Continue to use nanosecond-precision Timestamps in precision-sensitive areas (#7731)

spencerkclark · dcherian · keewis · web-flow · commit c9c1c6d681b6 · 2023-04-13T08:58:33.000-06:00
* [test-upstream] use nanosecond-precision timestamps for now

* [test-upstream] allow kwargs to be passed to nanosecond_precision_timestamp

* unpin `pandas`

* Add type hint for nanosecond_precision_timestamp

Co-authored-by: Illviljan &lt;14371165+Illviljan@users.noreply.github.com&gt;

* Add one more TODO comment

* Remove deleted attributes in CFTimeIndex documentation

* Add a what's new entry

* Remove one more attribute from api-hidden.rst

* Silence conversion warnings in tests

* Silence more conversion warnings

---------

Co-authored-by: Deepak Cherian &lt;dcherian@users.noreply.github.com&gt;
Co-authored-by: Justus Magin &lt;keewis@posteo.de&gt;
Co-authored-by: Illviljan &lt;14371165+Illviljan@users.noreply.github.com&gt;
diff --git a/ci/requirements/all-but-dask.yml b/ci/requirements/all-but-dask.yml
@@ -25,7 +25,7 @@ dependencies:
   - numbagg
   - numpy<1.24
   - packaging
-  - pandas<2
+  - pandas
   - pint
   - pip
   - pseudonetcdf
diff --git a/ci/requirements/doc.yml b/ci/requirements/doc.yml
@@ -19,7 +19,7 @@ dependencies:
   - numba
   - numpy>=1.21,<1.24
   - packaging>=21.3
-  - pandas>=1.4,<2
+  - pandas>=1.4
   - pooch
   - pip
   - pre-commit
diff --git a/ci/requirements/environment-py311.yml b/ci/requirements/environment-py311.yml
@@ -27,7 +27,7 @@ dependencies:
   - numexpr
   - numpy
   - packaging
-  - pandas<2
+  - pandas
   - pint
   - pip
   - pooch
diff --git a/ci/requirements/environment-windows-py311.yml b/ci/requirements/environment-windows-py311.yml
@@ -24,7 +24,7 @@ dependencies:
   # - numbagg
   - numpy
   - packaging
-  - pandas<2
+  - pandas
   - pint
   - pip
   - pre-commit
diff --git a/ci/requirements/environment-windows.yml b/ci/requirements/environment-windows.yml
@@ -24,7 +24,7 @@ dependencies:
   - numbagg
   - numpy<1.24
   - packaging
-  - pandas<2
+  - pandas
   - pint
   - pip
   - pre-commit
diff --git a/ci/requirements/environment.yml b/ci/requirements/environment.yml
@@ -27,7 +27,7 @@ dependencies:
   - numexpr
   - numpy<1.24
   - packaging
-  - pandas<2
+  - pandas
   - pint
   - pip
   - pooch
diff --git a/doc/api-hidden.rst b/doc/api-hidden.rst
@@ -375,10 +375,8 @@
    CFTimeIndex.is_floating
    CFTimeIndex.is_integer
    CFTimeIndex.is_interval
-   CFTimeIndex.is_mixed
    CFTimeIndex.is_numeric
    CFTimeIndex.is_object
-   CFTimeIndex.is_type_compatible
    CFTimeIndex.isin
    CFTimeIndex.isna
    CFTimeIndex.isnull
@@ -399,7 +397,6 @@
    CFTimeIndex.round
    CFTimeIndex.searchsorted
    CFTimeIndex.set_names
-   CFTimeIndex.set_value
    CFTimeIndex.shift
    CFTimeIndex.slice_indexer
    CFTimeIndex.slice_locs
@@ -413,7 +410,6 @@
    CFTimeIndex.to_flat_index
    CFTimeIndex.to_frame
    CFTimeIndex.to_list
-   CFTimeIndex.to_native_types
    CFTimeIndex.to_numpy
    CFTimeIndex.to_series
    CFTimeIndex.tolist
@@ -438,8 +434,6 @@
    CFTimeIndex.hasnans
    CFTimeIndex.hour
    CFTimeIndex.inferred_type
-   CFTimeIndex.is_all_dates
-   CFTimeIndex.is_monotonic
    CFTimeIndex.is_monotonic_increasing
    CFTimeIndex.is_monotonic_decreasing
    CFTimeIndex.is_unique
diff --git a/doc/user-guide/weather-climate.rst b/doc/user-guide/weather-climate.rst
@@ -57,14 +57,14 @@ CF-compliant coordinate variables
 
 .. _CFTimeIndex:
 
-Non-standard calendars and dates outside the Timestamp-valid range
-------------------------------------------------------------------
+Non-standard calendars and dates outside the nanosecond-precision range
+-----------------------------------------------------------------------
 
 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 `Timestamp-valid range`_
+using a standard calendar, but outside the `nanosecond-precision range`_
 (approximately between years 1678 and 2262).
 
 .. note::
@@ -75,13 +75,19 @@ using a standard calendar, but outside the `Timestamp-valid range`_
    any of the following are true:
 
    - The dates are from a non-standard calendar
-   - Any dates are outside the Timestamp-valid range.
+   - Any dates are outside the nanosecond-precision range.
 
    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.
 
+   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.
+
 For example, you can create a DataArray indexed by a time
 coordinate with dates from a no-leap calendar and a
 :py:class:`~xarray.CFTimeIndex` will automatically be used:
@@ -235,6 +241,6 @@ For data indexed by a :py:class:`~xarray.CFTimeIndex` xarray currently supports:
 
     da.resample(time="81T", closed="right", label="right", offset="3T").mean()
 
-.. _Timestamp-valid range: https://pandas.pydata.org/pandas-docs/stable/user_guide/timeseries.html#timestamp-limitations
+.. _nanosecond-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
diff --git a/doc/whats-new.rst b/doc/whats-new.rst
@@ -88,6 +88,12 @@ Internal Changes
 - Added a config.yml file with messages for the welcome bot when a Github user creates their first ever issue or pull request or has their first PR merged. (:issue:`7685`, :pull:`7685`)
   By `Nishtha P <https://github.com/nishthap981>`_.
 
+- Ensure that only nanosecond-precision :py:class:`pd.Timestamp` objects
+  continue to be used internally under pandas version 2.0.0.  This is mainly to
+  ease the transition to this latest version of pandas.  It should be relaxed
+  when addressing :issue:`7493`.  By `Spencer Clark
+  <https://github.com/spencerkclark>`_ (:issue:`7707`, :pull:`7731`).
+
 .. _whats-new.2023.03.0:
 
 v2023.03.0 (March 22, 2023)
diff --git a/setup.cfg b/setup.cfg
@@ -76,7 +76,7 @@ include_package_data = True
 python_requires = >=3.9
 install_requires =
     numpy >= 1.21  # recommended to use >= 1.22 for full quantile method support
-    pandas >= 1.4, <2
+    pandas >= 1.4
     packaging >= 21.3
 
 [options.extras_require]
diff --git a/xarray/coding/cftime_offsets.py b/xarray/coding/cftime_offsets.py
@@ -57,7 +57,12 @@
     format_cftime_datetime,
 )
 from xarray.core.common import _contains_datetime_like_objects, is_np_datetime_like
-from xarray.core.pdcompat import NoDefault, count_not_none, no_default
+from xarray.core.pdcompat import (
+    NoDefault,
+    count_not_none,
+    nanosecond_precision_timestamp,
+    no_default,
+)
 from xarray.core.utils import emit_user_level_warning
 
 try:
@@ -1286,8 +1291,10 @@ 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"
-        source_start = pd.Timestamp(source_start)
-        source_end = pd.Timestamp(source_end)
+        # 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)
     else:
         if isinstance(source, CFTimeIndex):
             source_calendar = source.calendar
diff --git a/xarray/coding/cftimeindex.py b/xarray/coding/cftimeindex.py
@@ -613,7 +613,7 @@ def to_datetimeindex(self, unsafe=False):
         ------
         ValueError
             If the CFTimeIndex contains dates that are not possible in the
-            standard calendar or outside the pandas.Timestamp-valid range.
+            standard calendar or outside the nanosecond-precision range.
 
         Warns
         -----
diff --git a/xarray/coding/times.py b/xarray/coding/times.py
@@ -23,6 +23,7 @@
 from xarray.core import indexing
 from xarray.core.common import contains_cftime_datetimes, is_np_datetime_like
 from xarray.core.formatting import first_n_items, format_timestamp, last_item
+from xarray.core.pdcompat import nanosecond_precision_timestamp
 from xarray.core.pycompat import is_duck_dask_array
 from xarray.core.variable import Variable
 
@@ -224,7 +225,9 @@ def _decode_datetime_with_pandas(
     delta, ref_date = _unpack_netcdf_time_units(units)
     delta = _netcdf_to_numpy_timeunit(delta)
     try:
-        ref_date = pd.Timestamp(ref_date)
+        # TODO: the strict enforcement of nanosecond precision Timestamps can be
+        # relaxed when addressing GitHub issue #7493.
+        ref_date = nanosecond_precision_timestamp(ref_date)
     except ValueError:
         # ValueError is raised by pd.Timestamp for non-ISO timestamp
         # strings, in which case we fall back to using cftime
@@ -391,7 +394,9 @@ def infer_datetime_units(dates) -> str:
         dates = to_datetime_unboxed(dates)
         dates = dates[pd.notnull(dates)]
         reference_date = dates[0] if len(dates) > 0 else "1970-01-01"
-        reference_date = pd.Timestamp(reference_date)
+        # TODO: the strict enforcement of nanosecond precision Timestamps can be
+        # relaxed when addressing GitHub issue #7493.
+        reference_date = nanosecond_precision_timestamp(reference_date)
     else:
         reference_date = dates[0] if len(dates) > 0 else "1970-01-01"
         reference_date = format_cftime_datetime(reference_date)
@@ -432,14 +437,16 @@ def cftime_to_nptime(times, raise_on_invalid: bool = True) -> np.ndarray:
     If raise_on_invalid is True (default), invalid dates trigger a ValueError.
     Otherwise, the invalid element is replaced by np.NaT."""
     times = np.asarray(times)
+    # TODO: the strict enforcement of nanosecond precision datetime values can
+    # be relaxed when addressing GitHub issue #7493.
     new = np.empty(times.shape, dtype="M8[ns]")
     for i, t in np.ndenumerate(times):
         try:
             # Use pandas.Timestamp in place of datetime.datetime, because
             # NumPy casts it safely it np.datetime64[ns] for dates outside
             # 1678 to 2262 (this is not currently the case for
             # datetime.datetime).
-            dt = pd.Timestamp(
+            dt = nanosecond_precision_timestamp(
                 t.year, t.month, t.day, t.hour, t.minute, t.second, t.microsecond
             )
         except ValueError as e:
@@ -498,6 +505,10 @@ def convert_time_or_go_back(date, date_type):
 
     This is meant to convert end-of-month dates into a new calendar.
     """
+    # TODO: the strict enforcement of nanosecond precision Timestamps can be
+    # relaxed when addressing GitHub issue #7493.
+    if date_type == pd.Timestamp:
+        date_type = nanosecond_precision_timestamp
     try:
         return date_type(
             date.year,
@@ -641,7 +652,10 @@ def encode_cf_datetime(
 
         delta_units = _netcdf_to_numpy_timeunit(delta)
         time_delta = np.timedelta64(1, delta_units).astype("timedelta64[ns]")
-        ref_date = pd.Timestamp(_ref_date)
+
+        # TODO: the strict enforcement of nanosecond precision Timestamps can be
+        # relaxed when addressing GitHub issue #7493.
+        ref_date = nanosecond_precision_timestamp(_ref_date)
 
         # If the ref_date Timestamp is timezone-aware, convert to UTC and
         # make it timezone-naive (GH 2649).
diff --git a/xarray/core/pdcompat.py b/xarray/core/pdcompat.py
@@ -39,6 +39,7 @@
 from typing import Literal
 
 import pandas as pd
+from packaging.version import Version
 
 from xarray.coding import cftime_offsets
 
@@ -91,3 +92,15 @@ def _convert_base_to_offset(base, freq, index):
             return base * freq.as_timedelta() // freq.n
     else:
         raise ValueError("Can only resample using a DatetimeIndex or CFTimeIndex.")
+
+
+def nanosecond_precision_timestamp(*args, **kwargs) -> pd.Timestamp:
+    """Return a nanosecond-precision Timestamp object.
+
+    Note this function should no longer be needed after addressing GitHub issue
+    #7493.
+    """
+    if Version(pd.__version__) >= Version("2.0.0"):
+        return pd.Timestamp(*args, **kwargs).as_unit("ns")
+    else:
+        return pd.Timestamp(*args, **kwargs)
diff --git a/xarray/tests/test_cftime_offsets.py b/xarray/tests/test_cftime_offsets.py
@@ -1373,6 +1373,7 @@ def test_date_range_like_same_calendar():
     assert src is out
 
 
+@pytest.mark.filterwarnings("ignore:Converting non-nanosecond")
 def test_date_range_like_errors():
     src = date_range("1899-02-03", periods=20, freq="D", use_cftime=False)
     src = src[np.arange(20) != 10]  # Remove 1 day so the frequency is not inferable.
diff --git a/xarray/tests/test_concat.py b/xarray/tests/test_concat.py
@@ -297,6 +297,7 @@ def test_concat_multiple_datasets_with_multiple_missing_variables() -> None:
     assert_identical(actual, expected)
 
 
+@pytest.mark.filterwarnings("ignore:Converting non-nanosecond")
 def test_concat_type_of_missing_fill() -> None:
     datasets = create_typed_datasets(2, seed=123)
     expected1 = concat(datasets, dim="day", fill_value=dtypes.NA)
diff --git a/xarray/tests/test_conventions.py b/xarray/tests/test_conventions.py
@@ -168,6 +168,7 @@ def test_do_not_overwrite_user_coordinates(self) -> None:
         with pytest.raises(ValueError, match=r"'coordinates' found in both attrs"):
             conventions.encode_dataset_coordinates(orig)
 
+    @pytest.mark.filterwarnings("ignore:Converting non-nanosecond")
     def test_emit_coordinates_attribute_in_attrs(self) -> None:
         orig = Dataset(
             {"a": 1, "b": 1},
@@ -185,6 +186,7 @@ def test_emit_coordinates_attribute_in_attrs(self) -> None:
         assert enc["b"].attrs.get("coordinates") == "t"
         assert "coordinates" not in enc["b"].encoding
 
+    @pytest.mark.filterwarnings("ignore:Converting non-nanosecond")
     def test_emit_coordinates_attribute_in_encoding(self) -> None:
         orig = Dataset(
             {"a": 1, "b": 1},
diff --git a/xarray/tests/test_dataset.py b/xarray/tests/test_dataset.py
diff --git a/xarray/tests/test_groupby.py b/xarray/tests/test_groupby.py
diff --git a/xarray/tests/test_interp.py b/xarray/tests/test_interp.py
diff --git a/xarray/tests/test_plot.py b/xarray/tests/test_plot.py
diff --git a/xarray/tests/test_variable.py b/xarray/tests/test_variable.py
