stats: Test failure of test_plot_iv because of a Python deprecation in Python 3.12

[WarrenWeckesser]

With '1.12.0.dev0+2038.f34c611', I get the following failure when I run the tests with Python 3.12 on Linux. I haven't investigated further; this might be a problem in maplotlib or one of its dependencies that is out of our hands.

Short summary:

FAILED scipy/stats/tests/test_survival.py::TestSurvival::test_plot_iv - DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal i...

Full error report

______________________________________ TestSurvival.test_plot_iv ______________________________________
[gw6] linux -- Python 3.12.0 /home/warren/py3.12.0/bin/python3
scipy/stats/tests/test_survival.py:382: in test_plot_iv
    import matplotlib.pyplot as plt  # noqa: F401
        _          = array([False, False, False, False, False, False, False, False, False,
       False, False, False, False, False, False,...False, False, False,
       False, False,  True, False, False, False, False, False, False,
       False, False, False])
        n_unique   = 83
        res        = ECDFResult(cdf=EmpiricalDistributionFunction(quantiles=array([0.01327326, 0.01406269, 0.0302765 , 0.03673028, 0.052658...85899,
       0.10301113, 0.08716326, 0.07923933, 0.06933441, 0.04952458,
       0.03961966, 0.02641311, 0.        ])))
        rng        = Generator(PCG64) at 0x7FC434978820
        sample     = CensoredData(uncensored=array([0.8165432 , 0.65078278, 0.26971902, 0.23666593, 0.85843935, 0.19714283, 0.27266022, 0.6...5842522, 0.0302765 , 0.36740916, 0.96576494, 0.39879276, 0.62778709]), interval=array([], shape=(0, 2), dtype=float64))
        self       = <scipy.stats.tests.test_survival.TestSurvival object at 0x7fc33352d2b0>
/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/pyplot.py:66: in <module>
    from matplotlib.figure import Figure, FigureBase, figaspect
        AbstractContextManager = <class 'contextlib.AbstractContextManager'>
        Enum       = <enum 'Enum'>
        ExitStack  = <class 'contextlib.ExitStack'>
        FigureCanvasBase = <class 'matplotlib.backend_bases.FigureCanvasBase'>
        FigureManagerBase = <class 'matplotlib.backend_bases.FigureManagerBase'>
        MouseButton = <enum 'MouseButton'>
        __annotations__ = {}
        __builtins__ = <builtins>
        __cached__ = '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/__pycache__/pyplot.cpython-312.pyc'
        __doc__    = '\n`matplotlib.pyplot` is a state-based interface to matplotlib. It provides\nan implicit,  MATLAB-like, way of plotti...y)\n\n\nSee :ref:`api_interfaces` for an explanation of the tradeoffs between the\nimplicit and explicit interfaces.\n'
        __file__   = '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/pyplot.py'
        __loader__ = <_frozen_importlib_external.SourceFileLoader object at 0x7fc336bc83e0>
        __name__   = 'matplotlib.pyplot'
        __package__ = 'matplotlib'
        __spec__   = ModuleSpec(name='matplotlib.pyplot', loader=<_frozen_importlib_external.SourceFileLoader object at 0x7fc336bc83e0>, origin='/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/pyplot.py')
        _api       = <module 'matplotlib._api' from '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/_api/__init__.py'>
        _docstring = <module 'matplotlib._docstring' from '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/_docstring.py'>
        _pylab_helpers = <module 'matplotlib._pylab_helpers' from '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/_pylab_helpers.py'>
        annotations = _Feature((3, 7, 0, 'beta', 1), None, 16777216)
        cast       = <function cast at 0x7fc437e9cea0>
        cbook      = <module 'matplotlib.cbook' from '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/cbook.py'>
        cm         = <module 'matplotlib.cm' from '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/cm.py'>
        cycler     = <function cycler at 0x7fc334af47c0>
        functools  = <module 'functools' from '/home/warren/py3.12.0/lib/python3.12/functools.py'>
        get_backend = <function get_backend at 0x7fc33492e700>
        importlib  = <module 'importlib' from '/home/warren/py3.12.0/lib/python3.12/importlib/__init__.py'>
        inspect    = <module 'inspect' from '/home/warren/py3.12.0/lib/python3.12/inspect.py'>
        interactive = <function interactive at 0x7fc33492e7a0>
        logging    = <module 'logging' from '/home/warren/py3.12.0/lib/python3.12/logging/__init__.py'>
        matplotlib = <module 'matplotlib' from '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/__init__.py'>
        overload   = <function overload at 0x7fc437e9d580>
        rcParams   = RcParams({'_internal.classic_mode': False,
          'agg.path.chunksize': 0,
          'animation.bitrate': -1,
     ...ize': 2.0,
          'ytick.minor.visible': False,
          'ytick.minor.width': 0.6,
          'ytick.right': False})
        re         = <module 're' from '/home/warren/py3.12.0/lib/python3.12/re/__init__.py'>
        style      = <module 'matplotlib.style' from '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/style/__init__.py'>
        sys        = <module 'sys' (built-in)>
        threading  = <module 'threading' from '/home/warren/py3.12.0/lib/python3.12/threading.py'>
        time       = <module 'time' (built-in)>
/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/figure.py:43: in <module>
    from matplotlib import _blocking_input, backend_bases, _docstring, projections
        ExitStack  = <class 'contextlib.ExitStack'>
        Integral   = <class 'numbers.Integral'>
        __builtins__ = <builtins>
        __cached__ = '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/__pycache__/figure.cpython-312.pyc'
        __doc__    = '\n`matplotlib.figure` implements the following classes:\n\n`Figure`\n    Top level `~matplotlib.artist.Artist`, which...f:`user_interfaces` for a\nlist of examples) .  More information about Figures can be found at\n:ref:`figure-intro`.\n'
        __file__   = '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/figure.py'
        __loader__ = <_frozen_importlib_external.SourceFileLoader object at 0x7fc3333600e0>
        __name__   = 'matplotlib.figure'
        __package__ = 'matplotlib'
        __spec__   = ModuleSpec(name='matplotlib.figure', loader=<_frozen_importlib_external.SourceFileLoader object at 0x7fc3333600e0>, origin='/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/figure.py')
        inspect    = <module 'inspect' from '/home/warren/py3.12.0/lib/python3.12/inspect.py'>
        itertools  = <module 'itertools' (built-in)>
        logging    = <module 'logging' from '/home/warren/py3.12.0/lib/python3.12/logging/__init__.py'>
        mpl        = <module 'matplotlib' from '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/__init__.py'>
        np         = <module 'numpy' from '/home/warren/py3.12.0/lib/python3.12/site-packages/numpy/__init__.py'>
        threading  = <module 'threading' from '/home/warren/py3.12.0/lib/python3.12/threading.py'>
/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/projections/__init__.py:55: in <module>
    from .. import axes, _docstring
        __builtins__ = <builtins>
        __cached__ = '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/projections/__pycache__/__init__.cpython-312.pyc'
        __doc__    = '\nNon-separable transforms that map from data space to screen space.\n\nProjections are defined as `~.axes.Axes` subc...y/misc/custom_projection`.  The polar plot functionality in\n`matplotlib.projections.polar` may also be of interest.\n'
        __file__   = '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/projections/__init__.py'
        __loader__ = <_frozen_importlib_external.SourceFileLoader object at 0x7fc3333a4680>
        __name__   = 'matplotlib.projections'
        __package__ = 'matplotlib.projections'
        __path__   = ['/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/projections']
        __spec__   = ModuleSpec(name='matplotlib.projections', loader=<_frozen_importlib_external.SourceFileLoader object at 0x7fc3333a4680...__init__.py', submodule_search_locations=['/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/projections'])
/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/axes/__init__.py:2: in <module>
    from ._axes import *
        __builtins__ = <builtins>
        __cached__ = '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/axes/__pycache__/__init__.cpython-312.pyc'
        __doc__    = None
        __file__   = '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/axes/__init__.py'
        __loader__ = <_frozen_importlib_external.SourceFileLoader object at 0x7fc3333a43e0>
        __name__   = 'matplotlib.axes'
        __package__ = 'matplotlib.axes'
        __path__   = ['/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/axes']
        __spec__   = ModuleSpec(name='matplotlib.axes', loader=<_frozen_importlib_external.SourceFileLoader object at 0x7fc3333a43e0>, orig...b/axes/__init__.py', submodule_search_locations=['/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/axes'])
        _base      = <module 'matplotlib.axes._base' from '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/axes/_base.py'>
/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/axes/_axes.py:11: in <module>
    import matplotlib.category  # Register category unit converter as side effect.
        Integral   = <class 'numbers.Integral'>
        Number     = <class 'numbers.Number'>
        Real       = <class 'numbers.Real'>
        __builtins__ = <builtins>
        __cached__ = '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/axes/__pycache__/_axes.cpython-312.pyc'
        __doc__    = None
        __file__   = '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/axes/_axes.py'
        __loader__ = <_frozen_importlib_external.SourceFileLoader object at 0x7fc3333a4c20>
        __name__   = 'matplotlib.axes._axes'
        __package__ = 'matplotlib.axes'
        __spec__   = ModuleSpec(name='matplotlib.axes._axes', loader=<_frozen_importlib_external.SourceFileLoader object at 0x7fc3333a4c20>, origin='/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/axes/_axes.py')
        functools  = <module 'functools' from '/home/warren/py3.12.0/lib/python3.12/functools.py'>
        itertools  = <module 'itertools' (built-in)>
        logging    = <module 'logging' from '/home/warren/py3.12.0/lib/python3.12/logging/__init__.py'>
        ma         = <module 'numpy.ma' from '/home/warren/py3.12.0/lib/python3.12/site-packages/numpy/ma/__init__.py'>
        math       = <module 'math' from '/home/warren/py3.12.0/lib/python3.12/lib-dynload/math.cpython-312-x86_64-linux-gnu.so'>
        mpl        = <module 'matplotlib' from '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/__init__.py'>
        np         = <module 'numpy' from '/home/warren/py3.12.0/lib/python3.12/site-packages/numpy/__init__.py'>
/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/category.py:14: in <module>
    import dateutil.parser
        OrderedDict = <class 'collections.OrderedDict'>
        __builtins__ = <builtins>
        __cached__ = '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/__pycache__/category.cpython-312.pyc'
        __doc__    = '\nPlotting of string "category" data: ``plot([\'d\', \'f\', \'a\'], [1, 2, 3])`` will\nplot three points with x-axis ... a tick locator, a tick formatter, and the\n`.UnitData` class that creates and stores the string-to-integer mapping.\n'
        __file__   = '/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/category.py'
        __loader__ = <_frozen_importlib_external.SourceFileLoader object at 0x7fc3333dede0>
        __name__   = 'matplotlib.category'
        __package__ = 'matplotlib'
        __spec__   = ModuleSpec(name='matplotlib.category', loader=<_frozen_importlib_external.SourceFileLoader object at 0x7fc3333dede0>, origin='/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/category.py')
/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/parser/__init__.py:2: in <module>
    from ._parser import parse, parser, parserinfo, ParserError
        __builtins__ = <builtins>
        __cached__ = '/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/parser/__pycache__/__init__.cpython-312.pyc'
        __doc__    = None
        __file__   = '/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/parser/__init__.py'
        __loader__ = <_frozen_importlib_external.SourceFileLoader object at 0x7fc3333a6120>
        __name__   = 'dateutil.parser'
        __package__ = 'dateutil.parser'
        __path__   = ['/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/parser']
        __spec__   = ModuleSpec(name='dateutil.parser', loader=<_frozen_importlib_external.SourceFileLoader object at 0x7fc3333a6120>, orig...parser/__init__.py', submodule_search_locations=['/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/parser'])
/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/parser/_parser.py:50: in <module>
    from .. import tz
        Decimal    = <class 'decimal.Decimal'>
        StringIO   = <class '_io.StringIO'>
        __builtins__ = <builtins>
        __cached__ = '/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/parser/__pycache__/_parser.cpython-312.pyc'
        __doc__    = '\nThis module offers a generic date/time string parser which is able to parse\nmost known formats to represent a date...>`_\n- `Java SimpleDateFormat Class\n  <https://docs.oracle.com/javase/6/docs/api/java/text/SimpleDateFormat.html>`_\n'
        __file__   = '/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/parser/_parser.py'
        __loader__ = <_frozen_importlib_external.SourceFileLoader object at 0x7fc3333a6300>
        __name__   = 'dateutil.parser._parser'
        __package__ = 'dateutil.parser'
        __spec__   = ModuleSpec(name='dateutil.parser._parser', loader=<_frozen_importlib_external.SourceFileLoader object at 0x7fc3333a6300>, origin='/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/parser/_parser.py')
        datetime   = <module 'datetime' from '/home/warren/py3.12.0/lib/python3.12/datetime.py'>
        integer_types = (<class 'int'>,)
        monthrange = <function monthrange at 0x7fc436e52e80>
        re         = <module 're' from '/home/warren/py3.12.0/lib/python3.12/re/__init__.py'>
        relativedelta = <module 'dateutil.relativedelta' from '/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/relativedelta.py'>
        six        = <module 'six' from '/home/warren/py3.12.0/lib/python3.12/site-packages/six.py'>
        string     = <module 'string' from '/home/warren/py3.12.0/lib/python3.12/string.py'>
        text_type  = <class 'str'>
        time       = <module 'time' (built-in)>
        unicode_literals = _Feature((2, 6, 0, 'alpha', 2), (3, 0, 0, 'alpha', 0), 2097152)
        warn       = <built-in function warn>
        warnings   = <module 'warnings' from '/home/warren/py3.12.0/lib/python3.12/warnings.py'>
/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/tz/__init__.py:2: in <module>
    from .tz import *
        __builtins__ = <builtins>
        __cached__ = '/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/tz/__pycache__/__init__.cpython-312.pyc'
        __doc__    = None
        __file__   = '/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/tz/__init__.py'
        __loader__ = <_frozen_importlib_external.SourceFileLoader object at 0x7fc3333a72f0>
        __name__   = 'dateutil.tz'
        __package__ = 'dateutil.tz'
        __path__   = ['/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/tz']
        __spec__   = ModuleSpec(name='dateutil.tz', loader=<_frozen_importlib_external.SourceFileLoader object at 0x7fc3333a72f0>, origin='...ateutil/tz/__init__.py', submodule_search_locations=['/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/tz'])
/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/tz/tz.py:37: in <module>
    EPOCH = datetime.datetime.utcfromtimestamp(0)
E   DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC).
        OrderedDict = <class 'collections.OrderedDict'>
        ZERO       = datetime.timedelta(0)
        _TzOffsetFactory = <class 'dateutil.tz._factories._TzOffsetFactory'>
        _TzSingleton = <class 'dateutil.tz._factories._TzSingleton'>
        _TzStrFactory = <class 'dateutil.tz._factories._TzStrFactory'>
        __builtins__ = <builtins>
        __cached__ = '/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/tz/__pycache__/tz.cpython-312.pyc'
        __doc__    = '\nThis module offers timezone implementations subclassing the abstract\n:py:class:`datetime.tzinfo` type. There are c...), given ranges (with help\nfrom relative deltas), local machine timezone, fixed offset timezone, and UTC\ntimezone.\n'
        __file__   = '/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/tz/tz.py'
        __loader__ = <_frozen_importlib_external.SourceFileLoader object at 0x7fc3333a7410>
        __name__   = 'dateutil.tz.tz'
        __package__ = 'dateutil.tz'
        __spec__   = ModuleSpec(name='dateutil.tz.tz', loader=<_frozen_importlib_external.SourceFileLoader object at 0x7fc3333a7410>, origin='/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/tz/tz.py')
        __warningregistry__ = {'version': 22181}
        _thread    = <module '_thread' (built-in)>
        _tzinfo    = <class 'dateutil.tz._common._tzinfo'>
        _validate_fromutc_inputs = <function _validate_fromutc_inputs at 0x7fc334257c40>
        bisect     = <module 'bisect' from '/home/warren/py3.12.0/lib/python3.12/bisect.py'>
        datetime   = <module 'datetime' from '/home/warren/py3.12.0/lib/python3.12/datetime.py'>
        enfold     = <function enfold at 0x7fc334257ba0>
        os         = <module 'os' (frozen)>
        six        = <module 'six' from '/home/warren/py3.12.0/lib/python3.12/site-packages/six.py'>
        string_types = (<class 'str'>,)
        struct     = <module 'struct' from '/home/warren/py3.12.0/lib/python3.12/struct.py'>
        sys        = <module 'sys' (built-in)>
        time       = <module 'time' (built-in)>
        tzname_in_python2 = <function tzname_in_python2 at 0x7fc334257b00>
        tzrangebase = <class 'dateutil.tz._common.tzrangebase'>
        tzwin      = None
        tzwinlocal = None
        warn       = <built-in function warn>
        weakref    = <module 'weakref' from '/home/warren/py3.12.0/lib/python3.12/weakref.py'>

[mdhaber]

this might be a problem in maplotlib or one of its dependencies that is out of our hands.

Looks like it, since the offending line appears to be import matplotlib.pyplot as plt. Can you try just that import on the same system?

[WarrenWeckesser]

Right, the warning arises during the import of matplotlib.pyplot:

$ python3 -Werror -c "import matplotlib.pyplot"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/pyplot.py", line 66, in <module>
    from matplotlib.figure import Figure, FigureBase, figaspect
  File "/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/figure.py", line 43, in <module>
    from matplotlib import _blocking_input, backend_bases, _docstring, projections
  File "/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/projections/__init__.py", line 55, in <module>
    from .. import axes, _docstring
  File "/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/axes/__init__.py", line 2, in <module>
    from ._axes import *
  File "/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/axes/_axes.py", line 11, in <module>
    import matplotlib.category  # Register category unit converter as side effect.
    ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/warren/py3.12.0/lib/python3.12/site-packages/matplotlib/category.py", line 14, in <module>
    import dateutil.parser
  File "/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/parser/__init__.py", line 2, in <module>
    from ._parser import parse, parser, parserinfo, ParserError
  File "/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/parser/_parser.py", line 50, in <module>
    from .. import tz
  File "/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/tz/__init__.py", line 2, in <module>
    from .tz import *
  File "/home/warren/py3.12.0/lib/python3.12/site-packages/dateutil/tz/tz.py", line 37, in <module>
    EPOCH = datetime.datetime.utcfromtimestamp(0)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
DeprecationWarning: datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC: datetime.datetime.fromtimestamp(timestamp, datetime.UTC).

The root cause is in the dateutil module that is used by matplotlib; see dateutil/dateutil#1285, and the request for an updated release of dateutil at dateutil/dateutil#1314.

[jenshnielsen]

@WarrenWeckesser Usually this kind of issue can be worked around by adding this warning to the ignore list here

scipy/pytest.ini

Line 18 in d664abf

ignore:.*In the future `np.long` will be defined as.*:FutureWarning

[AtsushiSakai]

I think the new release 2.9.0 of the dateutil has been released. We can solve this issue by installing the latest matplotlib. So we can close this issue.