TST, MAINT: test_thread_limit_apply failure with NumPy 2.1.0.dev

[tylerjereddy]

Using branch from gh-4482 locally on x86-64 Linux alongside NumPy main branch:

python -m pytest MDAnalysisTests/transformations/test_base.py::test_thread_limit_apply

______________________________________________________________________________________________________ test_thread_limit_apply _______________________________________________________________________________________________________

u = <Universe with 3341 atoms>

    def test_thread_limit_apply(u):
        default_thread_info = threadpool_info()
        default_num_thread_limit_list = [thread_info['num_threads']
                                         for thread_info in default_thread_info]
    
        new_trans = CustomTransformation(max_threads=2)
        _ = new_trans(u.trajectory.ts)
        for thread_info in new_trans.runtime_info:
>           assert thread_info['num_threads'] == 2
E           assert 1 == 2

MDAnalysisTests/transformations/test_base.py:98: AssertionError

I don't have any specific advice on this one yet, queried upstream at: numpy/numpy#26318

[tylerjereddy]

Sounds like it'll be fixed upstream in either NumPy or threadpoolctl, though the discussion is too complex to figure out who will ultimately solve it just yet.

[IAlibay]

@tylerjereddy do you know if this is still an issue? I'm fixing our tests against nightly wheels here https://github.com/MDAnalysis/mdanalysis/actions/runs/8870195702/job/24351713441?pr=4502#step:9:127 and can't seem to be able to reproduce the test failure.

[tylerjereddy]

I think the threadpoolctl fix/release isn't out yet per this table: numpy/numpy#26191

Maybe the NumPy bump to use OpenBLAS 0.3.27 in main and 2.0.0rc2 somehow fixed it. Anyway, if you want to close this I don't mind. Could always reopen if someone actually observes it again.

[IAlibay]

Thanks for the update @tylerjereddy - I'd say let's leave it open. At least on my end I'm not 100% sure the nightly CI is working exactly as expected, I'll try a local build to see if I can reproduce.