Merge branch 'main' of https://github.com/pydata/xarray

Author: TomNicholas

ci/requirements/environment.yml

@@ -56,6 +56,7 @@ dependencies:
   - types-pytz
   - types-PyYAML
   - types-setuptools
+  - types-openpyxl
   - typing_extensions
   - zarr
   - pip:

conftest.py

@@ -22,7 +22,9 @@ def pytest_runtest_setup(item):
         pytest.skip(
             "set --run-network-tests to run test requiring an internet connection"
         )
-    if "mypy" in item.keywords and not item.config.getoption("--run-mypy"):
+    if any("mypy" in m.name for m in item.own_markers) and not item.config.getoption(
+        "--run-mypy"
+    ):
         pytest.skip("set --run-mypy option to run mypy tests")
 
 

doc/api-hidden.rst

@@ -28,22 +28,22 @@
    core.coordinates.DatasetCoordinates.equals
    core.coordinates.DatasetCoordinates.identical
 
-   core.rolling.DatasetCoarsen.boundary
-   core.rolling.DatasetCoarsen.coord_func
-   core.rolling.DatasetCoarsen.obj
-   core.rolling.DatasetCoarsen.side
-   core.rolling.DatasetCoarsen.trim_excess
-   core.rolling.DatasetCoarsen.windows
-
-   core.rolling.DatasetRolling.center
-   core.rolling.DatasetRolling.dim
-   core.rolling.DatasetRolling.min_periods
-   core.rolling.DatasetRolling.obj
-   core.rolling.DatasetRolling.rollings
-   core.rolling.DatasetRolling.window
-
-   core.weighted.DatasetWeighted.obj
-   core.weighted.DatasetWeighted.weights
+   computation.rolling.DatasetCoarsen.boundary
+   computation.rolling.DatasetCoarsen.coord_func
+   computation.rolling.DatasetCoarsen.obj
+   computation.rolling.DatasetCoarsen.side
+   computation.rolling.DatasetCoarsen.trim_excess
+   computation.rolling.DatasetCoarsen.windows
+
+   computation.rolling.DatasetRolling.center
+   computation.rolling.DatasetRolling.dim
+   computation.rolling.DatasetRolling.min_periods
+   computation.rolling.DatasetRolling.obj
+   computation.rolling.DatasetRolling.rollings
+   computation.rolling.DatasetRolling.window
+
+   computation.weighted.DatasetWeighted.obj
+   computation.weighted.DatasetWeighted.weights
 
    Dataset.load_store
    Dataset.dump_to_store
@@ -70,22 +70,22 @@
    core.coordinates.DataArrayCoordinates.equals
    core.coordinates.DataArrayCoordinates.identical
 
-   core.rolling.DataArrayCoarsen.boundary
-   core.rolling.DataArrayCoarsen.coord_func
-   core.rolling.DataArrayCoarsen.obj
-   core.rolling.DataArrayCoarsen.side
-   core.rolling.DataArrayCoarsen.trim_excess
-   core.rolling.DataArrayCoarsen.windows
-
-   core.rolling.DataArrayRolling.center
-   core.rolling.DataArrayRolling.dim
-   core.rolling.DataArrayRolling.min_periods
-   core.rolling.DataArrayRolling.obj
-   core.rolling.DataArrayRolling.window
-   core.rolling.DataArrayRolling.window_labels
-
-   core.weighted.DataArrayWeighted.obj
-   core.weighted.DataArrayWeighted.weights
+   computation.rolling.DataArrayCoarsen.boundary
+   computation.rolling.DataArrayCoarsen.coord_func
+   computation.rolling.DataArrayCoarsen.obj
+   computation.rolling.DataArrayCoarsen.side
+   computation.rolling.DataArrayCoarsen.trim_excess
+   computation.rolling.DataArrayCoarsen.windows
+
+   computation.rolling.DataArrayRolling.center
+   computation.rolling.DataArrayRolling.dim
+   computation.rolling.DataArrayRolling.min_periods
+   computation.rolling.DataArrayRolling.obj
+   computation.rolling.DataArrayRolling.window
+   computation.rolling.DataArrayRolling.window_labels
+
+   computation.weighted.DataArrayWeighted.obj
+   computation.weighted.DataArrayWeighted.weights
 
    core.coordinates.DataTreeCoordinates.get
    core.coordinates.DataTreeCoordinates.items

doc/api.rst

@@ -1334,7 +1334,7 @@ Grouper Objects
 Rolling objects
 ===============
 
-.. currentmodule:: xarray.core.rolling
+.. currentmodule:: xarray.computation.rolling
 
 Dataset
 -------
@@ -1427,7 +1427,7 @@ DataArray
 Exponential rolling objects
 ===========================
 
-.. currentmodule:: xarray.core.rolling_exp
+.. currentmodule:: xarray.computation.rolling_exp
 
 .. autosummary::
    :toctree: generated/
@@ -1439,7 +1439,7 @@ Exponential rolling objects
 Weighted objects
 ================
 
-.. currentmodule:: xarray.core.weighted
+.. currentmodule:: xarray.computation.weighted
 
 Dataset
 -------
@@ -1591,6 +1591,8 @@ Tutorial
 
    tutorial.open_dataset
    tutorial.load_dataset
+   tutorial.open_datatree
+   tutorial.load_datatree
 
 Testing
 =======

doc/user-guide/data-structures.rst

@@ -558,7 +558,7 @@ specifying the nodes' relationship to one another as you create each one.
 The :py:class:`~xarray.DataTree` constructor takes:
 
 - ``dataset``: The data that will be stored in this node, represented by a single
-  :py:class:`xarray.Dataset`, or a named :py:class:`xarray.DataArray`.
+  :py:class:`xarray.Dataset`.
 - ``children``: The various child nodes (if there are any), given as a mapping
   from string keys to :py:class:`~xarray.DataTree` objects.
 - ``name``: A string to use as the name of this node.

doc/user-guide/reshaping.rst

@@ -305,7 +305,7 @@ Reshaping via coarsen
 
 Whilst :py:class:`~xarray.DataArray.coarsen` is normally used for reducing your data's resolution by applying a reduction function
 (see the :ref:`page on computation<compute.coarsen>`),
-it can also be used to reorganise your data without applying a computation via :py:meth:`~xarray.core.rolling.DataArrayCoarsen.construct`.
+it can also be used to reorganise your data without applying a computation via :py:meth:`~xarray.computation.rolling.DataArrayCoarsen.construct`.
 
 Taking our example tutorial air temperature dataset over the Northern US
 
@@ -324,7 +324,7 @@ Taking our example tutorial air temperature dataset over the Northern US
     @savefig pre_coarsening.png
     air.isel(time=0).plot(x="lon", y="lat")
 
-we can split this up into sub-regions of size ``(9, 18)`` points using :py:meth:`~xarray.core.rolling.DataArrayCoarsen.construct`:
+we can split this up into sub-regions of size ``(9, 18)`` points using :py:meth:`~xarray.computation.rolling.DataArrayCoarsen.construct`:
 
 .. ipython:: python
 

doc/whats-new.rst

@@ -21,6 +21,8 @@ v2025.02.0 (unreleased)
 
 New Features
 ~~~~~~~~~~~~
+- Added :py:meth:`tutorial.open_datatree` and :py:meth:`tutorial.load_datatree`
+  By `Eni Awowale <https://github.com/eni-awowale>`_.
 - Added :py:meth:`DataTree.filter_like` to conveniently restructure a DataTree like another DataTree (:issue:`10096`, :pull:`10097`).
   By `Kobe Vandelanotte <https://github.com/kobebryant432>`_.
 - Added :py:meth:`Coordinates.from_xindex` as convenience for creating a new :py:class:`Coordinates` object
@@ -32,11 +34,25 @@ New Features
   By `Justus Magin <https://github.com/keewis>`_.
 - Added experimental support for coordinate transforms (not ready for public use yet!) (:pull:`9543`)
   By `Benoit Bovy <https://github.com/benbovy>`_.
+- Similar to our :py:class:`numpy.datetime64` encoding path, automatically
+  modify the units when an integer dtype is specified during eager cftime
+  encoding, but the specified units would not allow for an exact round trip
+  (:pull:`9498`). By `Spencer Clark <https://github.com/spencerkclark>`_.
 - Support reading to `GPU memory with Zarr <https://zarr.readthedocs.io/en/stable/user-guide/gpu.html>`_ (:pull:`10078`).
   By `Deepak Cherian <https://github.com/dcherian>`_.
 
+Performance
+~~~~~~~~~~~
+- :py:meth:`DatasetGroupBy.first` and :py:meth:`DatasetGroupBy.last` can now use ``flox`` if available. (:issue:`9647`)
+  By `Deepak Cherian <https://github.com/dcherian>`_.
+
 Breaking changes
 ~~~~~~~~~~~~~~~~
+- Rolled back code that would attempt to catch integer overflow when encoding
+  times with small integer dtypes (:issue:`8542`), since it was inconsistent
+  with xarray's handling of standard integers, and interfered with encoding
+  times with small integer dtypes and missing values (:pull:`9498`). By
+  `Spencer Clark <https://github.com/spencerkclark>`_.
 - Warn instead of raise if phony_dims are detected when using h5netcdf-backend and ``phony_dims=None`` (:issue:`10049`, :pull:`10058`)
   By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
 
@@ -62,6 +78,12 @@ Bug fixes
 - Fix DataArray().drop_attrs(deep=False) and add support for attrs to
   DataArray()._replace(). (:issue:`10027`, :pull:`10030`). By `Jan
   Haacker <https://github.com/j-haacker>`_.
+- Fix bug preventing encoding times with missing values with small integer
+  dtype (:issue:`9134`, :pull:`9498`). By `Spencer Clark
+  <https://github.com/spencerkclark>`_.
+- More robustly raise an error when lazily encoding times and an integer dtype
+  is specified with units that do not allow for an exact round trip
+  (:pull:`9498`). By `Spencer Clark <https://github.com/spencerkclark>`_.
 - Prevent false resolution change warnings from being emitted when decoding
   timedeltas encoded with floating point values, and make it clearer how to
   silence this warning message in the case that it is rightfully emitted
@@ -157,8 +179,6 @@ New Features
   :py:class:`pandas.DatetimeIndex` (:pull:`9965`). By `Spencer Clark
   <https://github.com/spencerkclark>`_ and `Kai Mühlbauer
   <https://github.com/kmuehlbauer>`_.
-- :py:meth:`DatasetGroupBy.first` and :py:meth:`DatasetGroupBy.last` can now use ``flox`` if available. (:issue:`9647`)
-  By `Deepak Cherian <https://github.com/dcherian>`_.
 
 Breaking changes
 ~~~~~~~~~~~~~~~~
@@ -1473,7 +1493,7 @@ Bug fixes
   special case ``NaT`` handling in :py:meth:`~core.accessor_dt.DatetimeAccessor.isocalendar`
   (:issue:`7928`, :pull:`8084`).
   By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
-- Fix :py:meth:`~core.rolling.DatasetRolling.construct` with stride on Datasets without indexes.
+- Fix :py:meth:`~computation.rolling.DatasetRolling.construct` with stride on Datasets without indexes.
   (:issue:`7021`, :pull:`7578`).
   By `Amrest Chinkamol <https://github.com/p4perf4ce>`_ and `Michael Niklas <https://github.com/headtr1ck>`_.
 - Calling plot with kwargs ``col``, ``row`` or ``hue`` no longer squeezes dimensions passed via these arguments
@@ -2488,8 +2508,8 @@ New Features
 
 - The ``zarr`` backend is now able to read NCZarr.
   By `Mattia Almansi <https://github.com/malmans2>`_.
-- Add a weighted ``quantile`` method to :py:class:`~core.weighted.DatasetWeighted` and
-  :py:class:`~core.weighted.DataArrayWeighted` (:pull:`6059`).
+- Add a weighted ``quantile`` method to :py:class:`.computation.weighted.DatasetWeighted` and
+  :py:class:`~computation.weighted.DataArrayWeighted` (:pull:`6059`).
   By `Christian Jauvin <https://github.com/cjauvin>`_ and `David Huard <https://github.com/huard>`_.
 - Add a ``create_index=True`` parameter to :py:meth:`Dataset.stack` and
   :py:meth:`DataArray.stack` so that the creation of multi-indexes is optional
@@ -2871,7 +2891,7 @@ Thomas Nicholas, Tomas Chor, Tom Augspurger, Victor Negîrneac, Zachary Blackwoo
 
 New Features
 ~~~~~~~~~~~~
-- Add ``std``, ``var``,  ``sum_of_squares`` to :py:class:`~core.weighted.DatasetWeighted` and :py:class:`~core.weighted.DataArrayWeighted`.
+- Add ``std``, ``var``,  ``sum_of_squares`` to :py:class:`~computation.weighted.DatasetWeighted` and :py:class:`~computation.weighted.DataArrayWeighted`.
   By `Christian Jauvin <https://github.com/cjauvin>`_.
 - Added a :py:func:`get_options` method to xarray's root namespace (:issue:`5698`, :pull:`5716`)
   By `Pushkar Kopparla <https://github.com/pkopparla>`_.
@@ -3507,7 +3527,7 @@ New Features
   By `Justus Magin <https://github.com/keewis>`_.
 - Allow installing from git archives (:pull:`4897`).
   By `Justus Magin <https://github.com/keewis>`_.
-- :py:class:`~core.rolling.DataArrayCoarsen` and :py:class:`~core.rolling.DatasetCoarsen`
+- :py:class:`~computation.rolling.DataArrayCoarsen` and :py:class:`~computation.rolling.DatasetCoarsen`
   now implement a ``reduce`` method, enabling coarsening operations with custom
   reduction functions (:issue:`3741`, :pull:`4939`).
   By `Spencer Clark <https://github.com/spencerkclark>`_.
@@ -4352,8 +4372,8 @@ New Features
 - :py:meth:`Dataset.quantile`, :py:meth:`DataArray.quantile` and ``GroupBy.quantile``
   now work with dask Variables.
   By `Deepak Cherian <https://github.com/dcherian>`_.
-- Added the ``count`` reduction method to both :py:class:`~core.rolling.DatasetCoarsen`
-  and :py:class:`~core.rolling.DataArrayCoarsen` objects. (:pull:`3500`)
+- Added the ``count`` reduction method to both :py:class:`~computation.rolling.DatasetCoarsen`
+  and :py:class:`~computation.rolling.DataArrayCoarsen` objects. (:pull:`3500`)
   By `Deepak Cherian <https://github.com/dcherian>`_
 - Add ``meta`` kwarg to :py:func:`~xarray.apply_ufunc`;
   this is passed on to :py:func:`dask.array.blockwise`. (:pull:`3660`)
@@ -4705,7 +4725,7 @@ Bug fixes
 - Fix error in concatenating unlabeled dimensions (:pull:`3362`).
   By `Deepak Cherian <https://github.com/dcherian>`_.
 - Warn if the ``dim`` kwarg is passed to rolling operations. This is redundant since a dimension is
-  specified when the :py:class:`~core.rolling.DatasetRolling` or :py:class:`~core.rolling.DataArrayRolling` object is created.
+  specified when the :py:class:`~computation.rolling.DatasetRolling` or :py:class:`~computation.rolling.DataArrayRolling` object is created.
   (:pull:`3362`). By `Deepak Cherian <https://github.com/dcherian>`_.
 
 Documentation
@@ -5936,7 +5956,7 @@ Enhancements
   supplied list, returning a bool array. See :ref:`selecting values with isin`
   for full details. Similar to the ``np.isin`` function.
   By `Maximilian Roos <https://github.com/max-sixty>`_.
-- Some speed improvement to construct :py:class:`~xarray.core.rolling.DataArrayRolling`
+- Some speed improvement to construct :py:class:`~xarray.computation.rolling.DataArrayRolling`
   object (:issue:`1993`)
   By `Keisuke Fujii <https://github.com/fujiisoup>`_.
 - Handle variables with different values for ``missing_value`` and
@@ -6016,8 +6036,8 @@ Enhancements
   NumPy. By `Stephan Hoyer <https://github.com/shoyer>`_.
 
 - Improve :py:func:`~xarray.DataArray.rolling` logic.
-  :py:func:`~xarray.core.rolling.DataArrayRolling` object now supports
-  :py:func:`~xarray.core.rolling.DataArrayRolling.construct` method that returns a view
+  :py:func:`~xarray.computation.rolling.DataArrayRolling` object now supports
+  :py:func:`~xarray.computation.rolling.DataArrayRolling.construct` method that returns a view
   of the DataArray / Dataset object with the rolling-window dimension added
   to the last axis. This enables more flexible operation, such as strided
   rolling, windowed rolling, ND-rolling, short-time FFT and convolution.
@@ -6791,7 +6811,7 @@ Enhancements
   By `Stephan Hoyer <https://github.com/shoyer>`_ and
   `Phillip J. Wolfram <https://github.com/pwolfram>`_.
 
-- New aggregation on rolling objects :py:meth:`~core.rolling.DataArrayRolling.count`
+- New aggregation on rolling objects :py:meth:`~computation.rolling.DataArrayRolling.count`
   which providing a rolling count of valid values (:issue:`1138`).
 
 Bug fixes

pyproject.toml

@@ -30,22 +30,6 @@ dependencies = ["numpy>=1.24", "packaging>=23.2", "pandas>=2.1"]
 [project.optional-dependencies]
 accel = ["scipy", "bottleneck", "numbagg", "numba>=0.54", "flox", "opt_einsum"]
 complete = ["xarray[accel,etc,io,parallel,viz]"]
-dev = [
-  "hypothesis",
-  "jinja2",
-  "mypy",
-  "pre-commit",
-  "pytest",
-  "pytest-cov",
-  "pytest-env",
-  "pytest-mypy-plugins",
-  "pytest-timeout",
-  "pytest-xdist",
-  "ruff>=0.8.0",
-  "sphinx",
-  "sphinx_autosummary_accessors",
-  "xarray[complete,types]",
-]
 io = [
   "netCDF4",
   "h5netcdf",
@@ -71,11 +55,30 @@ types = [
   "types-pexpect",
   "types-psutil",
   "types-pycurl",
+  "types-openpyxl",
   "types-python-dateutil",
   "types-pytz",
   "types-setuptools",
 ]
 
+[dependency-groups]
+dev = [
+  "hypothesis",
+  "jinja2",
+  "mypy",
+  "pre-commit",
+  "pytest",
+  "pytest-cov",
+  "pytest-env",
+  "pytest-mypy-plugins",
+  "pytest-timeout",
+  "pytest-xdist",
+  "ruff>=0.8.0",
+  "sphinx",
+  "sphinx_autosummary_accessors",
+  "xarray[complete,types]",
+]
+
 [project.urls]
 Documentation = "https://docs.xarray.dev"
 SciPy2015-talk = "https://www.youtube.com/watch?v=X0pAhJgySxk"
@@ -99,10 +102,10 @@ fallback_version = "9999"
 [tool.coverage.run]
 omit = [
   "*/xarray/tests/*",
-  "*/xarray/core/dask_array_compat.py",
-  "*/xarray/core/npcompat.py",
-  "*/xarray/core/pdcompat.py",
-  "*/xarray/core/pycompat.py",
+  "*/xarray/compat/dask_array_compat.py",
+  "*/xarray/compat/npcompat.py",
+  "*/xarray/compat/pdcompat.py",
+  "*/xarray/namedarray/pycompat.py",
   "*/xarray/core/types.py",
 ]
 source = ["xarray"]
@@ -166,9 +169,8 @@ check_untyped_defs = true
 module = [
   "xarray.core.accessor_dt",
   "xarray.core.accessor_str",
-  "xarray.core.alignment",
-  "xarray.core.computation",
-  "xarray.core.rolling_exp",
+  "xarray.structure.alignment",
+  "xarray.computation.*",
   "xarray.indexes.*",
   "xarray.tests.*",
 ]
@@ -359,7 +361,7 @@ markers = [
   "slow_hypothesis: slow hypothesis tests",
 ]
 minversion = "7"
-python_files = "test_*.py"
+python_files = ["test_*.py"]
 testpaths = ["xarray/tests", "properties"]
 
 [tool.aliases]