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python311Packages.pybind11: 2.11.1 -> 2.12.0#299864

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dotlambda:python3Packages.pybind11
Apr 6, 2024
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python311Packages.pybind11: 2.11.1 -> 2.12.0#299864
doronbehar merged 2 commits intoNixOS:stagingfrom
dotlambda:python3Packages.pybind11

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@dotlambda dotlambda commented Mar 28, 2024

Description of changes

Diff: pybind/pybind11@v2.11.1...v2.12.0

Changelog: https://github.com/pybind/pybind11/blob/v2.12.0/docs/changelog.rst

Things done

  • Built on platform(s)
    • x86_64-linux
    • aarch64-linux
    • x86_64-darwin
    • aarch64-darwin
  • For non-Linux: Is sandboxing enabled in nix.conf? (See Nix manual)
    • sandbox = relaxed
    • sandbox = true
  • Tested, as applicable:
  • Tested compilation of all packages that depend on this change using nix-shell -p nixpkgs-review --run "nixpkgs-review rev HEAD". Note: all changes have to be committed, also see nixpkgs-review usage
  • Tested basic functionality of all binary files (usually in ./result/bin/)
  • 24.05 Release Notes (or backporting 23.05 and 23.11 Release notes)
    • (Package updates) Added a release notes entry if the change is major or breaking
    • (Module updates) Added a release notes entry if the change is significant
    • (Module addition) Added a release notes entry if adding a new NixOS module
  • Fits CONTRIBUTING.md.

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@github-actions github-actions bot added the 6.topic: python Python is a high-level, general-purpose programming language. label Mar 28, 2024
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dotlambda commented Mar 31, 2024

@ofborg eval

@ofborg ofborg bot requested review from FRidh and doronbehar March 31, 2024 22:53
@ofborg ofborg bot added 10.rebuild-darwin: 501+ This PR causes many rebuilds on Darwin and should normally target the staging branches. 10.rebuild-darwin: 5001+ This PR causes many rebuilds on Darwin and must target the staging branches. 10.rebuild-linux: 501+ This PR causes many rebuilds on Linux and should normally target the staging branches. 10.rebuild-linux: 5001+ This PR causes many rebuilds on Linux and must target the staging branches. labels Mar 31, 2024
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doronbehar commented Apr 1, 2024

Hmm I see a failing test in scipy in CI:

=================================== FAILURES ===================================
___ test_milp_timeout_16545[options0-Time limit reached. (HiGHS Status 13:] ____
[gw34] linux -- Python 3.11.8 /nix/store/gd3shnza1i50zn8zs04fa729ribr88m9-python3-3.11.8/bin/python3.11
options = {'time_limit': 0.1}, msg = 'Time limit reached. (HiGHS Status 13:'
    @pytest.mark.skipif(np.intp(0).itemsize < 8,
                        reason="Unhandled 32-bit GCC FP bug")
    @pytest.mark.slow
    @pytest.mark.parametrize(["options", "msg"], [({"time_limit": 0.1}, _msg_time),
                                                  ({"node_limit": 1}, _msg_iter)])
    def test_milp_timeout_16545(options, msg):
        # Ensure solution is not thrown away if MILP solver times out
        # -- see gh-16545
        rng = np.random.default_rng(5123833489170494244)
        A = rng.integers(0, 5, size=(100, 100))
        b_lb = np.full(100, fill_value=-np.inf)
        b_ub = np.full(100, fill_value=25)
        constraints = LinearConstraint(A, b_lb, b_ub)
        variable_lb = np.zeros(100)
        variable_ub = np.ones(100)
        variable_bounds = Bounds(variable_lb, variable_ub)
        integrality = np.ones(100)
        c_vector = -np.ones(100)
        res = milp(
            c_vector,
            integrality=integrality,
            bounds=variable_bounds,
            constraints=constraints,
            options=options,
        )
    
        assert res.message.startswith(msg)
>       assert res["x"] is not None
E       assert None is not None
lib/python3.11/site-packages/scipy/optimize/tests/test_milp.py:323: AssertionError
=============================== warnings summary ===============================
lib/python3.11/site-packages/scipy/conftest.py:9: 64 warnings
  /nix/store/m067dwmf2yslbz013vhyfn1c8yj4z1gq-python3.11-scipy-1.12.0/lib/python3.11/site-packages/scipy/conftest.py:9: UserWarning: The numpy.array_api submodule is still experimental. See NEP 47.
    import numpy.array_api
lib/python3.11/site-packages/scipy/stats/tests/test_qmc.py::TestUtils::test_geometric_discrepancy_mst_with_zero_distances
  /nix/store/m067dwmf2yslbz013vhyfn1c8yj4z1gq-python3.11-scipy-1.12.0/lib/python3.11/site-packages/scipy/stats/tests/test_qmc.py:232: UserWarning: Sample contains duplicate points.
    assert_allclose(qmc.geometric_discrepancy(sample, method='mst'), 0.5)
-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
=========================== short test summary info ============================
FAILED lib/python3.11/site-packages/scipy/optimize/tests/test_milp.py::test_milp_timeout_16545[options0-Time limit reached. (HiGHS Status 13:] - assert None is not None
= 1 failed, 58921 passed, 2699 skipped, 237 xfailed, 16 xpassed, 65 warnings in 541.07s (0:09:01) =

I wonder if that is related to the pybind update. Maybe this should be reported upstream? Or perhaps it is a sort of timeout failure that will not exist on Hydra?

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doronbehar commented Apr 3, 2024

We can also open a PR for scipy 1.13.0.

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doronbehar commented Apr 3, 2024

Haven't tested the update, will wait for CI.

@doronbehar doronbehar force-pushed the python3Packages.pybind11 branch 3 times, most recently from 60e4d1b to f7739e6 Compare April 5, 2024 06:15
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doronbehar commented Apr 5, 2024

@ofborg eval

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doronbehar commented Apr 5, 2024

Hmm I saw earlier deeper errors in ofborg from dependencies of pybind. I tested a better but similar version of this change upon the master branch, and it seems to be fine.

I also don't understand the cython_3 error in ansible-pylibssh that ofborg reports upon.. I sort of fixed it but it won't pick up my change. I think this can be cooked in staging, the ofborg error is not fatal of course because it's not the master branch. cc @mweinelt .

@doronbehar doronbehar mentioned this pull request Apr 5, 2024
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mweinelt commented Apr 5, 2024

Eval fix in 243c22a

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SuperSandro2000 commented Apr 5, 2024

@ofborg eval

@wegank wegank added the 12.approvals: 1 This PR was reviewed and approved by one person. label Apr 5, 2024
@doronbehar doronbehar force-pushed the python3Packages.pybind11 branch from 0355829 to f7739e6 Compare April 6, 2024 20:07
@doronbehar doronbehar force-pushed the python3Packages.pybind11 branch from f7739e6 to 11d0dfa Compare April 6, 2024 20:08
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doronbehar commented Apr 6, 2024

OK thanks for the links - I think what caused the issue was that staging without this PR didn't eval so ofborg couldn't compute the different attributes. I rebased and removed my ansible-pylibssh commit, to clean the PR. Will merge after eval finishes, I don't expect it to build, as I said earlier.

@doronbehar doronbehar merged commit 4eae5f9 into NixOS:staging Apr 6, 2024
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vcunat commented Apr 15, 2024

FYI the build of scipy now regressed on x86_64-darwin (but not the other three platforms):
https://hydra.nixos.org/build/256212026#tabs-buildsteps
https://hydra.nixos.org/build/256034246#tabs-buildsteps
/cc the staging-next PR #303527

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doronbehar commented Apr 15, 2024

Thanks for the link! scipy/scipy#20300 is the upstream issue. Here's a fix: #304226

@dotlambda dotlambda deleted the python3Packages.pybind11 branch April 15, 2024 15:19
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@SuperSandro2000 SuperSandro2000 SuperSandro2000 approved these changes

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6.topic: python Python is a high-level, general-purpose programming language. 10.rebuild-darwin: 501+ This PR causes many rebuilds on Darwin and should normally target the staging branches. 10.rebuild-darwin: 5001+ This PR causes many rebuilds on Darwin and must target the staging branches. 10.rebuild-linux: 501+ This PR causes many rebuilds on Linux and should normally target the staging branches. 10.rebuild-linux: 5001+ This PR causes many rebuilds on Linux and must target the staging branches. 12.approvals: 1 This PR was reviewed and approved by one person.

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