanpy as sc
522 >>> adata = AnnData(np.array([[1, 0], [3, 0], [5, 6]], dtype=np.float32))
523 >>> print(adata.X.sum(axis=1))
524 [ 1.  3. 11.]
525 >>> sc.pp.normalize_per_cell(adata)
Expected:
    FutureWarning: Use `sc.pp.normalize_total` instead.
        sc.pp.normalize_per_cell(adata)
Got:
    FutureWarning: The function normalize_per_cell is deprecated and will be removed in the future. Use :func:`~scanpy.pp.normalize_total` instead.
    The new function is equivalent to the present
    function, except that
    <BLANKLINE>
    * the new function doesn't filter cells based on `min_counts`,
        use :func:`~scanpy.pp.filter_cells` if filtering is needed.
    * some arguments were renamed
    * `copy` is replaced by `inplace`
        sc.pp.normalize_per_cell(adata)
    FutureWarning: The function normalize_per_cell is deprecated and will be removed in the future. Use :func:`~scanpy.pp.normalize_total` instead.
    The new function is equivalent to the present
    function, except that
    <BLANKLINE>
    * the new function doesn't filter cells based on `min_counts`,
        use :func:`~scanpy.pp.filter_cells` if filtering is needed.
    * some arguments were renamed
    * `copy` is replaced by `inplace`
        normalize_per_cell(

#x1B[1m#x1B[.../scanpy/preprocessing/_simple.py#x1B[0m:525: DocTestFailure

tests/test_score_genes.py::test_add_score

Stack Traces | 0.01s run time

#x1B[1m#x1B[31mE   Failed: DID NOT WARN. No warnings of type (<class 'FutureWarning'>,) matching the regex were emitted.#x1B[0m
#x1B[1m#x1B[31m     Regex: sc\.pp\.normalize_total#x1B[0m
#x1B[1m#x1B[31m     Emitted warnings: [ FutureWarning("The function normalize_per_cell is deprecated and will be removed in the future. Use :func:`~scanpy.pp.normalize_total` instead.\nThe new function is equivalent to the present\nfunction, except that\n\n* the new function doesn't filter cells based on `min_counts`,\n    use :func:`~scanpy.pp.filter_cells` if filtering is needed.\n* some arguments were renamed\n* `copy` is replaced by `inplace`"),#x1B[0m
#x1B[1m#x1B[31m      FutureWarning("The function normalize_per_cell is deprecated and will be removed in the future. Use :func:`~scanpy.pp.normalize_total` instead.\nThe new function is equivalent to the present\nfunction, except that\n\n* the new function doesn't filter cells based on `min_counts`,\n    use :func:`~scanpy.pp.filter_cells` if filtering is needed.\n* some arguments were renamed\n* `copy` is replaced by `inplace`")].#x1B[0m
All traceback entries are hidden. Pass `--full-trace` to see hidden and internal frames.

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

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_add_score#x1B[39;49;00m():#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Check the dtype of the scores and that non-existing genes get ignored."""#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# TODO: write a test that costs less resources and is more meaningful#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        adata = _create_adata(#x1B[94m100#x1B[39;49;00m, #x1B[94m1000#x1B[39;49;00m, p_zero=#x1B[94m0#x1B[39;49;00m, p_nan=#x1B[94m0#x1B[39;49;00m)#x1B[90m#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.normalize_total#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       FutureWarning: The function normalize_per_cell is deprecated and will be removed in the future. Use :func:`~scanpy.pp.normalize_total` instead.#x1B[0m
#x1B[1m#x1B[31mE       The new function is equivalent to the present#x1B[0m
#x1B[1m#x1B[31mE       function, except that#x1B[0m
#x1B[1m#x1B[31mE       #x1B[0m
#x1B[1m#x1B[31mE       * the new function doesn't filter cells based on `min_counts`,#x1B[0m
#x1B[1m#x1B[31mE           use :func:`~scanpy.pp.filter_cells` if filtering is needed.#x1B[0m
#x1B[1m#x1B[31mE       * some arguments were renamed#x1B[0m
#x1B[1m#x1B[31mE       * `copy` is replaced by `inplace`#x1B[0m

#x1B[1m#x1B[31mtests/test_score_genes.py#x1B[0m:82: FutureWarning

tests/test_score_genes.py::test_layer

Stack Traces | 0.014s run time

#x1B[1m#x1B[31mE   Failed: DID NOT WARN. No warnings of type (<class 'FutureWarning'>,) matching the regex were emitted.#x1B[0m
#x1B[1m#x1B[31m     Regex: sc\.pp\.normalize_total#x1B[0m
#x1B[1m#x1B[31m     Emitted warnings: [ FutureWarning("The function normalize_per_cell is deprecated and will be removed in the future. Use :func:`~scanpy.pp.normalize_total` instead.\nThe new function is equivalent to the present\nfunction, except that\n\n* the new function doesn't filter cells based on `min_counts`,\n    use :func:`~scanpy.pp.filter_cells` if filtering is needed.\n* some arguments were renamed\n* `copy` is replaced by `inplace`"),#x1B[0m
#x1B[1m#x1B[31m      FutureWarning("The function normalize_per_cell is deprecated and will be removed in the future. Use :func:`~scanpy.pp.normalize_total` instead.\nThe new function is equivalent to the present\nfunction, except that\n\n* the new function doesn't filter cells based on `min_counts`,\n    use :func:`~scanpy.pp.filter_cells` if filtering is needed.\n* some arguments were renamed\n* `copy` is replaced by `inplace`")].#x1B[0m
All traceback entries are hidden. Pass `--full-trace` to see hidden and internal frames.

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

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_layer#x1B[39;49;00m():#x1B[90m#x1B[39;49;00m
        adata = _create_adata(#x1B[94m100#x1B[39;49;00m, #x1B[94m1000#x1B[39;49;00m, p_zero=#x1B[94m0#x1B[39;49;00m, p_nan=#x1B[94m0#x1B[39;49;00m)#x1B[90m#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.normalize_total#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       FutureWarning: The function normalize_per_cell is deprecated and will be removed in the future. Use :func:`~scanpy.pp.normalize_total` instead.#x1B[0m
#x1B[1m#x1B[31mE       The new function is equivalent to the present#x1B[0m
#x1B[1m#x1B[31mE       function, except that#x1B[0m
#x1B[1m#x1B[31mE       #x1B[0m
#x1B[1m#x1B[31mE       * the new function doesn't filter cells based on `min_counts`,#x1B[0m
#x1B[1m#x1B[31mE           use :func:`~scanpy.pp.filter_cells` if filtering is needed.#x1B[0m
#x1B[1m#x1B[31mE       * some arguments were renamed#x1B[0m
#x1B[1m#x1B[31mE       * `copy` is replaced by `inplace`#x1B[0m

#x1B[1m#x1B[31mtests/test_score_genes.py#x1B[0m:236: FutureWarning

tests/test_score_genes.py::test_score_with_reference

Stack Traces | 0.444s run time

#x1B[1m#x1B[31mE   Failed: DID NOT WARN. No warnings of type (<class 'FutureWarning'>,) matching the regex were emitted.#x1B[0m
#x1B[1m#x1B[31m     Regex: sc\.pp\.normalize_total#x1B[0m
#x1B[1m#x1B[31m     Emitted warnings: [ FutureWarning("The function normalize_per_cell is deprecated and will be removed in the future. Use :func:`~scanpy.pp.normalize_total` instead.\nThe new function is equivalent to the present\nfunction, except that\n\n* the new function doesn't filter cells based on `min_counts`,\n    use :func:`~scanpy.pp.filter_cells` if filtering is needed.\n* some arguments were renamed\n* `copy` is replaced by `inplace`"),#x1B[0m
#x1B[1m#x1B[31m      FutureWarning("The function normalize_per_cell is deprecated and will be removed in the future. Use :func:`~scanpy.pp.normalize_total` instead.\nThe new function is equivalent to the present\nfunction, except that\n\n* the new function doesn't filter cells based on `min_counts`,\n    use :func:`~scanpy.pp.filter_cells` if filtering is needed.\n* some arguments were renamed\n* `copy` is replaced by `inplace`")].#x1B[0m
All traceback entries are hidden. Pass `--full-trace` to see hidden and internal frames.

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

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_score_with_reference#x1B[39;49;00m():#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Checks if score_genes output agrees with pre-computed reference values.#x1B[39;49;00m
    #x1B[33m#x1B[39;49;00m
    #x1B[33m    The reference values had been generated using the same code#x1B[39;49;00m
    #x1B[33m    and stored as a pickle object in `./data`.#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        adata = paul15()#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.normalize_total#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       FutureWarning: The function normalize_per_cell is deprecated and will be removed in the future. Use :func:`~scanpy.pp.normalize_total` instead.#x1B[0m
#x1B[1m#x1B[31mE       The new function is equivalent to the present#x1B[0m
#x1B[1m#x1B[31mE       function, except that#x1B[0m
#x1B[1m#x1B[31mE       #x1B[0m
#x1B[1m#x1B[31mE       * the new function doesn't filter cells based on `min_counts`,#x1B[0m
#x1B[1m#x1B[31mE           use :func:`~scanpy.pp.filter_cells` if filtering is needed.#x1B[0m
#x1B[1m#x1B[31mE       * some arguments were renamed#x1B[0m
#x1B[1m#x1B[31mE       * `copy` is replaced by `inplace`#x1B[0m

#x1B[1m#x1B[31mtests/test_score_genes.py#x1B[0m:66: FutureWarning

To view more test analytics, go to the Test Analytics Dashboard
_{📋 Got 3 mins? Take this short survey to help us improve Test Analytics.}

Backport PR #4096: chore: use scverse-misc’s @deprecated

8f837c9

flying-sheep enabled auto-merge (squash) May 7, 2026 16:10

flying-sheep added 3 commits May 7, 2026 18:15

backport to since-removed functions

ce436ff

add dep

ecfab98

whoops

5232e1c

flying-sheep mentioned this pull request May 7, 2026

deprecated creates bad docstring when passed a multiline message scverse/scverse-misc#27

Closed

correct warning suppression

81e0922

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Backport PR #4096 on branch 1.12.x (chore: use scverse-misc’s `@deprecated`)#4109

Backport PR #4096 on branch 1.12.x (chore: use scverse-misc’s `@deprecated`)#4109
flying-sheep wants to merge 5 commits into1.12.xfrom
auto-backport-of-pr-4096-on-1.12.x

flying-sheep commented May 7, 2026 •

edited

Loading

Uh oh!

codecov Bot commented May 7, 2026 •

edited

Loading

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

1 participant

Conversation

flying-sheep commented May 7, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

codecov Bot commented May 7, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

❌ 5 Tests Failed:

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

1 participant

flying-sheep commented May 7, 2026 •

edited

Loading

codecov Bot commented May 7, 2026 •

edited

Loading