2 tests fail

[yurivict]

Description

========================================================================================== FAILURES ==========================================================================================
_________________________________________________________________________ test_itercb_minimizer_class[leastsq-False] _________________________________________________________________________

method = 'leastsq', calc_covar = False

    @pytest.mark.parametrize("calc_covar", calc_covar_options)
    @pytest.mark.parametrize("method", fitmethods)
    def test_itercb_minimizer_class(method, calc_covar):
        """Test the iteration callback for all solvers."""
        if method in ('nelder', 'differential_evolution'):
            pytest.xfail("scalar_minimizers behave differently, but shouldn't!!")

        mini = Minimizer(residual, pars, fcn_args=(x, y), iter_cb=per_iteration,
                         calc_covar=calc_covar)
        out = mini.minimize(method=method)

>       assert out.nfev == 23
E       assert 21 == 23
E        +  where 21 = <lmfit.minimizer.MinimizerResult object at 0x9816362e0>.nfev

tests/test_itercb.py:76: AssertionError
____________________________________________________________________________________ test_manypeaks_speed ____________________________________________________________________________________

    @pytest.mark.flaky(max_runs=5)
    def test_manypeaks_speed():
        model = None
        t0 = time.time()
        for i in np.arange(500):
            g = Model(gaussian, prefix=f'g{i}')
            if model is None:
                model = g
            else:
                model += g
        t1 = time.time()
        pars = model.make_params()
        t2 = time.time()
        _cpars = deepcopy(pars)  # noqa: F841
        t3 = time.time()

        # these are very conservative tests that
        # should be satisfied on nearly any machine
>       assert (t3-t2) < 0.5
E       assert (1660084394.21768 - 1660084393.5360963) < 0.5

tests/test_manypeaks_speed.py:33: AssertionError
====================================================================================== warnings summary ======================================================================================
../../../../../../usr/local/lib/python3.9/site-packages/matplotlib/__init__.py:152
../../../../../../usr/local/lib/python3.9/site-packages/matplotlib/__init__.py:152
../../../../../../usr/local/lib/python3.9/site-packages/matplotlib/__init__.py:152
../../../../../../usr/local/lib/python3.9/site-packages/matplotlib/__init__.py:152
../../../../../../usr/local/lib/python3.9/site-packages/matplotlib/__init__.py:152
  /usr/local/lib/python3.9/site-packages/matplotlib/__init__.py:152: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
    if LooseVersion(module.__version__) < minver:

../../../../../../usr/local/lib/python3.9/site-packages/setuptools/_distutils/version.py:346
../../../../../../usr/local/lib/python3.9/site-packages/setuptools/_distutils/version.py:346
../../../../../../usr/local/lib/python3.9/site-packages/setuptools/_distutils/version.py:346
../../../../../../usr/local/lib/python3.9/site-packages/setuptools/_distutils/version.py:346
../../../../../../usr/local/lib/python3.9/site-packages/setuptools/_distutils/version.py:346
  /usr/local/lib/python3.9/site-packages/setuptools/_distutils/version.py:346: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
    other = LooseVersion(other)

tests/test_dual_annealing.py: 3 warnings
tests/test_itercb.py: 2 warnings
tests/test_max_nfev.py: 4 warnings
tests/test_model_saveload.py: 1 warning
  /disk-samsung/freebsd-ports/math/py-lmfit/work-py39/lmfit-1.0.3/lmfit/minimizer.py:2232: DeprecationWarning: dual_annealing argument 'local_search_options' is deprecated in favor of 'minimizer_kwargs'
    ret = scipy_dual_annealing(self.penalty, bounds, **da_kws)

tests/test_lineshapes.py::test_x_float_value[step]
tests/test_lineshapes.py::test_x_float_value[rectangle]
  <__array_function__ internals>:180: DeprecationWarning: Calling nonzero on 0d arrays is deprecated, as it behaves surprisingly. Use `atleast_1d(cond).nonzero()` if the old behavior was intended. If the context of this warning is of the form `arr[nonzero(cond)]`, just use `arr[cond]`.

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

test_manypeaks_speed failed (4 runs remaining out of 5).
    <class 'AssertionError'>
    assert (1660084382.1485593 - 1660084381.4555016) < 0.5
    [<TracebackEntry /disk-samsung/freebsd-ports/math/py-lmfit/work-py39/lmfit-1.0.3/tests/test_manypeaks_speed.py:33>]
test_manypeaks_speed failed (3 runs remaining out of 5).
    <class 'AssertionError'>
    assert (1660084385.2885222 - 1660084384.6056588) < 0.5
    [<TracebackEntry /disk-samsung/freebsd-ports/math/py-lmfit/work-py39/lmfit-1.0.3/tests/test_manypeaks_speed.py:33>]
test_manypeaks_speed failed (2 runs remaining out of 5).
    <class 'AssertionError'>
    assert (1660084388.2647245 - 1660084387.5893734) < 0.5
    [<TracebackEntry /disk-samsung/freebsd-ports/math/py-lmfit/work-py39/lmfit-1.0.3/tests/test_manypeaks_speed.py:33>]
test_manypeaks_speed failed (1 runs remaining out of 5).
    <class 'AssertionError'>
    assert (1660084391.2338388 - 1660084390.564811) < 0.5
    [<TracebackEntry /disk-samsung/freebsd-ports/math/py-lmfit/work-py39/lmfit-1.0.3/tests/test_manypeaks_speed.py:33>]
test_manypeaks_speed failed; it passed 0 out of the required 1 times.
    <class 'AssertionError'>
    assert (1660084394.21768 - 1660084393.5360963) < 0.5
    [<TracebackEntry /disk-samsung/freebsd-ports/math/py-lmfit/work-py39/lmfit-1.0.3/tests/test_manypeaks_speed.py:33>]

===End Flaky Test Report===
================================================================================== short test summary info ===================================================================================
SKIPPED [2] tests/test_covariance_matrix.py:113: could not import 'numdifftools': No module named 'numdifftools'
SKIPPED [5] tests/test_covariance_matrix.py:156: could not import 'numdifftools': No module named 'numdifftools'
SKIPPED [1] tests/test_covariance_matrix.py:202: could not import 'numdifftools': No module named 'numdifftools'
SKIPPED [2] tests/test_model.py:1297: ConstantModel has not independent_vars.
SKIPPED [1] tests/test_nose.py:460: Pytest fails with multiprocessing
======================================================= 2 failed, 591 passed, 11 skipped, 2 xfailed, 22 warnings in 365.55s (0:06:05) ========================================================

A Minimal, Complete, and Verifiable example

n/a

Error message:

see above

Version information

1.0.3

Python-3.9 FreeBSD 13.1

[newville]

@yurivict Thanks, but I'm not sure we're going to act on this. We don't really promise that a) all tests will always pass on all platforms and contexts, or that b) we view such failures as "actionable". Specifically, we do not test with FreeBSD and do not intend to do so. Tests are targeted for our CI systems and used so that we have confidence that we have not broken expected behavior during development. While the results of running tests on other platforms are interesting, they are not necessarily something that we will address.

Do these failures present a problem for you? If so, can you explain what that problem is?

[yurivict]

No, I just ran them once and 2 of them failed.

[reneeotten]

the first failure is fixed already in 753db613be7641a62244f0451ee641a1d74bf244 ; it turns out that with some change in SciPy the fit converges quicker than before and that's where the failure originated from.

The second one I already marked as "flaky" in 58919491afca59aaebaf90c36890e0451a8fef19 to try and avoid these failures; it should really be able to run within the time unless the hardware is really old...

[newville]

@reneeotten thanks, yeah to me this says "lmfit runs fine of FreeBSD even though we don't test it". So, thanks @yurivict but there is no further action needed here.