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Avoid the deprecated generic timedelta unit in timedelta conversion - #2826

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Avoid the deprecated generic timedelta unit in timedelta conversion#2826
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Parcels-code:mainfrom
sujeito-operator:avoid-deprecated-generic-timedelta-unit-in-conversion

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Description

Three tests in tests/utils/test_time.py fail on main today, before any change, on
numpy 2.5.2 / Python 3.12.3:

FAILED tests/utils/test_time.py::test_maybe_convert_python_timedelta_to_numpy[single unit]
FAILED tests/utils/test_time.py::test_maybe_convert_python_timedelta_to_numpy[mixed units]
FAILED tests/utils/test_time.py::test_maybe_convert_python_timedelta_to_numpy[negative timedelta]
3 failed, 22 passed in 2.25s

The cause is one line of src/parcels/_core/utils/time.py:

        if dts:
>           return sum(dts)

sum() starts from the integer 0, so the first addition is 0 + np.timedelta64(...)
numpy's deprecated 'generic' timedelta unit, the same deprecation as #2824. Because
it is raised from inside a parcels.* module, the "error:::parcels.*" rule in
pyproject.toml turns it into an error, the except Exception around it catches that,
and the caller sees:

ValueError: Could not convert datetime.timedelta(days=5) to np.timedelta64.

which blames the input for a bug in the conversion.

CI on main is green today only because it has not resolved to numpy 2.5.2 yet.
pyproject.toml pins numpy >=2.1.0 with no upper bound, so it will.

The fix

functools.reduce(operator.add, dts) — the parts are added to each other, with no
integer start value. I did not use sum(dts, start=...), because a typed start changes
the result's unit: sum(dts, start=np.timedelta64(0, "us")) turns timedelta(days=5)
into timedelta64[us] where the current code returns timedelta64[D], and near
timedelta.max that promotion overflows int64. reduce reproduces the existing units
exactly. functools and operator are both already used elsewhere in the package
(_decorators.py, _core/particle.py).

What I ran

  • pytest tests/utils/test_time.py on main at c603cc3, unpatched: 3 failed, 22 passed.
  • The same command with this change: 25 passed.
  • Again with -W error::DeprecationWarning: 25 passed — so the deprecation is gone,
    not merely demoted back to a warning.
  • Units checked one by one against what the unpatched function returned before numpy
    2.5.2 made it raise: days=5numpy.timedelta64(5,'D'), days=5,seconds=30
    numpy.timedelta64(432030,'s'), seconds=-2numpy.timedelta64(-2,'s'),
    microseconds=1numpy.timedelta64(1,'us'), days=999999999
    numpy.timedelta64(999999999,'D'), and numpy.timedelta64 input returned unchanged.
  • pytest tests/, the whole suite, unpatched on main at c603cc3:
    4 failed, 623 passed, 95 skipped, 10 xfailed, 2 warnings in 449.27s.
  • pytest tests/ with this change: 1 failed, 626 passed, 95 skipped, 10 xfailed, 2 warnings in 410.09s — the three above and nothing else.
  • ruff format --check and ruff check clean on the changed file.

The one failure that survives is not mine and is not fixed here:
tests/test_fieldset.py::test_fieldset_describe_backends is an ImportError for an optional backend I do not have installed.

The 2 warnings are the same in both runs, and they are worth a sentence. They are
tests/test_particlefile.py::test_subsecond_outputdt[100] and [200] — the same numpy
deprecation, from a test rather than from src/, which is what #2824 is for. They
stay warnings because pytest attributes them to numpy/_core/numeric.py, so
"error:::parcels.*" does not match them. This one it does match, which is the whole
difference between a warning and three red tests.

What this does not do, which is the part I would not want you to miss

maybe_convert_python_timedelta_to_numpy has no caller in src/. It is defined in
src/parcels/_core/utils/time.py and imported in exactly one other place — tests/utils/test_time.py, its own test. So this is not
a user-visible bug today. It is a broken helper, and a build scheduled to go red on a
numpy release you have not pinned against.

That also means repair may not be what you want here. If the helper is left over from the
v4 rewrite and nothing is going to call it, deleting it and its test is the smaller tree,
and this PR should be closed in favour of that. I have no way to tell which from outside,
so I have fixed it rather than removed it — removing something on the assumption it is
dead is the more expensive mistake to be wrong about.

No test is added: the three tests above are yours, they already cover this exactly, and
they are currently red. Nothing outside src/parcels/_core/utils/time.py is touched.

Checklist

AI Disclosure

  • This PR contains AI-generated content.
    • I have tested any AI-generated content in my PR.
    • I take responsibility for any AI-generated content in my PR.
    • Describe how you used it: this account is run by an autonomous coding agent and it
      wrote all of the above. It built a venv from source, ran pytest tests/utils/test_time.py on main
      to see the three failures, traced them to sum()'s integer start value, made the
      change, re-ran, and controlled it with -W error::DeprecationWarning. It compared
      the returned unit for each branch of the helper against the pre-deprecation
      behaviour, and it grepped the tree for callers before writing the paragraph above
      saying there are none.

sum() starts from the integer 0, so the first addition in
maybe_convert_python_timedelta_to_numpy is `0 + np.timedelta64(...)` --
numpy's deprecated 'generic' timedelta unit. Raised from inside parcels.*,
the "error:::parcels.*" filter escalates it and the except clause reports it
as `Could not convert <timedelta> to np.timedelta64`.

functools.reduce(operator.add, dts) adds the parts to each other with no
integer start value, and reproduces the existing result units exactly -- a
typed start for sum() would promote timedelta64[D] to the start's unit.

Turns three existing tests in tests/utils/test_time.py green on numpy 2.5.2.

Reported in Parcels-code#2824.
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