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@dependabot dependabot bot commented on behalf of github Dec 15, 2025

Bumps actions/upload-artifact from 5 to 6.

Release notes

Sourced from actions/upload-artifact's releases.

v6.0.0

v6 - What's new

[!IMPORTANT] actions/upload-artifact@v6 now runs on Node.js 24 (runs.using: node24) and requires a minimum Actions Runner version of 2.327.1. If you are using self-hosted runners, ensure they are updated before upgrading.

Node.js 24

This release updates the runtime to Node.js 24. v5 had preliminary support for Node.js 24, however this action was by default still running on Node.js 20. Now this action by default will run on Node.js 24.

What's Changed

Full Changelog: actions/upload-artifact@v5.0.0...v6.0.0

Commits
  • b7c566a Merge pull request #745 from actions/upload-artifact-v6-release
  • e516bc8 docs: correct description of Node.js 24 support in README
  • ddc45ed docs: update README to correct action name for Node.js 24 support
  • 615b319 chore: release v6.0.0 for Node.js 24 support
  • 017748b Merge pull request #744 from actions/fix-storage-blob
  • 38d4c79 chore: rebuild dist
  • 7d27270 chore: add missing license cache files for @​actions/core, @​actions/io, and mi...
  • 5f643d3 chore: update license files for @​actions/artifact@​5.0.1 dependencies
  • 1df1684 chore: update package-lock.json with @​actions/artifact@​5.0.1
  • b5b1a91 fix: update @​actions/artifact to ^5.0.0 for Node.js 24 punycode fix
  • Additional commits viewable in compare view

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Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 5 to 6.
- [Release notes](https://github.com/actions/upload-artifact/releases)
- [Commits](actions/upload-artifact@v5...v6)

---
updated-dependencies:
- dependency-name: actions/upload-artifact
  dependency-version: '6'
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file github_actions Pull requests that update GitHub Actions code labels Dec 15, 2025
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codecov bot commented Dec 15, 2025

❌ 2 Tests Failed:

Tests completed Failed Passed Skipped
2336 2 2334 348
View the top 2 failed test(s) by shortest run time
tests/test_rank_genes_groups.py::test_wilcoxon_tie_correction[False]
Stack Traces | 0.086s run time
reference = False

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[33m"#x1B[39;49;00m#x1B[33mreference#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, [#x1B[94mTrue#x1B[39;49;00m, #x1B[94mFalse#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_wilcoxon_tie_correction#x1B[39;49;00m(reference):#x1B[90m#x1B[39;49;00m
        pbmc = pbmc68k_reduced()#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        groups = [#x1B[33m"#x1B[39;49;00m#x1B[33mCD14+ Monocyte#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mDendritic#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
        groupby = #x1B[33m"#x1B[39;49;00m#x1B[33mbulk_labels#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        _, groups_masks = select_groups(pbmc, groups, groupby)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        x = pbmc.raw.X[groups_masks[#x1B[94m0#x1B[39;49;00m]].toarray()#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        mask_rest = groups_masks[#x1B[94m1#x1B[39;49;00m] #x1B[94mif#x1B[39;49;00m reference #x1B[94melse#x1B[39;49;00m ~groups_masks[#x1B[94m0#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
        y = pbmc.raw.X[mask_rest].toarray()#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        pvals = mannwhitneyu(x, y, use_continuity=#x1B[94mFalse#x1B[39;49;00m, alternative=#x1B[33m"#x1B[39;49;00m#x1B[33mtwo-sided#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m).pvalue#x1B[90m#x1B[39;49;00m
        pvals[np.isnan(pvals)] = #x1B[94m1.0#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m reference:#x1B[90m#x1B[39;49;00m
            ref = groups[#x1B[94m1#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
        #x1B[94melse#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            ref = #x1B[33m"#x1B[39;49;00m#x1B[33mrest#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            groups = groups[:#x1B[94m1#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        test_obj = _RankGenes(pbmc, groups, groupby, reference=ref)#x1B[90m#x1B[39;49;00m
        #x1B[94mwith#x1B[39;49;00m (#x1B[90m#x1B[39;49;00m
            pytest.warns(#x1B[96mRuntimeWarning#x1B[39;49;00m, match=#x1B[33mr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33minvalid value encountered#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m reference#x1B[90m#x1B[39;49;00m
            #x1B[94melse#x1B[39;49;00m nullcontext()#x1B[90m#x1B[39;49;00m
        ):#x1B[90m#x1B[39;49;00m
            test_obj.compute_statistics(#x1B[33m"#x1B[39;49;00m#x1B[33mwilcoxon#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, tie_correct=#x1B[94mTrue#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
>       np.testing.assert_allclose(test_obj.stats[groups[#x1B[94m0#x1B[39;49;00m]][#x1B[33m"#x1B[39;49;00m#x1B[33mpvals#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m], pvals)#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: 465 / 765 (60.8%)#x1B[0m
#x1B[1m#x1B[31mE       Max absolute difference among violations: 7.0936388474e-07#x1B[0m
#x1B[1m#x1B[31mE       Max relative difference among violations: 0.435111574#x1B[0m
#x1B[1m#x1B[31mE        ACTUAL: array([4.747381e-47, 2.910919e-01, 9.350926e-01, 1.204920e-01,#x1B[0m
#x1B[1m#x1B[31mE              6.826701e-18, 4.262317e-04, 6.489862e-01, 3.630759e-11,#x1B[0m
#x1B[1m#x1B[31mE              3.053055e-17, 3.037204e-01, 2.432239e-01, 5.370464e-01,...#x1B[0m
#x1B[1m#x1B[31mE        DESIRED: array([0.000000e+00, 2.910920e-01, 9.350926e-01, 1.204920e-01,#x1B[0m
#x1B[1m#x1B[31mE              6.826711e-18, 4.262317e-04, 6.489862e-01, 3.630755e-11,#x1B[0m
#x1B[1m#x1B[31mE              3.053048e-17, 3.037204e-01, 2.432239e-01, 5.370464e-01,...#x1B[0m

#x1B[1m#x1B[31mtests/test_rank_genes_groups.py#x1B[0m:301: AssertionError
tests/test_rank_genes_groups.py::test_wilcoxon_tie_correction[True]
Stack Traces | 6.03s run time
reference = True

    #x1B[0m#x1B[37m@pytest#x1B[39;49;00m.mark.parametrize(#x1B[33m"#x1B[39;49;00m#x1B[33mreference#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, [#x1B[94mTrue#x1B[39;49;00m, #x1B[94mFalse#x1B[39;49;00m])#x1B[90m#x1B[39;49;00m
    #x1B[94mdef#x1B[39;49;00m#x1B[90m #x1B[39;49;00m#x1B[92mtest_wilcoxon_tie_correction#x1B[39;49;00m(reference):#x1B[90m#x1B[39;49;00m
        pbmc = pbmc68k_reduced()#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        groups = [#x1B[33m"#x1B[39;49;00m#x1B[33mCD14+ Monocyte#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, #x1B[33m"#x1B[39;49;00m#x1B[33mDendritic#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
        groupby = #x1B[33m"#x1B[39;49;00m#x1B[33mbulk_labels#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        _, groups_masks = select_groups(pbmc, groups, groupby)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        x = pbmc.raw.X[groups_masks[#x1B[94m0#x1B[39;49;00m]].toarray()#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        mask_rest = groups_masks[#x1B[94m1#x1B[39;49;00m] #x1B[94mif#x1B[39;49;00m reference #x1B[94melse#x1B[39;49;00m ~groups_masks[#x1B[94m0#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
        y = pbmc.raw.X[mask_rest].toarray()#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        pvals = mannwhitneyu(x, y, use_continuity=#x1B[94mFalse#x1B[39;49;00m, alternative=#x1B[33m"#x1B[39;49;00m#x1B[33mtwo-sided#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m).pvalue#x1B[90m#x1B[39;49;00m
        pvals[np.isnan(pvals)] = #x1B[94m1.0#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        #x1B[94mif#x1B[39;49;00m reference:#x1B[90m#x1B[39;49;00m
            ref = groups[#x1B[94m1#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
        #x1B[94melse#x1B[39;49;00m:#x1B[90m#x1B[39;49;00m
            ref = #x1B[33m"#x1B[39;49;00m#x1B[33mrest#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[90m#x1B[39;49;00m
            groups = groups[:#x1B[94m1#x1B[39;49;00m]#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
        test_obj = _RankGenes(pbmc, groups, groupby, reference=ref)#x1B[90m#x1B[39;49;00m
        #x1B[94mwith#x1B[39;49;00m (#x1B[90m#x1B[39;49;00m
            pytest.warns(#x1B[96mRuntimeWarning#x1B[39;49;00m, match=#x1B[33mr#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m#x1B[33minvalid value encountered#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
            #x1B[94mif#x1B[39;49;00m reference#x1B[90m#x1B[39;49;00m
            #x1B[94melse#x1B[39;49;00m nullcontext()#x1B[90m#x1B[39;49;00m
        ):#x1B[90m#x1B[39;49;00m
            test_obj.compute_statistics(#x1B[33m"#x1B[39;49;00m#x1B[33mwilcoxon#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m, tie_correct=#x1B[94mTrue#x1B[39;49;00m)#x1B[90m#x1B[39;49;00m
    #x1B[90m#x1B[39;49;00m
>       np.testing.assert_allclose(test_obj.stats[groups[#x1B[94m0#x1B[39;49;00m]][#x1B[33m"#x1B[39;49;00m#x1B[33mpvals#x1B[39;49;00m#x1B[33m"#x1B[39;49;00m], pvals)#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: 383 / 765 (50.1%)#x1B[0m
#x1B[1m#x1B[31mE       Max absolute difference among violations: 2.4703574419e-07#x1B[0m
#x1B[1m#x1B[31mE       Max relative difference among violations: 4.4790295425e-05#x1B[0m
#x1B[1m#x1B[31mE        ACTUAL: array([2.029091e-18, 6.430380e-01, 6.164863e-01, 7.551346e-02,#x1B[0m
#x1B[1m#x1B[31mE              1.590458e-08, 1.884037e-03, 5.290635e-01, 1.314833e-05,#x1B[0m
#x1B[1m#x1B[31mE              5.756106e-08, 2.646892e-01, 2.670054e-02, 4.151307e-01,...#x1B[0m
#x1B[1m#x1B[31mE        DESIRED: array([2.029090e-18, 6.430379e-01, 6.164863e-01, 7.551347e-02,#x1B[0m
#x1B[1m#x1B[31mE              1.590460e-08, 1.884038e-03, 5.290635e-01, 1.314831e-05,#x1B[0m
#x1B[1m#x1B[31mE              5.756110e-08, 2.646892e-01, 2.670054e-02, 4.151307e-01,...#x1B[0m

#x1B[1m#x1B[31mtests/test_rank_genes_groups.py#x1B[0m:301: AssertionError

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