Merge branch 'main' into groupby-dask

* main:
  Add `DataTree.persist` (pydata#9682)
  Typing annotations for arithmetic overrides (e.g., DataArray + Dataset) (pydata#9688)
  Raise `ValueError` for unmatching chunks length in `DataArray.chunk()` (pydata#9689)
  Fix inadvertent deep-copying of child data in DataTree (pydata#9684)
  new blank whatsnew (pydata#9679)
  v2024.10.0 release summary (pydata#9678)
  drop the length from `numpy`'s fixed-width string dtypes (pydata#9586)
  fixing behaviour for group parameter in `open_datatree` (pydata#9666)
  Use zarr v3 dimension_names (pydata#9669)
  fix(zarr): use inplace array.resize for zarr 2 and 3 (pydata#9673)
  implement `dask` methods on `DataTree` (pydata#9670)
  support `chunks` in `open_groups` and `open_datatree` (pydata#9660)
  Compatibility for zarr-python 3.x (pydata#9552)
  Update to_dataframe doc to match current behavior (pydata#9662)
  Reduce graph size through writing indexes directly into graph for ``map_blocks`` (pydata#9658)

.github/workflows/ci-additional.yaml

@@ -92,7 +92,7 @@ jobs:
         shell: bash -l {0}
     env:
       CONDA_ENV_FILE: ci/requirements/environment.yml
-      PYTHON_VERSION: "3.11"
+      PYTHON_VERSION: "3.12"
 
     steps:
       - uses: actions/checkout@v4

ci/install-upstream-wheels.sh

@@ -45,15 +45,15 @@ python -m pip install \
     --pre \
     --upgrade \
     pyarrow
-# manually install `pint` to pull in new dependencies
-python -m pip install --upgrade pint
+# manually install `pint`, `donfig`, and `crc32c` to pull in new dependencies
+python -m pip install --upgrade pint donfig crc32c
 python -m pip install \
     --no-deps \
     --upgrade \
     git+https://github.com/dask/dask \
     git+https://github.com/dask/dask-expr \
     git+https://github.com/dask/distributed \
-    git+https://github.com/zarr-developers/zarr.git@main \
+    git+https://github.com/zarr-developers/zarr \
     git+https://github.com/Unidata/cftime \
     git+https://github.com/pypa/packaging \
     git+https://github.com/hgrecco/pint \

doc/api.rst

@@ -656,6 +656,7 @@ This interface echoes that of ``xarray.Dataset``.
    DataTree.has_attrs
    DataTree.is_empty
    DataTree.is_hollow
+   DataTree.chunksizes
 
 Dictionary Interface
 --------------------
@@ -968,6 +969,10 @@ DataTree methods
    DataTree.to_dict
    DataTree.to_netcdf
    DataTree.to_zarr
+   DataTree.chunk
+   DataTree.load
+   DataTree.compute
+   DataTree.persist
 
 .. ..
 

doc/user-guide/io.rst

@@ -823,8 +823,9 @@ For example:
 .. ipython:: python
 
     import zarr
+    from numcodecs.blosc import Blosc
 
-    compressor = zarr.Blosc(cname="zstd", clevel=3, shuffle=2)
+    compressor = Blosc(cname="zstd", clevel=3, shuffle=2)
     ds.to_zarr("foo.zarr", encoding={"foo": {"compressor": compressor}})
 
 .. note::

doc/whats-new.rst

@@ -14,34 +14,18 @@ What's New
 
     np.random.seed(123456)
 
-.. _whats-new.2024.09.1:
+.. _whats-new.2024.10.1:
 
-v2024.09.1 (unreleased)
------------------------
+v.2024.10.1 (unreleased)
+------------------------
 
 New Features
 ~~~~~~~~~~~~
-- ``DataTree`` related functionality is now exposed in the main ``xarray`` public
-  API. This includes: ``xarray.DataTree``, ``xarray.open_datatree``, ``xarray.open_groups``,
-  ``xarray.map_over_datasets``, ``xarray.group_subtrees``,
-  ``xarray.register_datatree_accessor`` and ``xarray.testing.assert_isomorphic``.
-  By `Owen Littlejohns <https://github.com/owenlittlejohns>`_,
-  `Eni Awowale <https://github.com/eni-awowale>`_,
-  `Matt Savoie <https://github.com/flamingbear>`_,
-  `Stephan Hoyer <https://github.com/shoyer>`_ and
-  `Tom Nicholas <https://github.com/TomNicholas>`_.
-- A migration guide for users of the prototype `xarray-contrib/datatree repository <https://github.com/xarray-contrib/datatree>`_ has been added, and can be found in the `DATATREE_MIGRATION_GUIDE.md` file in the repository root.
-  By `Tom Nicholas <https://github.com/TomNicholas>`_.
-- Added zarr backends for :py:func:`open_groups` (:issue:`9430`, :pull:`9469`).
-  By `Eni Awowale <https://github.com/eni-awowale>`_.
+- Added :py:meth:`DataTree.persist` method (:issue:`9675`, :pull:`9682`).
+  By `Sam Levang <https://github.com/slevang>`_.
 - Support lazy grouping by dask arrays, and allow specifying ordered groups with ``UniqueGrouper(labels=["a", "b", "c"])``
   (:issue:`2852`, :issue:`757`).
   By `Deepak Cherian <https://github.com/dcherian>`_.
-- Added support for vectorized interpolation using additional interpolators
-  from the ``scipy.interpolate`` module (:issue:`9049`, :pull:`9526`).
-  By `Holly Mandel <https://github.com/hollymandel>`_.
-- Implement handling of complex numbers (netcdf4/h5netcdf) and enums (h5netcdf) (:issue:`9246`, :issue:`3297`, :pull:`9509`).
-  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
 
 Breaking changes
 ~~~~~~~~~~~~~~~~
@@ -55,6 +39,62 @@ Deprecations
   provide expected group labels using the ``labels`` kwarg to a grouper object such as
   :py:class:`grouper.UniqueGrouper` or :py:class:`grouper.BinGrouper`.
 
+Bug fixes
+~~~~~~~~~
+
+- Fix inadvertent deep-copying of child data in DataTree.
+  By `Stephan Hoyer <https://github.com/shoyer>`_.
+
+Documentation
+~~~~~~~~~~~~~
+
+
+Internal Changes
+~~~~~~~~~~~~~~~~
+- ``persist`` methods now route through the :py:class:`xr.core.parallelcompat.ChunkManagerEntrypoint` (:pull:`9682`).
+  By `Sam Levang <https://github.com/slevang>`_.
+
+.. _whats-new.2024.10.0:
+
+v2024.10.0 (Oct 24th, 2024)
+---------------------------
+
+This release brings official support for `xarray.DataTree`, and compatibility with zarr-python v3!
+
+Aside from these two huge features, it also improves support for vectorised interpolation and fixes various bugs.
+
+Thanks to the 31 contributors to this release:
+Alfonso Ladino, DWesl, Deepak Cherian, Eni, Etienne Schalk, Holly Mandel, Ilan Gold, Illviljan, Joe Hamman, Justus Magin, Kai Mühlbauer, Karl Krauth, Mark Harfouche, Martey Dodoo, Matt Savoie, Maximilian Roos, Patrick Hoefler, Peter Hill, Renat Sibgatulin, Ryan Abernathey, Spencer Clark, Stephan Hoyer, Tom Augspurger, Tom Nicholas, Vecko, Virgile Andreani, Yvonne Fröhlich, carschandler, joseph nowak, mgunyho and owenlittlejohns
+
+New Features
+~~~~~~~~~~~~
+- ``DataTree`` related functionality is now exposed in the main ``xarray`` public
+  API. This includes: ``xarray.DataTree``, ``xarray.open_datatree``, ``xarray.open_groups``,
+  ``xarray.map_over_datasets``, ``xarray.group_subtrees``,
+  ``xarray.register_datatree_accessor`` and ``xarray.testing.assert_isomorphic``.
+  By `Owen Littlejohns <https://github.com/owenlittlejohns>`_,
+  `Eni Awowale <https://github.com/eni-awowale>`_,
+  `Matt Savoie <https://github.com/flamingbear>`_,
+  `Stephan Hoyer <https://github.com/shoyer>`_,
+  `Tom Nicholas <https://github.com/TomNicholas>`_,
+  `Justus Magin <https://github.com/keewis>`_, and
+  `Alfonso Ladino <https://github.com/aladinor>`_.
+- A migration guide for users of the prototype `xarray-contrib/datatree repository <https://github.com/xarray-contrib/datatree>`_ has been added, and can be found in the `DATATREE_MIGRATION_GUIDE.md` file in the repository root.
+  By `Tom Nicholas <https://github.com/TomNicholas>`_.
+- Support for Zarr-Python 3 (:issue:`95515`, :pull:`9552`).
+  By `Tom Augspurger <https://github.com/TomAugspurger>`_,
+  `Ryan Abernathey <https://github.com/rabernat>`_ and
+  `Joe Hamman <https://github.com/jhamman>`_.
+- Added zarr backends for :py:func:`open_groups` (:issue:`9430`, :pull:`9469`).
+  By `Eni Awowale <https://github.com/eni-awowale>`_.
+- Added support for vectorized interpolation using additional interpolators
+  from the ``scipy.interpolate`` module (:issue:`9049`, :pull:`9526`).
+  By `Holly Mandel <https://github.com/hollymandel>`_.
+- Implement handling of complex numbers (netcdf4/h5netcdf) and enums (h5netcdf) (:issue:`9246`, :issue:`3297`, :pull:`9509`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Fix passing missing arguments to when opening hdf5 and netCDF4 datatrees
+  (:issue:`9427`, :pull: `9428`).
+  By `Alfonso Ladino <https://github.com/aladinor>`_.
 
 Bug fixes
 ~~~~~~~~~
@@ -78,6 +118,8 @@ Bug fixes
   <https://github.com/josephnowak>`_.
 - Fix binning by multiple variables where some bins have no observations. (:issue:`9630`).
   By `Deepak Cherian <https://github.com/dcherian>`_.
+- Fix issue where polyfit wouldn't handle non-dimension coordinates. (:issue:`4375`, :pull:`9369`)
+  By `Karl Krauth <https://github.com/Karl-Krauth>`_.
 
 Documentation
 ~~~~~~~~~~~~~
@@ -88,12 +130,9 @@ Documentation
   By `Owen Littlejohns <https://github.com/owenlittlejohns>`_, `Matt Savoie <https://github.com/flamingbear>`_, and
   `Tom Nicholas <https://github.com/TomNicholas>`_.
 
-
-
 Internal Changes
 ~~~~~~~~~~~~~~~~
 
-
 .. _whats-new.2024.09.0:
 
 v2024.09.0 (Sept 11, 2024)
@@ -161,17 +200,12 @@ Bug fixes
   date "0001-01-01". (:issue:`9108`, :pull:`9116`) By `Spencer Clark
   <https://github.com/spencerkclark>`_ and `Deepak Cherian
   <https://github.com/dcherian>`_.
-- Fix issue where polyfit wouldn't handle non-dimension coordinates. (:issue:`4375`, :pull:`9369`)
-  By `Karl Krauth <https://github.com/Karl-Krauth>`_.
 - Fix issue with passing parameters to ZarrStore.open_store when opening
   datatree in zarr format (:issue:`9376`, :pull:`9377`).
   By `Alfonso Ladino <https://github.com/aladinor>`_
 - Fix deprecation warning that was raised when calling ``np.array`` on an ``xr.DataArray``
   in NumPy 2.0 (:issue:`9312`, :pull:`9393`)
   By `Andrew Scherer <https://github.com/andrew-s28>`_.
-- Fix passing missing arguments to when opening hdf5 and netCDF4 datatrees
-  (:issue:`9427`, :pull: `9428`).
-  By `Alfonso Ladino <https://github.com/aladinor>`_.
 - Fix support for using ``pandas.DateOffset``, ``pandas.Timedelta``, and
   ``datetime.timedelta`` objects as ``resample`` frequencies
   (:issue:`9408`, :pull:`9413`).

pyproject.toml

@@ -37,6 +37,7 @@ accel = ["scipy", "bottleneck", "numbagg", "numba>=0.54", "flox", "opt_einsum"]
 complete = ["xarray[accel,etc,io,parallel,viz]"]
 dev = [
   "hypothesis",
+  "jinja2",
   "mypy",
   "pre-commit",
   "pytest",
@@ -49,7 +50,7 @@ dev = [
   "sphinx_autosummary_accessors",
   "xarray[complete]",
 ]
-io = ["netCDF4", "h5netcdf", "scipy", 'pydap; python_version<"3.10"', "zarr<3", "fsspec", "cftime", "pooch"]
+io = ["netCDF4", "h5netcdf", "scipy", 'pydap; python_version<"3.10"', "zarr", "fsspec", "cftime", "pooch"]
 etc = ["sparse"]
 parallel = ["dask[complete]"]
 viz = ["cartopy", "matplotlib", "nc-time-axis", "seaborn"]
@@ -124,6 +125,7 @@ module = [
   "nc_time_axis.*",
   "netCDF4.*",
   "netcdftime.*",
+  "numcodecs.*",
   "opt_einsum.*",
   "pint.*",
   "pooch.*",