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fix: moran's calculation parallelization#4148

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fix: moran's calculation parallelization#4148
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ig/moran_numba_66

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@ilan-gold

@ilan-gold ilan-gold commented Jun 8, 2026 •
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Was getting the following beginning with numba>=0.66rc1:

Details =================================== FAILURES =================================== __________________ test_consistency[morans_i-single-threaded] __________________ [gw1] linux -- Python 3.14.5 /home/runner/.local/share/hatch/env/virtual/scanpy/B9PcT7QG/hatch-test.pre/bin/python3

metric = <function morans_i at 0x7fae9eda6140>

@pytest.mark.usefixtures("_threading")
def test_consistency(metric) -> None:
    pbmc = pbmc68k_reduced()
    pbmc.layers["raw"] = pbmc.raw.X.copy()
    g = pbmc.obsp["connectivities"]
    equality_check = partial(np.testing.assert_allclose, atol=1e-11)

    # This can fail
    equality_check(
        metric(g, pbmc.obs["percent_mito"]),
        metric(g, pbmc.obs["percent_mito"]),
    )
    equality_check(
        metric(g, pbmc.obs["percent_mito"]),
        metric(pbmc, vals=pbmc.obs["percent_mito"]),
    )

    equality_check(  # Test that series and vectors return same value
        metric(g, pbmc.obs["percent_mito"]),
        metric(g, pbmc.obs["percent_mito"].values),
    )

    equality_check(
        metric(pbmc, obsm="X_pca"),
        metric(g, pbmc.obsm["X_pca"].T),
    )

    all_genes = metric(pbmc, layer="raw")
    first_gene = metric(
        pbmc, vals=pbmc[:, pbmc.var_names[0]].layers["raw"].toarray().ravel()
    )

  np.testing.assert_allclose(all_genes[0], first_gene, rtol=1e-9)

E AssertionError:
E Not equal to tolerance rtol=1e-09, atol=0
E
E Mismatched elements: 1 / 1 (100%)
E Max absolute difference among violations: 7.9750179849e-08
E Max relative difference among violations: 1.8702209022e-07
E ACTUAL: array(0.426421)
E DESIRED: array(0.426421)

tests/test_metrics.py:72: AssertionError
__________________ test_consistency[morans_i-multi-threaded] ___________________
[gw1] linux -- Python 3.14.5 /home/runner/.local/share/hatch/env/virtual/scanpy/B9PcT7QG/hatch-test.pre/bin/python3
data[i] -= regressor[i] @ coeff

tests/test_scaling.py::test_scale[mask-center-int64-array-csc_matrix]
tests/test_scaling.py::test_scale[mask-center-int64-anndata-csc_matrix]
tests/test_scaling.py::test_scale[mask-center-float32-anndata-csc_matrix]
tests/test_scaling.py::test_scale[mask-center-float32-array-csc_matrix]
/home/runner/.local/share/hatch/env/virtual/scanpy/B9PcT7QG/hatch-test.pre/lib/python3.14/site-packages/scipy/sparse/_index.py:216: SparseEfficiencyWarning: Changing the sparsity structure of a csc_matrix is expensive. lil and dok are more efficient.
self._set_arrayXarray(i, j, x)

tests/test_scaling.py::test_scale[mask-center-int64-anndata-csr_matrix]
tests/test_scaling.py::test_scale[mask-center-float32-array-csr_matrix]
tests/test_scaling.py::test_scale[mask-center-float32-anndata-csr_matrix]
tests/test_scaling.py::test_scale[mask-center-int64-array-csr_matrix]
/home/runner/.local/share/hatch/env/virtual/scanpy/B9PcT7QG/hatch-test.pre/lib/python3.14/site-packages/scipy/sparse/_index.py:216: SparseEfficiencyWarning: Changing the sparsity structure of a csr_matrix is expensive. lil and dok are more efficient.
self._set_arrayXarray(i, j, x)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

  • generated xml file: /home/runner/work/scanpy/scanpy/test-data/test-results.xml -
    =========================== short test summary info ============================
    FAILED tests/test_metrics.py::test_consistency[morans_i-single-threaded] - AssertionError:
    Not equal to tolerance rtol=1e-09, atol=0

Mismatched elements: 1 / 1 (100%)
Max absolute difference among violations: 7.9750179849e-08
Max relative difference among violations: 1.8702209022e-07
ACTUAL: array(0.426421)
DESIRED: array(0.426421)
FAILED tests/test_metrics.py::test_consistency[morans_i-multi-threaded] - AssertionError:
Not equal to tolerance rtol=1e-09, atol=0

Mismatched elements: 1 / 1 (100%)
Max absolute difference among violations: 7.9750179849e-08
Max relative difference among violations: 1.8702209022e-07
ACTUAL: array(0.426421)
DESIRED: array(0.426421)

and suspect this could be the cause

  • Closes #
  • Tests included or not required because:
  • Release notes not necessary because: fix in preparation for upcoming release

@codecov

codecov Bot commented Jun 8, 2026 •
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❌ 2 Tests Failed:

Tests completed Failed Passed Skipped
2628 2 2626 150
View the top 3 failed test(s) by shortest run time 
tests/test_datasets.py::test_burczynski06
Stack Traces | 0.046s run time 
+ Exception Group Traceback (most recent call last):
  |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14....../site-packages/_pytest/runner.py", line 353, in from_call
  |     result: TResult | None = func()
  |                              ~~~~^^
  |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14....../site-packages/_pytest/runner.py", line 245, in <lambda>
  |     lambda: runtest_hook(item=item, **kwds),
  |             ~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
  |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14.../site-packages/pluggy/_hooks.py", line 512, in __call__
  |     return self._hookexec(self.name, self._hookimpls.copy(), kwargs, firstresult)
  |            ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14.../site-packages/pluggy/_manager.py", line 120, in _hookexec
  |     return self._inner_hookexec(hook_name, methods, kwargs, firstresult)
  |            ~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14............/site-packages/pluggy/_callers.py", line 167, in _multicall
  |     raise exception
  |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14............/site-packages/pluggy/_callers.py", line 139, in _multicall
  |     teardown.throw(exception)
  |     ~~~~~~~~~~~~~~^^^^^^^^^^^
  |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14.../site-packages/_pytest/logging.py", line 843, in pytest_runtest_setup
  |     yield
  |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14............/site-packages/pluggy/_callers.py", line 139, in _multicall
  |     teardown.throw(exception)
  |     ~~~~~~~~~~~~~~^^^^^^^^^^^
  |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14.../site-packages/_pytest/capture.py", line 895, in pytest_runtest_setup
  |     return (yield)
  |             ^^^^^
  |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14............/site-packages/pluggy/_callers.py", line 121, in _multicall
  |     res = hook_impl.function(*args)
  |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14...................../site-packages/_pytest/unraisableexception.py", line 153, in pytest_runtest_setup
  |     collect_unraisable(item.config)
  |     ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^
  |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14...................../site-packages/_pytest/unraisableexception.py", line 81, in collect_unraisable
  |     raise ExceptionGroup("multiple unraisable exception warnings", errors)
  | ExceptionGroup: multiple unraisable exception warnings (5 sub-exceptions)
  +-+---------------- 1 ----------------
    | Traceback (most recent call last):
    |   File ".../_temp/uv-python-dir/cpython-3.14.5-linux-x86_64-gnu/lib/python3.14/tempfile.py", line 484, in __del__
    |     _warnings.warn(self.warn_message, ResourceWarning)
    |     ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    | ResourceWarning: Implicitly cleaning up <HTTPError 500: 'Internal Server Error'>
    | 
    | The above exception was the direct cause of the following exception:
    | 
    | Traceback (most recent call last):
    |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14...................../site-packages/_pytest/unraisableexception.py", line 67, in collect_unraisable
    |     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
    |     ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    | pytest.PytestUnraisableExceptionWarning: Exception ignored while calling deallocator <function _TemporaryFileCloser.__del__ at 0x7f29d2ab85c0>: None
    | 
    +---------------- 2 ----------------
    | Traceback (most recent call last):
    |   File ".../_temp/uv-python-dir/cpython-3.14.5-linux-x86_64-gnu/lib/python3.14/tempfile.py", line 484, in __del__
    |     _warnings.warn(self.warn_message, ResourceWarning)
    |     ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    | ResourceWarning: Implicitly cleaning up <HTTPError 500: 'Internal Server Error'>
    | 
    | The above exception was the direct cause of the following exception:
    | 
    | Traceback (most recent call last):
    |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14...................../site-packages/_pytest/unraisableexception.py", line 67, in collect_unraisable
    |     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
    |     ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    | pytest.PytestUnraisableExceptionWarning: Exception ignored while calling deallocator <function _TemporaryFileCloser.__del__ at 0x7f29d2ab85c0>: None
    | 
    +---------------- 3 ----------------
    | Traceback (most recent call last):
    |   File ".../_temp/uv-python-dir/cpython-3.14.5-linux-x86_64-gnu/lib/python3.14/tempfile.py", line 484, in __del__
    |     _warnings.warn(self.warn_message, ResourceWarning)
    |     ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    | ResourceWarning: Implicitly cleaning up <HTTPError 500: 'Internal Server Error'>
    | 
    | The above exception was the direct cause of the following exception:
    | 
    | Traceback (most recent call last):
    |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14...................../site-packages/_pytest/unraisableexception.py", line 67, in collect_unraisable
    |     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
    |     ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    | pytest.PytestUnraisableExceptionWarning: Exception ignored while calling deallocator <function _TemporaryFileCloser.__del__ at 0x7f29d2ab85c0>: None
    | 
    +---------------- 4 ----------------
    | Traceback (most recent call last):
    |   File ".../_temp/uv-python-dir/cpython-3.14.5-linux-x86_64-gnu/lib/python3.14/tempfile.py", line 484, in __del__
    |     _warnings.warn(self.warn_message, ResourceWarning)
    |     ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    | ResourceWarning: Implicitly cleaning up <HTTPError 500: 'Internal Server Error'>
    | 
    | The above exception was the direct cause of the following exception:
    | 
    | Traceback (most recent call last):
    |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14...................../site-packages/_pytest/unraisableexception.py", line 67, in collect_unraisable
    |     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
    |     ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    | pytest.PytestUnraisableExceptionWarning: Exception ignored while calling deallocator <function _TemporaryFileCloser.__del__ at 0x7f29d2ab85c0>: None
    | 
    +---------------- 5 ----------------
    | Traceback (most recent call last):
    |   File ".../_temp/uv-python-dir/cpython-3.14.5-linux-x86_64-gnu/lib/python3.14/tempfile.py", line 484, in __del__
    |     _warnings.warn(self.warn_message, ResourceWarning)
    |     ~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    | ResourceWarning: Implicitly cleaning up <HTTPError 500: 'Internal Server Error'>
    | 
    | The above exception was the direct cause of the following exception:
    | 
    | Traceback (most recent call last):
    |   File ".................................................../home/runner/.local.../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14...................../site-packages/_pytest/unraisableexception.py", line 67, in collect_unraisable
    |     warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))
    |     ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    | pytest.PytestUnraisableExceptionWarning: Exception ignored while calling deallocator <function _TemporaryFileCloser.__del__ at 0x7f29d2ab85c0>: None
    | 
    +------------------------------------
tests/test_metrics.py::test_consistency[morans_i-multi-threaded]
Stack Traces | 0.124s run time 
metric = <function morans_i at 0x7fcc2bfa9b10>

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.usefixtures(#x1B[33m"#x1B[39;49;00m#x1B[33m_threading#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_consistency#x1B[39;49;00m(metric) -> #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
        pbmc = pbmc68k_reduced()#x1B[90m#x1B[39;49;00m
        pbmc.layers[#x1B[33m"#x1B[39;49;00m#x1B[33mraw#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] = pbmc.raw.X.copy()#x1B[90m#x1B[39;49;00m
        g = pbmc.obsp[#x1B[33m"#x1B[39;49;00m#x1B[33mconnectivities#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
        equality_check = partial(np.testing.assert_allclose, atol=#x1B[94m1e-11#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# This can fail#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        equality_check(#x1B[90m#x1B[39;49;00m
            metric(g, pbmc.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mpercent_mito#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]),#x1B[90m#x1B[39;49;00m
            metric(g, pbmc.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mpercent_mito#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]),#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
        equality_check(#x1B[90m#x1B[39;49;00m
            metric(g, pbmc.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mpercent_mito#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]),#x1B[90m#x1B[39;49;00m
            metric(pbmc, vals=pbmc.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mpercent_mito#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
        equality_check(  #x1B[90m# Test that series and vectors return same value#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            metric(g, pbmc.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mpercent_mito#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]),#x1B[90m#x1B[39;49;00m
            metric(g, pbmc.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mpercent_mito#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m].values),#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        equality_check(#x1B[90m#x1B[39;49;00m
            metric(pbmc, obsm=#x1B[33m"#x1B[39;49;00m#x1B[33mX_pca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
            metric(g, pbmc.obsm[#x1B[33m"#x1B[39;49;00m#x1B[33mX_pca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m].T),#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        all_genes = metric(pbmc, layer=#x1B[33m"#x1B[39;49;00m#x1B[33mraw#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        first_gene = metric(#x1B[90m#x1B[39;49;00m
            pbmc, vals=pbmc[:, pbmc.var_names[#x1B[94m0#x1B[39;49;00m]].layers[#x1B[33m"#x1B[39;49;00m#x1B[33mraw#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m].toarray().ravel()#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
>       np.testing.assert_allclose(all_genes[#x1B[94m0#x1B[39;49;00m], first_gene, rtol=#x1B[94m1e-7#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=1e-07, atol=0#x1B[0m
#x1B[1m#x1B[31mE       #x1B[0m
#x1B[1m#x1B[31mE       Mismatched elements: 1 / 1 (100%)#x1B[0m
#x1B[1m#x1B[31mE       Max absolute difference among violations: 7.9750179849e-08#x1B[0m
#x1B[1m#x1B[31mE       Max relative difference among violations: 1.8702209022e-07#x1B[0m
#x1B[1m#x1B[31mE        ACTUAL: array(0.426421)#x1B[0m
#x1B[1m#x1B[31mE        DESIRED: array(0.426421)#x1B[0m

#x1B[1m#x1B[31mtests/test_metrics.py#x1B[0m:72: AssertionError
tests/test_metrics.py::test_consistency[morans_i-single-threaded]
Stack Traces | 4.05s run time 
metric = <function morans_i at 0x7fcc2bfa9b10>

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.usefixtures(#x1B[33m"#x1B[39;49;00m#x1B[33m_threading#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_consistency#x1B[39;49;00m(metric) -> #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
        pbmc = pbmc68k_reduced()#x1B[90m#x1B[39;49;00m
        pbmc.layers[#x1B[33m"#x1B[39;49;00m#x1B[33mraw#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m] = pbmc.raw.X.copy()#x1B[90m#x1B[39;49;00m
        g = pbmc.obsp[#x1B[33m"#x1B[39;49;00m#x1B[33mconnectivities#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
        equality_check = partial(np.testing.assert_allclose, atol=#x1B[94m1e-11#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# This can fail#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        equality_check(#x1B[90m#x1B[39;49;00m
            metric(g, pbmc.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mpercent_mito#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]),#x1B[90m#x1B[39;49;00m
            metric(g, pbmc.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mpercent_mito#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]),#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
        equality_check(#x1B[90m#x1B[39;49;00m
            metric(g, pbmc.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mpercent_mito#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]),#x1B[90m#x1B[39;49;00m
            metric(pbmc, vals=pbmc.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mpercent_mito#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
        equality_check(  #x1B[90m# Test that series and vectors return same value#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            metric(g, pbmc.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mpercent_mito#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]),#x1B[90m#x1B[39;49;00m
            metric(g, pbmc.obs[#x1B[33m"#x1B[39;49;00m#x1B[33mpercent_mito#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m].values),#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        equality_check(#x1B[90m#x1B[39;49;00m
            metric(pbmc, obsm=#x1B[33m"#x1B[39;49;00m#x1B[33mX_pca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m),#x1B[90m#x1B[39;49;00m
            metric(g, pbmc.obsm[#x1B[33m"#x1B[39;49;00m#x1B[33mX_pca#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m].T),#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        all_genes = metric(pbmc, layer=#x1B[33m"#x1B[39;49;00m#x1B[33mraw#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        first_gene = metric(#x1B[90m#x1B[39;49;00m
            pbmc, vals=pbmc[:, pbmc.var_names[#x1B[94m0#x1B[39;49;00m]].layers[#x1B[33m"#x1B[39;49;00m#x1B[33mraw#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m].toarray().ravel()#x1B[90m#x1B[39;49;00m
        )#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
>       np.testing.assert_allclose(all_genes[#x1B[94m0#x1B[39;49;00m], first_gene, rtol=#x1B[94m1e-7#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=1e-07, atol=0#x1B[0m
#x1B[1m#x1B[31mE       #x1B[0m
#x1B[1m#x1B[31mE       Mismatched elements: 1 / 1 (100%)#x1B[0m
#x1B[1m#x1B[31mE       Max absolute difference among violations: 7.9750179849e-08#x1B[0m
#x1B[1m#x1B[31mE       Max relative difference among violations: 1.8702209022e-07#x1B[0m
#x1B[1m#x1B[31mE        ACTUAL: array(0.426421)#x1B[0m
#x1B[1m#x1B[31mE        DESIRED: array(0.426421)#x1B[0m

#x1B[1m#x1B[31mtests/test_metrics.py#x1B[0m:72: AssertionError
tests/test_datasets.py::test_ebi_expression_atlas
Stack Traces | 4.83s run time 
monkeypatch = <_pytest.monkeypatch.MonkeyPatch object at 0x7f294c4f0d70>

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.internet#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_ebi_expression_atlas#x1B[39;49;00m(monkeypatch: pytest.MonkeyPatch):#x1B[90m#x1B[39;49;00m
        #x1B[94mfrom#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[04m#x1B[96mscanpy#x1B[39;49;00m#x1B[04m#x1B[96m.#x1B[39;49;00m#x1B[04m#x1B[96mdatasets#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[94mimport#x1B[39;49;00m _ebi_expression_atlas #x1B[94mas#x1B[39;49;00m ea_mod#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[90m# make sure we use chunks when testing.#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[90m# This dataset has <8M entries, so 4M entries/chunk = 2 chunks#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[94massert#x1B[39;49;00m #x1B[96mhasattr#x1B[39;49;00m(ea_mod, #x1B[33m"#x1B[39;49;00m#x1B[33mCHUNK_SIZE#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
        monkeypatch.setattr(ea_mod, #x1B[33m"#x1B[39;49;00m#x1B[33mCHUNK_SIZE#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[96mint#x1B[39;49;00m(#x1B[94m4e6#x1B[39;49;00m))#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
>       adata = sc.datasets.ebi_expression_atlas(#x1B[33m"#x1B[39;49;00m#x1B[33mE-MTAB-4888#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[31mtests/test_datasets.py#x1B[0m:84: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[.../scanpy/datasets/_ebi_expression_atlas.py#x1B[0m:159: in ebi_expression_atlas
    #x1B[0mdownload_experiment(accession)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/datasets/_utils.py#x1B[0m:16: in wrapper
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m f(*args, **kwargs)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/datasets/_ebi_expression_atlas.py#x1B[0m:48: in download_experiment
    #x1B[0msniff_url(accession)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[.../scanpy/datasets/_ebi_expression_atlas.py#x1B[0m:39: in sniff_url
    #x1B[0m#x1B[94mwith#x1B[39;49;00m urlopen(base_url):  #x1B[90m# Check if server up/ dataset exists#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
         ^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../..................../_temp/uv-python-dir/cpython-3.14.5-linux-x86_64-gnu/lib/python3.14/urllib/request.py#x1B[0m:187: in urlopen
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m opener.open(url, data, timeout)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../..................../_temp/uv-python-dir/cpython-3.14.5-linux-x86_64-gnu/lib/python3.14/urllib/request.py#x1B[0m:493: in open
    #x1B[0mresponse = meth(req, response)#x1B[90m#x1B[39;49;00m
               ^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../..................../_temp/uv-python-dir/cpython-3.14.5-linux-x86_64-gnu/lib/python3.14/urllib/request.py#x1B[0m:602: in http_response
    #x1B[0mresponse = #x1B[96mself#x1B[39;49;00m.parent.error(#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../..................../_temp/uv-python-dir/cpython-3.14.5-linux-x86_64-gnu/lib/python3.14/urllib/request.py#x1B[0m:531: in error
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._call_chain(*args)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../..................../_temp/uv-python-dir/cpython-3.14.5-linux-x86_64-gnu/lib/python3.14/urllib/request.py#x1B[0m:464: in _call_chain
    #x1B[0mresult = func(*args)#x1B[90m#x1B[39;49;00m
             ^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

self = <urllib.request.HTTPDefaultErrorHandler object at 0x7f2978bbf380>
req = <urllib.request.Request object at 0x7f294c2bc050>
fp = <http.client.HTTPResponse object at 0x7f294c2b7790>, code = 500
msg = 'Internal Server Error'
hdrs = <http.client.HTTPMessage object at 0x7f29683ef200>

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mhttp_error_default#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m, req, fp, code, msg, hdrs):#x1B[90m#x1B[39;49;00m
>       #x1B[94mraise#x1B[39;49;00m HTTPError(req.full_url, code, msg, hdrs, fp)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE       urllib.error.HTTPError: HTTP Error 500: Internal Server Error#x1B[0m
#x1B[1m#x1B[31mE       https://www.ebi.ac..../sc/experiments/E-MTAB-4888/#x1B[0m

#x1B[1m#x1B[31m../..................../_temp/uv-python-dir/cpython-3.14.5-linux-x86_64-gnu/lib/python3.14/urllib/request.py#x1B[0m:611: HTTPError
tests/test_pca.py::test_pca_chunked
Stack Traces | 8.7s run time 
self = <tempfile._TemporaryFileCloser object at 0x7f2978bbc2f0>

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92m__del__#x1B[39;49;00m(#x1B[96mself#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
        close_called = #x1B[96mself#x1B[39;49;00m.close_called#x1B[90m#x1B[39;49;00m
        #x1B[96mself#x1B[39;49;00m.cleanup()#x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m #x1B[95mnot#x1B[39;49;00m close_called:#x1B[90m#x1B[39;49;00m
>           _warnings.warn(#x1B[96mself#x1B[39;49;00m.warn_message, #x1B[96mResourceWarning#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE           ResourceWarning: Implicitly cleaning up <HTTPError 500: 'Internal Server Error'>#x1B[0m

#x1B[1m#x1B[31m../...../_temp/uv-python-dir/cpython-3.14.5-linux-x86_64-gnu/lib/python3.14/tempfile.py#x1B[0m:484: ResourceWarning

#x1B[33mThe above exception was the direct cause of the following exception:#x1B[0m

cls = <class '_pytest.runner.CallInfo'>
func = <function call_and_report.<locals>.<lambda> at 0x7f29208b3ed0>
when = 'call'
reraise = (<class '_pytest.outcomes.Exit'>, <class 'KeyboardInterrupt'>)

    #x1B[0m#x1B[37m@classmethod#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mfrom_call#x1B[39;49;00m(#x1B[90m#x1B[39;49;00m
        #x1B[96mcls#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
        func: Callable[[], TResult],#x1B[90m#x1B[39;49;00m
        when: Literal[#x1B[33m"#x1B[39;49;00m#x1B[33mcollect#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33msetup#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mcall#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mteardown#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m],#x1B[90m#x1B[39;49;00m
        reraise: #x1B[96mtype#x1B[39;49;00m[#x1B[96mBaseException#x1B[39;49;00m] | #x1B[96mtuple#x1B[39;49;00m[#x1B[96mtype#x1B[39;49;00m[#x1B[96mBaseException#x1B[39;49;00m], ...] | #x1B[94mNone#x1B[39;49;00m = #x1B[94mNone#x1B[39;49;00m,#x1B[90m#x1B[39;49;00m
    ) -> CallInfo[TResult]:#x1B[90m#x1B[39;49;00m
    #x1B[90m    #x1B[39;49;00m#x1B[33m"""Call func, wrapping the result in a CallInfo.#x1B[39;49;00m
    #x1B[33m#x1B[39;49;00m
    #x1B[33m    :param func:#x1B[39;49;00m
    #x1B[33m        The function to call. Called without arguments.#x1B[39;49;00m
    #x1B[33m    :type func: Callable[[], _pytest.runner.TResult]#x1B[39;49;00m
    #x1B[33m    :param when:#x1B[39;49;00m
    #x1B[33m        The phase in which the function is called.#x1B[39;49;00m
    #x1B[33m    :param reraise:#x1B[39;49;00m
    #x1B[33m        Exception or exceptions that shall propagate if raised by the#x1B[39;49;00m
    #x1B[33m        function, instead of being wrapped in the CallInfo.#x1B[39;49;00m
    #x1B[33m    """#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        excinfo = #x1B[94mNone#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        instant = timing.Instant()#x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>           result: TResult | #x1B[94mNone#x1B[39;49;00m = func()#x1B[90m#x1B[39;49;00m
                                     ^^^^^^#x1B[90m#x1B[39;49;00m

#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14....../site-packages/_pytest/runner.py#x1B[0m:353: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14....../site-packages/_pytest/runner.py#x1B[0m:245: in <lambda>
    #x1B[0m#x1B[94mlambda#x1B[39;49;00m: runtest_hook(item=item, **kwds),#x1B[90m#x1B[39;49;00m
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14.../site-packages/pluggy/_hooks.py#x1B[0m:512: in __call__
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._hookexec(#x1B[96mself#x1B[39;49;00m.name, #x1B[96mself#x1B[39;49;00m._hookimpls.copy(), kwargs, firstresult)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14.../site-packages/pluggy/_manager.py#x1B[0m:120: in _hookexec
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m #x1B[96mself#x1B[39;49;00m._inner_hookexec(hook_name, methods, kwargs, firstresult)#x1B[90m#x1B[39;49;00m
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14.../site-packages/_pytest/logging.py#x1B[0m:850: in pytest_runtest_call
    #x1B[0m#x1B[94myield#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14.../site-packages/_pytest/capture.py#x1B[0m:900: in pytest_runtest_call
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m (#x1B[94myield#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
            ^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14.../site-packages/_pytest/skipping.py#x1B[0m:268: in pytest_runtest_call
    #x1B[0m#x1B[94mreturn#x1B[39;49;00m (#x1B[94myield#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
            ^^^^^#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14........./site-packages/_pytest/unraisableexception.py#x1B[0m:158: in pytest_runtest_call
    #x1B[0mcollect_unraisable(item.config)#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14........./site-packages/_pytest/unraisableexception.py#x1B[0m:79: in collect_unraisable
    #x1B[0m#x1B[94mraise#x1B[39;49;00m errors[#x1B[94m0#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

config = <_pytest.config.Config object at 0x7f29d27b74d0>

    #x1B[0m#x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mcollect_unraisable#x1B[39;49;00m(config: Config) -> #x1B[94mNone#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
        pop_unraisable = config.stash[unraisable_exceptions].pop#x1B[90m#x1B[39;49;00m
        errors: #x1B[96mlist#x1B[39;49;00m[pytest.PytestUnraisableExceptionWarning | #x1B[96mRuntimeError#x1B[39;49;00m] = []#x1B[90m#x1B[39;49;00m
        meta = #x1B[94mNone#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        hook_error = #x1B[94mNone#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
        #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            #x1B[94mwhile#x1B[39;49;00m #x1B[94mTrue#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                    meta = pop_unraisable()#x1B[90m#x1B[39;49;00m
                #x1B[94mexcept#x1B[39;49;00m #x1B[96mIndexError#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
                    #x1B[94mbreak#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(meta, #x1B[96mBaseException#x1B[39;49;00m):#x1B[90m#x1B[39;49;00m
                    hook_error = #x1B[96mRuntimeError#x1B[39;49;00m(#x1B[33m"#x1B[39;49;00m#x1B[33mFailed to process unraisable exception#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
                    hook_error.__cause__ = meta#x1B[90m#x1B[39;49;00m
                    errors.append(hook_error)#x1B[90m#x1B[39;49;00m
                    #x1B[94mcontinue#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
                msg = meta.msg#x1B[90m#x1B[39;49;00m
                #x1B[94mtry#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
>                   warnings.warn(pytest.PytestUnraisableExceptionWarning(msg))#x1B[90m#x1B[39;49;00m
#x1B[1m#x1B[31mE                   pytest.PytestUnraisableExceptionWarning: Exception ignored while calling deallocator <function _TemporaryFileCloser.__del__ at 0x7f29d2ab85c0>: None#x1B[0m

#x1B[1m#x1B[31m../../../..../scanpy/B9PcT7QG/hatch-test.stable/lib/python3.14........./site-packages/_pytest/unraisableexception.py#x1B[0m:67: PytestUnraisableExceptionWarning

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@ilan-gold

ilan-gold commented Jun 8, 2026

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At this point, I think this may just be worth reporting upstream to numba and loosening our tolerance

@ilan-gold ilan-gold force-pushed the ig/moran_numba_66 branch from c1f7f7a to 02d5793 Compare June 8, 2026 15:22
@ilan-gold ilan-gold added this to the 1.12.2 milestone Jun 8, 2026
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