Merge branch 'main' into concat_default_kwargs

Author: jsignell

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
 -------

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

@@ -1473,7 +1473,7 @@ 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 +2488,8 @@ 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 +2871,7 @@ 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 +3507,7 @@ 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 +4352,8 @@ 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 +4705,7 @@ 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 +5936,7 @@ 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 +6016,8 @@ 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 +6791,7 @@ 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]

xarray/__init__.py

@@ -15,12 +15,10 @@
 from xarray.coding.cftime_offsets import cftime_range, date_range, date_range_like
 from xarray.coding.cftimeindex import CFTimeIndex
 from xarray.coding.frequencies import infer_freq
-from xarray.conventions import SerializationWarning, decode_cf
-from xarray.core.alignment import align, broadcast
-from xarray.core.combine import combine_by_coords, combine_nested
-from xarray.core.common import ALL_DIMS, full_like, ones_like, zeros_like
-from xarray.core.computation import (
+from xarray.computation.apply_ufunc import (
     apply_ufunc,
+)
+from xarray.computation.computation import (
     corr,
     cov,
     cross,
@@ -29,7 +27,8 @@
     unify_chunks,
     where,
 )
-from xarray.core.concat import concat
+from xarray.conventions import SerializationWarning, decode_cf
+from xarray.core.common import ALL_DIMS, full_like, ones_like, zeros_like
 from xarray.core.coordinates import Coordinates
 from xarray.core.dataarray import DataArray
 from xarray.core.dataset import Dataset
@@ -42,7 +41,6 @@
 )
 from xarray.core.indexes import Index
 from xarray.core.indexing import IndexSelResult
-from xarray.core.merge import Context, MergeError, merge
 from xarray.core.options import get_options, set_options
 from xarray.core.parallel import map_blocks
 from xarray.core.treenode import (
@@ -53,6 +51,10 @@
 )
 from xarray.core.variable import IndexVariable, Variable, as_variable
 from xarray.namedarray.core import NamedArray
+from xarray.structure.alignment import align, broadcast
+from xarray.structure.combine import combine_by_coords, combine_nested
+from xarray.structure.concat import concat
+from xarray.structure.merge import Context, MergeError, merge
 from xarray.util.print_versions import show_versions
 
 try:

xarray/backends/api.py

@@ -36,11 +36,6 @@
 from xarray.coders import CFDatetimeCoder, CFTimedeltaCoder
 from xarray.core import dtypes, indexing
 from xarray.core.chunk import _get_chunk, _maybe_chunk
-from xarray.core.combine import (
-    _infer_concat_order_from_positions,
-    _nested_combine,
-    combine_by_coords,
-)
 from xarray.core.dataarray import DataArray
 from xarray.core.dataset import Dataset
 from xarray.core.datatree import DataTree
@@ -50,6 +45,11 @@
 from xarray.core.utils import is_remote_uri
 from xarray.namedarray.daskmanager import DaskManager
 from xarray.namedarray.parallelcompat import guess_chunkmanager
+from xarray.structure.combine import (
+    _infer_concat_order_from_positions,
+    _nested_combine,
+    combine_by_coords,
+)
 from xarray.util.deprecation_helpers import (
     _COMPAT_DEFAULT,
     _COORDS_DEFAULT,