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

Author: TomNicholas

.github/workflows/nightly-wheels.yml

@@ -38,7 +38,7 @@ jobs:
           fi
 
       - name: Upload wheel
-        uses: scientific-python/upload-nightly-action@82396a2ed4269ba06c6b2988bb4fd568ef3c3d6b # 0.6.1
+        uses: scientific-python/upload-nightly-action@b36e8c0c10dbcfd2e05bf95f17ef8c14fd708dbf # 0.6.2
         with:
           anaconda_nightly_upload_token: ${{ secrets.ANACONDA_NIGHTLY }}
           artifacts_path: dist

.github/workflows/upstream-dev-ci.yaml

@@ -84,7 +84,7 @@ jobs:
         if: success()
         id: status
         run: |
-          python -m pytest --timeout=60 -rf \
+          python -m pytest --timeout=60 -rf -nauto \
             --report-log output-${{ matrix.python-version }}-log.jsonl
       - name: Generate and publish the report
         if: |

ci/install-upstream-wheels.sh

@@ -53,7 +53,7 @@ python -m pip install \
     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+https://github.com/zarr-developers/zarr-python \
     git+https://github.com/Unidata/cftime \
     git+https://github.com/pypa/packaging \
     git+https://github.com/hgrecco/pint \

doc/getting-started-guide/faq.rst

@@ -191,7 +191,7 @@ To open format X file in xarray, you need to know the `format of the data <https
    :header: "File Format", "Open via", " Related Packages"
    :widths: 15, 45, 15
 
-   "NetCDF (.nc, .nc4, .cdf)","``open_dataset()`` OR ``open_mfdataset()``", "`netCDF4 <https://pypi.org/project/netCDF4/>`_, `netcdf <https://pypi.org/project/netcdf/>`_ , `cdms2 <https://cdms.readthedocs.io/en/latest/cdms2.html>`_"
+   "NetCDF (.nc, .nc4, .cdf)","``open_dataset()`` OR ``open_mfdataset()``", "`netCDF4 <https://pypi.org/project/netCDF4/>`_, `cdms2 <https://cdms.readthedocs.io/en/latest/cdms2.html>`_"
    "HDF5 (.h5, .hdf5)","``open_dataset()`` OR ``open_mfdataset()``", "`h5py <https://www.h5py.org/>`_, `pytables <https://www.pytables.org/>`_ "
    "GRIB (.grb, .grib)", "``open_dataset()``", "`cfgrib <https://pypi.org/project/cfgrib/>`_, `pygrib <https://pypi.org/project/pygrib/>`_"
    "CSV (.csv)","``open_dataset()``", "`pandas`_ , `dask <https://www.dask.org/>`_"

doc/user-guide/indexing.rst

@@ -376,7 +376,7 @@ indexing for xarray is based on our
 :ref:`broadcasting rules <compute.broadcasting>`.
 See :ref:`indexing.rules` for the complete specification.
 
-.. _NumPy's advanced indexing: https://numpy.org/doc/stable/reference/arrays.indexing.html
+.. _NumPy's advanced indexing: https://numpy.org/doc/stable/user/basics.indexing.html#advanced-indexing
 
 Vectorized indexing also works with ``isel``, ``loc``, and ``sel``:
 

doc/user-guide/io.rst

@@ -1021,6 +1021,22 @@ reads. Because this fall-back option is so much slower, xarray issues a
        instead of falling back to try reading non-consolidated metadata.
 
 
+Fill Values
+~~~~~~~~~~~
+
+Zarr arrays have a ``fill_value`` that is used for chunks that were never written to disk.
+For the Zarr version 2 format, Xarray will set ``fill_value`` to be equal to the CF/NetCDF ``"_FillValue"``.
+This is ``np.nan`` by default for floats, and unset otherwise. Note that the Zarr library will set a
+default ``fill_value`` if not specified (usually ``0``).
+
+For the Zarr version 3 format, ``_FillValue`` and ```fill_value`` are decoupled.
+So you can set ``fill_value`` in ``encoding`` as usual.
+
+Note that at read-time, you can control whether ``_FillValue`` is masked using the
+``mask_and_scale`` kwarg; and whether Zarr's ``fill_value`` is treated as synonymous
+with ``_FillValue`` using the ``use_zarr_fill_value_as_mask`` kwarg to :py:func:`xarray.open_zarr`.
+
+
 .. _io.kerchunk:
 
 Kerchunk

doc/whats-new.rst

@@ -14,21 +14,20 @@ What's New
 
     np.random.seed(123456)
 
-.. _whats-new.2025.03.1:
+.. _whats-new.2025.04.0:
 
-v2025.03.1 (unreleased)
+v2025.04.0 (unreleased)
 -----------------------
 
 New Features
 ~~~~~~~~~~~~
 
+- Added `scipy-stubs <https://github.com/scipy/scipy-stubs>`_ to the ``xarray[types]`` dependencies.
+  By `Joren Hammudoglu <https://github.com/jorenham>`_.
 
 Breaking changes
 ~~~~~~~~~~~~~~~~
 
-- Explicitly forbid appending a :py:class:`~xarray.DataTree` to zarr using :py:meth:`~xarray.DataTree.to_zarr` with ``append_dim``, because the expected behaviour is currently undefined.
-  (:issue:`9858`, :pull:`10156`)
-  By `Tom Nicholas <https://github.com/TomNicholas>`_.
 
 Deprecations
 ~~~~~~~~~~~~
@@ -45,6 +44,43 @@ Documentation
 Internal Changes
 ~~~~~~~~~~~~~~~~
 
+.. _whats-new.2025.03.1:
+
+v2025.03.1 (Mar 30, 2025)
+-------------------------
+
+This release brings the ability to specify ``fill_value`` and ``write_empty_chunks`` for Zarr V3 stores, and a few bug fixes.
+Thanks to the 10 contributors to this release:
+Andrecho, Deepak Cherian, Ian Hunt-Isaak, Karl Krauth, Mathias Hauser, Maximilian Roos, Nick Hodgskin (🦎 Vecko), Spencer Clark, Tom Nicholas and wpbonelli.
+
+New Features
+~~~~~~~~~~~~
+
+- Allow setting a ``fill_value`` for Zarr format 3 arrays. Specify ``fill_value`` in ``encoding`` as usual.
+  (:issue:`10064`). By `Deepak Cherian <https://github.com/dcherian>`_.
+
+Breaking changes
+~~~~~~~~~~~~~~~~
+
+- Explicitly forbid appending a :py:class:`~xarray.DataTree` to zarr using :py:meth:`~xarray.DataTree.to_zarr` with ``append_dim``, because the expected behaviour is currently undefined.
+  (:issue:`9858`, :pull:`10156`)
+  By `Tom Nicholas <https://github.com/TomNicholas>`_.
+
+Bug fixes
+~~~~~~~~~
+
+- Update the parameters of :py:meth:`~xarray.DataArray.to_zarr` to match :py:meth:`~xarray.Dataset.to_zarr`.
+  This fixes the issue where using the ``zarr_version`` parameter would raise a deprecation warning telling the user to use
+  a non-existent ``zarr_format`` parameter instead. (:issue:`10163`, :pull:`10164`)
+  By `Karl Krauth <https://github.com/Karl-Krauth>`_.
+- :py:meth:`DataTree.sel` and :py:meth:`DataTree.isel` display the path of the first failed node again  (:pull:`10154`).
+  By `Mathias Hauser <https://github.com/mathause>`_.
+- Fix grouped and resampled ``first``, ``last`` with datetimes (:issue:`10169`, :pull:`10173`)
+  By `Deepak Cherian <https://github.com/dcherian>`_.
+- FacetGrid plots now include units in their axis labels when available (:issue:`10184`, :pull:`10185`)
+  By `Andre Wendlinger <https://github.com/andrewendlinger>`_.
+
+
 .. _whats-new.2025.03.0:
 
 v2025.03.0 (Mar 20, 2025)

pyproject.toml

@@ -45,6 +45,7 @@ parallel = ["dask[complete]"]
 viz = ["cartopy", "matplotlib", "nc-time-axis", "seaborn"]
 types = [
   "pandas-stubs",
+  "scipy-stubs",
   "types-PyYAML",
   "types-Pygments",
   "types-colorama",
@@ -276,11 +277,10 @@ ignore = [
   "RUF001",  # string contains ambiguous unicode character
   "RUF002",  # docstring contains ambiguous acute accent unicode character
   "RUF003",  # comment contains ambiguous no-break space unicode character
-  "RUF005",  # consider upacking operator instead of concatenation
+  "RUF005",  # consider unpacking operator instead of concatenation
   "RUF012",  # mutable class attributes
 ]
 
-
 [tool.ruff.lint.per-file-ignores]
 # don't enforce absolute imports
 "asv_bench/**" = ["TID252"]

xarray/__init__.py

@@ -24,7 +24,6 @@
     cross,
     dot,
     polyval,
-    unify_chunks,
     where,
 )
 from xarray.conventions import SerializationWarning, decode_cf
@@ -52,6 +51,7 @@
 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.chunks import unify_chunks
 from xarray.structure.combine import combine_by_coords, combine_nested
 from xarray.structure.concat import concat
 from xarray.structure.merge import Context, MergeError, merge

xarray/backends/api.py

@@ -35,7 +35,6 @@
 from xarray.backends.locks import _get_scheduler
 from xarray.coders import CFDatetimeCoder, CFTimedeltaCoder
 from xarray.core import indexing
-from xarray.core.chunk import _get_chunk, _maybe_chunk
 from xarray.core.dataarray import DataArray
 from xarray.core.dataset import Dataset
 from xarray.core.datatree import DataTree
@@ -45,6 +44,7 @@
 from xarray.core.utils import is_remote_uri
 from xarray.namedarray.daskmanager import DaskManager
 from xarray.namedarray.parallelcompat import guess_chunkmanager
+from xarray.structure.chunks import _get_chunk, _maybe_chunk
 from xarray.structure.combine import (
     _infer_concat_order_from_positions,
     _nested_combine,