(fix): sc.read with extension does not warn unnecessarily

[ilan-gold]

• Closes irrelevant warning in sc.read #2288
• Tests included or not required because:

• Release notes not necessary because:

[codecov]

❌ 2 Tests Failed:

Tests completed	Failed	Passed	Skipped
2131	2	2129	98

View the top 2 failed test(s) by shortest run time

tests/test_preprocessing.py::test_scale_zero_center_warns_dask_sparse[dask_array_sparse]

Stack Traces | 0.059s run time

array_type = <function as_sparse_dask_array at 0x7f902d3a60c0>

    @pytest.mark.parametrize("array_type", ARRAY_TYPES_SPARSE)
    def test_scale_zero_center_warns_dask_sparse(array_type):
        adata = pbmc68k_reduced()
        adata.X = adata.raw.X
        adata_casted = adata.copy()
        adata_casted.X = array_type(adata_casted.raw.X)
        with pytest.warns(UserWarning, match="zero-center.*sparse"):
            sc.pp.scale(adata_casted)
        sc.pp.scale(adata)
>       assert_allclose(adata_casted.X, adata.X, rtol=1e-5, atol=1e-5)
#x1B[1m#x1B[31mE       AssertionError: #x1B[0m
#x1B[1m#x1B[31mE       Not equal to tolerance rtol=1e-05, atol=1e-05#x1B[0m
#x1B[1m#x1B[31mE       #x1B[0m
#x1B[1m#x1B[31mE       Mismatched elements: 5581 / 535500 (1.04%)#x1B[0m
#x1B[1m#x1B[31mE       Max absolute difference among violations: 0.01053696#x1B[0m
#x1B[1m#x1B[31mE       Max relative difference among violations: 2.85978674#x1B[0m
#x1B[1m#x1B[31mE        ACTUAL: array([[-0.399906, -0.200817, -0.855342, ..., -0.258421, -0.684061,#x1B[0m
#x1B[1m#x1B[31mE                2.79155 ],#x1B[0m
#x1B[1m#x1B[31mE              [ 1.980319, -0.200817,  1.067341, ..., -0.258421,  2.087584,...#x1B[0m
#x1B[1m#x1B[31mE        DESIRED: array([[-0.399906, -0.200817, -0.86101 , ..., -0.258421, -0.684061,#x1B[0m
#x1B[1m#x1B[31mE                2.79155 ],#x1B[0m
#x1B[1m#x1B[31mE              [ 1.980319, -0.200817,  1.067071, ..., -0.258421,  2.087584,...#x1B[0m

#x1B[1m#x1B[31mtests/test_preprocessing.py#x1B[0m:287: AssertionError

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

Stack Traces | 0.069s run time

@pytest.mark.parametrize("func", ["hvg", "fgd"])
    @pytest.mark.parametrize(
        ("flavor", "params", "ref_path"),
        [
            pytest.param(
                "seurat", dict(min_mean=0.0125, max_mean=3, min_disp=0.5), FILE, id="seurat"
            ),
            pytest.param(
                "cell_ranger", dict(n_top_genes=100), FILE_CELL_RANGER, id="cell_ranger"
            ),
        ],
    )
    @pytest.mark.parametrize("array_type", ARRAY_TYPES)
    def test_compare_to_upstream(
        *,
        request: pytest.FixtureRequest,
        func: Literal["hvg", "fgd"],
        flavor: Literal["seurat", "cell_ranger"],
        params: dict[str, float | int],
        ref_path: Path,
        array_type: Callable,
    ):
        if func == "fgd" and flavor == "cell_ranger":
            reason = "The deprecated filter_genes_dispersion behaves differently with cell_ranger"
            request.applymarker(pytest.mark.xfail(reason=reason))
        hvg_info = pd.read_csv(ref_path)
    
        pbmc = pbmc68k_reduced()
        pbmc.X = pbmc.raw.X
        pbmc.X = array_type(pbmc.X)
        pbmc.var_names_make_unique()
        sc.pp.filter_cells(pbmc, min_counts=1)
        sc.pp.normalize_total(pbmc, target_sum=1e4)
    
        if func == "hvg":
            sc.pp.log1p(pbmc)
            sc.pp.highly_variable_genes(pbmc, flavor=flavor, **params, inplace=True)
        elif func == "fgd":
            sc.pp.filter_genes_dispersion(
                pbmc, flavor=flavor, **params, log=True, subset=False
            )
        else:
            raise AssertionError()
    
        np.testing.assert_array_equal(
            hvg_info["highly_variable"], pbmc.var["highly_variable"]
        )
    
        # (still) Not equal to tolerance rtol=2e-05, atol=2e-05
        # np.testing.assert_allclose(4, 3.9999, rtol=2e-05, atol=2e-05)
>       np.testing.assert_allclose(
            hvg_info["means"],
            pbmc.var["means"],
            rtol=2e-05,
            atol=2e-05,
        )
#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: 42 / 765 (5.49%)#x1B[0m
#x1B[1m#x1B[31mE       Max absolute difference among violations: 0.01178531#x1B[0m
#x1B[1m#x1B[31mE       Max relative difference among violations: 0.00858193#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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[codecov]

Codecov Report

Attention: Patch coverage is 88.88889% with 2 lines in your changes missing coverage. Please review.

Project coverage is 76.14%. Comparing base (82adc79) to head (f718bad).
Report is 1 commits behind head on main.

✅ All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
src/scanpy/readwrite.py	88.88%	2 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #3643   +/-   ##
=======================================
  Coverage   76.13%   76.14%           
=======================================
  Files         114      114           
  Lines       12736    12741    +5     
=======================================
+ Hits         9697     9702    +5     
  Misses       3039     3039           

Files with missing lines	Coverage Δ
src/scanpy/readwrite.py	77.55% <88.88%> (+0.24%)	⬆️

[lumberbot-app]

Owee, I'm MrMeeseeks, Look at me.

There seem to be a conflict, please backport manually. Here are approximate instructions:

1. Checkout backport branch and update it.

git checkout 1.11.x
git pull

2. Cherry pick the first parent branch of the this PR on top of the older branch:

git cherry-pick -x -m1 350c3424d2f96c4a3a7bb3b7d0428d38d842ebe8

3. You will likely have some merge/cherry-pick conflict here, fix them and commit:

git commit -am 'Backport PR #3643: (fix): `sc.read` with extension does not warn unnecessarily'

4. Push to a named branch:

git push YOURFORK 1.11.x:auto-backport-of-pr-3643-on-1.11.x

5. Create a PR against branch 1.11.x, I would have named this PR:

"Backport PR #3643 on branch 1.11.x ((fix): sc.read with extension does not warn unnecessarily)"

And apply the correct labels and milestones.

Congratulations — you did some good work! Hopefully your backport PR will be tested by the continuous integration and merged soon!

Remember to remove the Still Needs Manual Backport label once the PR gets merged.

If these instructions are inaccurate, feel free to suggest an improvement.