Maintenance: Support zarr>=3.0

ci/policy.yaml

@@ -26,6 +26,7 @@ policy:
     - hypothesis
     - pytz
     - pytest-reportlog
+    - pyarrow # transitive dependency of dask.dataframe, not an xarray dependency
   # these packages don't fail the CI, but will be printed in the report
   ignored_violations:
     - array-api-strict

conftest.py

@@ -41,12 +41,6 @@ def pytest_collection_modifyitems(items):
             item.add_marker(pytest.mark.mypy)
 
 
-@pytest.fixture(autouse=True)
-def set_zarr_v3_api(monkeypatch):
-    """Set ZARR_V3_EXPERIMENTAL_API environment variable for all tests."""
-    monkeypatch.setenv("ZARR_V3_EXPERIMENTAL_API", "1")
-
-
 @pytest.fixture(autouse=True)
 def add_standard_imports(doctest_namespace, tmpdir):
     import numpy as np

doc/whats-new.rst

@@ -17,6 +17,71 @@ New Features
 
 Breaking Changes
 ~~~~~~~~~~~~~~~~
+The minimum versions of some dependencies were changed:
+By `Joe Hamman <https://github.com/jhamman>`_.
+
+.. list-table::
+   :header-rows: 1
+   :widths: 30 20 20
+
+   * - Dependency
+     - Old Version
+     - New Version
+   * - boto3
+     - 1.34
+     - 1.37
+   * - cartopy
+     - 0.23
+     - 0.24
+   * - dask-core
+     - 2024.6
+     - 2025.2
+   * - distributed
+     - 2024.6
+     - 2025.2
+   * - flox
+     - 0.9
+     - 0.10
+   * - h5netcdf
+     - 1.4
+     - 1.5
+   * - h5py
+     - 3.11
+     - 3.13
+   * - iris
+     - 3.9
+     - 3.11
+   * - lxml
+     - 5.1
+     - 5.3
+   * - matplotlib-base
+     - 3.8
+     - 3.10
+   * - numba
+     - 0.60
+     - 0.61
+   * - numbagg
+     - 0.8
+     - 0.9
+   * - numpy
+     - 1.26
+     - 2.1
+   * - packaging
+     - 24.1
+     - 24.2
+   * - rasterio
+     - 1.3
+     - 1.4
+   * - scipy
+     - 1.13
+     - 1.15
+   * - toolz
+     - 0.12
+     - 1.0
+   * - zarr
+     - 2.18
+     - 3.0
+
 - Xarray will no longer by default decode a variable into a
   :py:class:`np.timedelta64` dtype based on the presence of a timedelta-like
   ``"units"`` attribute alone. Instead it will rely on the presence of a
@@ -31,6 +96,15 @@ Breaking Changes
   ``open_dataset`` and ``open_datatree`` the default behavior of fsspec is now to
   use block caching with a 4MB block size (:pull:`11216`). By `Julia Signell
   <https://github.com/jsignell>`_.
+- The minimum zarr version is now 3.0. All zarr-python 2.x compatibility code
+  has been removed from the zarr backend. The following parameters have been
+  removed:
+
+  - ``zarr_version``: Use ``zarr_format`` instead (was deprecated since 2024.9.1).
+  - ``synchronizer``: Not supported in zarr-python 3.x.
+  - ``chunk_store``: Not supported in zarr-python 3.x.
+
+  By `Joe Hamman <https://github.com/jhamman>`_ (:pull:`11232`).
 
 Deprecations
 ~~~~~~~~~~~~
@@ -41,6 +115,10 @@ Bug Fixes
 
 - Fix ``Source`` link in api docs (:pull:`11187`)
   By `Ian Hunt-Isaak <https://github.com/ianhi>`_
+- Fix async zarr tests using ``wraps`` with ``autospec=True`` on async methods,
+  which caused ``AsyncMock`` objects to leak through instead of real array data
+  (:pull:`11232`).
+  By `Joe Hamman <https://github.com/jhamman>`_.
 - Coerce masked dask arrays to filled (:issue:`9374` :pull:`11157`).
   By `Julia Signell <https://github.com/jsignell>`_
 

pixi.toml

@@ -20,7 +20,7 @@ python = "*"
 numpy = "*"
 pandas = "*"
 
-packaging = "24.1.*"
+packaging = "24.2.*"
 git = "*"            # needed for dynamic versioning
 
 [dependencies]
@@ -103,44 +103,45 @@ jax = "*" # no way to get cpu-only jaxlib from conda if gpu is present
 [feature.minimal.dependencies]
 # minimal versions
 python = "3.11.*"
-numpy = "1.26.*"
+numpy = "2.1.*"
 pandas = "2.2.*"
 
 [feature.minimum-scipy.dependencies]
-scipy = "1.13.*"
+scipy = "1.15.*"
 
 [feature.min-versions.dependencies]
 array-api-strict = "2.4.*" # dependency for testing the array api compat
-boto3 = "1.34.*"
+boto3 = "1.37.*"
 bottleneck = "1.4.*"
-cartopy = "0.23.*"
+cartopy = "0.24.*"
 cftime = "1.6.*"
-dask-core = "2024.6.*"
-distributed = "2024.6.*"
-flox = "0.9.*"
-h5netcdf = "1.4.*"
+dask-core = "2025.2.*"
+distributed = "2025.2.*"
+flox = "0.10.*"
+h5netcdf = "1.5.*"
 # h5py and hdf5 tend to cause conflicts
 # for e.g. hdf5 1.12 conflicts with h5py=3.1
 # prioritize bumping other packages instead
-h5py = "3.11.*"
+h5py = "3.13.*"
 hdf5 = "1.14.*"
-iris = "3.9.*"
-lxml = "5.1.*"            # Optional dep of pydap
-matplotlib-base = "3.8.*"
+iris = "3.11.*"
+lxml = "5.3.*"             # Optional dep of pydap
+matplotlib-base = "3.10.*"
 nc-time-axis = "1.4.*"
 # netcdf follows a 1.major.minor[.patch] convention
 # (see https://github.com/Unidata/netcdf4-python/issues/1090)
 netcdf4 = "1.6.*"
-numba = "0.60.*"
-numbagg = "0.8.*"
-packaging = "24.1.*"
+numba = "0.61.*"
+numbagg = "0.9.*"
+packaging = "24.2.*"
 pint = "0.24.*"
 pydap = "3.5.*"
-rasterio = "1.3.*"
+rasterio = "1.4.*"
 seaborn = "0.13.*"
 sparse = "0.15.*"
-toolz = "0.12.*"
-zarr = "2.18.*"
+toolz = "1.0.*"
+zarr = "3.0.*"
+pyarrow = "*"        # required by dask.dataframe
 
 # TODO: Remove `target.unix` restriction once pandas nightly has win-64 wheels again.
 # Without this, `pixi lock` fails because it can't solve the nightly feature for win-64,

pyproject.toml

@@ -18,7 +18,7 @@ name = "xarray"
 readme = "README.md"
 requires-python = ">=3.11"
 
-dependencies = ["numpy>=1.26", "packaging>=24.1", "pandas>=2.2"]
+dependencies = ["numpy>=2.1", "packaging>=24.2", "pandas>=2.2"]
 
 # We don't encode minimum requirements here (though if we can write a script to
 # generate the text from `min_deps_check.py`, that's welcome...). We do add
@@ -27,27 +27,27 @@ dependencies = ["numpy>=1.26", "packaging>=24.1", "pandas>=2.2"]
 
 [project.optional-dependencies]
 accel = [
-  "scipy>=1.13",
+  "scipy>=1.15",
   "bottleneck",
-  "numbagg>=0.8",
+  "numbagg>=0.9",
   "numba>=0.62",  # numba 0.62 added support for numpy 2.3
-  "flox>=0.9",
+  "flox>=0.10",
   "opt_einsum",
 ]
 complete = ["xarray[accel,etc,io,parallel,viz]"]
 io = [
   "netCDF4>=1.6.0",
-  "h5netcdf[h5py]>=1.4.0",
+  "h5netcdf[h5py]>=1.5.0",
   "pydap",
-  "scipy>=1.13",
-  "zarr>=2.18",
+  "scipy>=1.15",
+  "zarr>=3.0",
   "fsspec",
   "cftime",
   "pooch",
 ]
 etc = ["sparse>=0.15"]
 parallel = ["dask[complete]"]
-viz = ["cartopy>=0.23", "matplotlib>=3.8", "nc-time-axis", "seaborn"]
+viz = ["cartopy>=0.24", "matplotlib>=3.10", "nc-time-axis", "seaborn"]
 types = [
   "pandas-stubs",
   "scipy-stubs",
@@ -310,7 +310,6 @@ asyncio_default_fixture_loop_scope = "function"
 addopts = [
   "--strict-config",
   "--strict-markers",
-  "--mypy-only-local-stub",
   "--mypy-pyproject-toml-file=pyproject.toml",
 ]