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Relax nanosecond datetime restriction in CF time decoding #9618

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7b5f323
implement default_precision_timestamp, refactor coding/times.py and c…
kmuehlbauer Oct 10, 2024
8784f33
align tests with new time resolution behaviour
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b45ab23
timedelta decoding, fsspec handling
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39086ef
fixes in coding/times.py
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df49a40
add docs on time coding
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adb8ca3
attempt fixing doc tests
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266b1ed
fix issue where out-of-bounds floating point values slipped in the pr…
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6d5f13b
convert to UTC first before stripping of tz in _unpack_time_units_and…
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5d68bfe
reorganize pandas compatibility code, remove unneeded code, attempt t…
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07bba69
another attempt to finally fix mypy
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6e7f0bb
refactor out _check_date_is_after_shift
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b4a49bb
refactor out _maybe_strip_tz_from_timestamp
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2e1ff4f
more refactoring in coding.times.py
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d5a7da0
more refactoring in coding.times.py
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821b68d
minor fix in time-coding.rst
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d066edf
set default resolution to "s", which actually means, use pandas lowes…
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ed22da1
Add section for default units, fix options
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8bf23f4
attempt to fix typing
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c3a2b39
attempt to fix typing
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3c44aed
fix scalar datetime/timedelta
kmuehlbauer Oct 15, 2024
48be73a
fix user docs
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Fix variable tests, mostly datetime/timedelta is inittialized with us…
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b5d0795
revert changes in _possible_convert_objects, this needs to be checked…
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308091c
use set instead list
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remove global option
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mypy thinks `unit` is Literal, because the pandas-stubs suggest so, b…
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43f7d61
ignore mypy arg-type
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59934b9
fix docstring of `default_precision_timestamp`
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a01f9f3
add 'time_unit'-kwarg to decode_cf and descendent functions with "ns"…
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8b91128
fix tests
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0e351ca
fix more tests
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07a8e9c
fix docstring
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2be5739
use pd.Timestamp(np.datetime64(cftime)) to convert from cftime to numpy
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b9d0a8e
use dt = np.datetime64(cftime.isoformat()) to convert from cftime to …
kmuehlbauer Nov 18, 2024
08afc3b
fix time-coding.rst
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edc55e1
use us in to_datetimeindex
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bffe919
revert back to us for datetimeindex tests
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150b982
estimate fitting resolution for floating point values, when decoding …
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7113ceb
add test
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7f47f0b
refactor floating point decoding
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63c83f4
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2910250
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update time-coding.rst
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5333240
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try to fix test, remove stale print
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d0c17a4
another attempt to fix test
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b2b6bb1
debug failing test
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5dbc8a7
refactor cftime fallback in datetime decoding
kmuehlbauer Nov 21, 2024
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f95408a
fix merge-collission
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ec7f165
use CFDatetimeCoder instance to transport unit/use_cftime
kmuehlbauer Nov 22, 2024
1f1cf1c
decode_times with CFDatetimeCoder
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provide CFDatetimeCoder from xarray.coders
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provide CFDatetimeCoder from xarray.coders
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provide CFDatetimeCoder from xarray.coders
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fix tests as suggested by code review
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Add note on ``proleptic_gregorian`` calendar
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0ba848d
remove time_resolution from docstring
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6cb8702
update time.coding.rst wrt default time unit
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fix empty array
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revert some tests to align with scalar logic handling
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1 change: 1 addition & 0 deletions doc/internals/index.rst
Original file line number Diff line number Diff line change
Expand Up @@ -26,3 +26,4 @@ The pages in this section are intended for:
how-to-add-new-backend
how-to-create-custom-index
zarr-encoding-spec
time-coding
442 changes: 442 additions & 0 deletions doc/internals/time-coding.rst

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34 changes: 20 additions & 14 deletions doc/user-guide/time-series.rst
Original file line number Diff line number Diff line change
Expand Up @@ -21,20 +21,32 @@ core functionality.
Creating datetime64 data
------------------------

Xarray uses the numpy dtypes ``datetime64[ns]`` and ``timedelta64[ns]`` to
represent datetime data, which offer vectorized (if sometimes buggy) operations
with numpy and smooth integration with pandas.
Xarray uses the numpy dtypes ``datetime64[unit]`` and ``timedelta64[unit]``
(where unit is anything of "s", "ms", "us" and "ns") to represent datetime
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data, which offer vectorized (if sometimes buggy) operations with numpy and
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smooth integration with pandas.

To convert to or create regular arrays of ``datetime64`` data, we recommend
using :py:func:`pandas.to_datetime` and :py:func:`pandas.date_range`:

.. ipython:: python

pd.to_datetime(["2000-01-01", "2000-02-02"])
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can we add an example with xr.date_range too please?

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Honestly I might even just switch all of these to xr.date_range

pd.DatetimeIndex(
["2000-01-01 00:00:00", "2000-02-02 00:00:00"], dtype="datetime64[s]"
)
pd.date_range("2000-01-01", periods=365)
pd.date_range("2000-01-01", periods=365, unit="s")

.. note::
Care has to be taken to create the output with the wanted resolution.
For :py:func:`pandas.date_range` the ``unit``-kwarg has to be specified
and for :py:func:`pandas.to_datetime` the selection of the resolution
isn't possible at all. For that :py:class:`pd.DatetimeIndex` can be used
directly.

Alternatively, you can supply arrays of Python ``datetime`` objects. These get
converted automatically when used as arguments in xarray objects:
converted automatically when used as arguments in xarray objects (with us-resolution):

.. ipython:: python

Expand All @@ -51,7 +63,7 @@ attribute like ``'days since 2000-01-01'``).
.. note::

When decoding/encoding datetimes for non-standard calendars or for dates
before year 1678 or after year 2262, xarray uses the `cftime`_ library.
before 1582-10-15, xarray uses the `cftime`_ library.
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It was previously packaged with the ``netcdf4-python`` package under the
name ``netcdftime`` but is now distributed separately. ``cftime`` is an
:ref:`optional dependency<installing>` of xarray.
Expand All @@ -68,15 +80,9 @@ You can manual decode arrays in this form by passing a dataset to
ds = xr.Dataset({"time": ("time", [0, 1, 2, 3], attrs)})
xr.decode_cf(ds)

One unfortunate limitation of using ``datetime64[ns]`` is that it limits the
native representation of dates to those that fall between the years 1678 and
2262. When a netCDF file contains dates outside of these bounds, dates will be
returned as arrays of :py:class:`cftime.datetime` objects and a :py:class:`~xarray.CFTimeIndex`
will be used for indexing. :py:class:`~xarray.CFTimeIndex` enables a subset of
the indexing functionality of a :py:class:`pandas.DatetimeIndex` and is only
fully compatible with the standalone version of ``cftime`` (not the version
packaged with earlier versions ``netCDF4``). See :ref:`CFTimeIndex` for more
information.
From xarray 2024.11 the resolution of the dates can be tuned between "s", "ms", "us" and "ns". One limitation of using ``datetime64[ns]`` is that it limits the native representation of dates to those that fall between the years 1678 and 2262, which gets increased significantly with lower resolutions. When a netCDF file contains dates outside of these bounds (or dates < 1582-10-15), dates will be returned as arrays of :py:class:`cftime.datetime` objects and a :py:class:`~xarray.CFTimeIndex` will be used for indexing.
:py:class:`~xarray.CFTimeIndex` enables a subset of the indexing functionality of a :py:class:`pandas.DatetimeIndex` and is only fully compatible with the standalone version of ``cftime`` (not the version packaged with earlier versions ``netCDF4``).
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See :ref:`CFTimeIndex` for more information.

Datetime indexing
-----------------
Expand Down
23 changes: 9 additions & 14 deletions doc/user-guide/weather-climate.rst
Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@ Weather and climate data

import xarray as xr

Xarray can leverage metadata that follows the `Climate and Forecast (CF) conventions`_ if present. Examples include :ref:`automatic labelling of plots<plotting>` with descriptive names and units if proper metadata is present and support for non-standard calendars used in climate science through the ``cftime`` module(Explained in the :ref:`CFTimeIndex` section). There are also a number of :ref:`geosciences-focused projects that build on xarray<ecosystem>`.
Xarray can leverage metadata that follows the `Climate and Forecast (CF) conventions`_ if present. Examples include :ref:`automatic labelling of plots<plotting>` with descriptive names and units if proper metadata is present and support for non-standard calendars used in climate science through the ``cftime`` module (explained in the :ref:`CFTimeIndex` section). There are also a number of :ref:`geosciences-focused projects that build on xarray<ecosystem>`.

.. _Climate and Forecast (CF) conventions: https://cfconventions.org

Expand Down Expand Up @@ -64,8 +64,7 @@ Through the standalone ``cftime`` library and a custom subclass of
:py:class:`pandas.Index`, xarray supports a subset of the indexing
functionality enabled through the standard :py:class:`pandas.DatetimeIndex` for
dates from non-standard calendars commonly used in climate science or dates
using a standard calendar, but outside the `nanosecond-precision range`_
(approximately between years 1678 and 2262).
using a standard calendar, but outside the `precision range`_ and dates prior 1582-10-15.
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.. note::

Expand All @@ -75,18 +74,14 @@ using a standard calendar, but outside the `nanosecond-precision range`_
any of the following are true:

- The dates are from a non-standard calendar
- Any dates are outside the nanosecond-precision range.
- Any dates are outside the nanosecond-precision range (prior xarray version 2024.11)
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Todo: Fix version

- Any dates are outside the time span limited by the resolution (from xarray version v2024.11)
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TODO: Fix version


Otherwise pandas-compatible dates from a standard calendar will be
represented with the ``np.datetime64[ns]`` data type, enabling the use of a
:py:class:`pandas.DatetimeIndex` or arrays with dtype ``np.datetime64[ns]``
and their full set of associated features.
represented with the ``np.datetime64[unit]`` data type (where unit can be any of ["s", "ms", "us", "ns"], enabling the use of a :py:class:`pandas.DatetimeIndex` or arrays with dtype ``np.datetime64[unit]`` and their full set of associated features.
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As of pandas version 2.0.0, pandas supports non-nanosecond precision datetime
values. For the time being, xarray still automatically casts datetime values
to nanosecond-precision for backwards compatibility with older pandas
versions; however, this is something we would like to relax going forward.
See :issue:`7493` for more discussion.
values. From xarray version 2024.11 the relaxed non-nanosecond precision datetime values will be used.

For example, you can create a DataArray indexed by a time
coordinate with dates from a no-leap calendar and a
Expand Down Expand Up @@ -115,7 +110,7 @@ instance, we can create the same dates and DataArray we created above using:
Mirroring pandas' method with the same name, :py:meth:`~xarray.infer_freq` allows one to
infer the sampling frequency of a :py:class:`~xarray.CFTimeIndex` or a 1-D
:py:class:`~xarray.DataArray` containing cftime objects. It also works transparently with
``np.datetime64[ns]`` and ``np.timedelta64[ns]`` data.
``np.datetime64`` and ``np.timedelta64`` data (with "s", "ms", "us" or "ns" resolution).

.. ipython:: python

Expand All @@ -137,7 +132,7 @@ Conversion between non-standard calendar and to/from pandas DatetimeIndexes is
facilitated with the :py:meth:`xarray.Dataset.convert_calendar` method (also available as
:py:meth:`xarray.DataArray.convert_calendar`). Here, like elsewhere in xarray, the ``use_cftime``
argument controls which datetime backend is used in the output. The default (``None``) is to
use `pandas` when possible, i.e. when the calendar is standard and dates are within 1678 and 2262.
use `pandas` when possible, i.e. when the calendar is standard and dates starting with 1582-10-15.
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.. ipython:: python

Expand Down Expand Up @@ -241,6 +236,6 @@ For data indexed by a :py:class:`~xarray.CFTimeIndex` xarray currently supports:

da.resample(time="81min", closed="right", label="right", offset="3min").mean()

.. _nanosecond-precision range: https://pandas.pydata.org/pandas-docs/stable/user_guide/timeseries.html#timestamp-limitations
.. _precision range: https://pandas.pydata.org/pandas-docs/stable/user_guide/timeseries.html#timestamp-limitations
.. _ISO 8601 standard: https://en.wikipedia.org/wiki/ISO_8601
.. _partial datetime string indexing: https://pandas.pydata.org/pandas-docs/stable/user_guide/timeseries.html#partial-string-indexing
18 changes: 4 additions & 14 deletions xarray/coding/cftime_offsets.py
Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@
from xarray.core.pdcompat import (
NoDefault,
count_not_none,
nanosecond_precision_timestamp,
default_precision_timestamp,
no_default,
)
from xarray.core.utils import emit_user_level_warning
Expand All @@ -83,21 +83,13 @@
T_FreqStr = TypeVar("T_FreqStr", str, None)


def _nanosecond_precision_timestamp(*args, **kwargs):
# As of pandas version 3.0, pd.to_datetime(Timestamp(...)) will try to
# infer the appropriate datetime precision. Until xarray supports
# non-nanosecond precision times, we will use this constructor wrapper to
# explicitly create nanosecond-precision Timestamp objects.
return pd.Timestamp(*args, **kwargs).as_unit("ns")


def get_date_type(calendar, use_cftime=True):
"""Return the cftime date type for a given calendar name."""
if cftime is None:
raise ImportError("cftime is required for dates with non-standard calendars")
else:
if _is_standard_calendar(calendar) and not use_cftime:
return _nanosecond_precision_timestamp
return default_precision_timestamp

calendars = {
"noleap": cftime.DatetimeNoLeap,
Expand Down Expand Up @@ -1475,10 +1467,8 @@ def date_range_like(source, calendar, use_cftime=None):
if is_np_datetime_like(source.dtype):
# We want to use datetime fields (datetime64 object don't have them)
source_calendar = "standard"
# TODO: the strict enforcement of nanosecond precision Timestamps can be
# relaxed when addressing GitHub issue #7493.
source_start = nanosecond_precision_timestamp(source_start)
source_end = nanosecond_precision_timestamp(source_end)
source_start = default_precision_timestamp(source_start)
source_end = default_precision_timestamp(source_end)
else:
if isinstance(source, CFTimeIndex):
source_calendar = source.calendar
Expand Down
2 changes: 1 addition & 1 deletion xarray/coding/cftimeindex.py
Original file line number Diff line number Diff line change
Expand Up @@ -646,7 +646,7 @@ def to_datetimeindex(self, unsafe=False):
CFTimeIndex([2000-01-01 00:00:00, 2000-01-02 00:00:00],
dtype='object', length=2, calendar='standard', freq=None)
>>> times.to_datetimeindex()
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This seems like we should expose the unit kwarg and add a deprecation cycle?

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I'll look into it.

DatetimeIndex(['2000-01-01', '2000-01-02'], dtype='datetime64[ns]', freq=None)
DatetimeIndex(['2000-01-01', '2000-01-02'], dtype='datetime64[us]', freq=None)
"""

if not self._data.size:
Expand Down
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