Bump minimum dependency versions

.claude/skills/upgrade-min-versions/SKILL.md

@@ -73,7 +73,11 @@ This must pass. If it fails, there may be dependency conflicts to resolve.
 pixi run policy-min-versions
 ```
 
-All packages should now show `=`.
+All packages should now show `=`, and the command must exit with 0. Only a `>`
+(pin newer than the policy) fails the check; it is allowed for packages listed
+under `ignored_violations` in `ci/policy.yaml`.
+
+Remove `overrides` in `ci/policy.yaml` that are no longer needed.
 
 ### 6. Clean Up Obsolete Test Decorators
 
@@ -93,47 +97,120 @@ rg "has_scipy_ge_|has_dask_ge_|has_zarr_v3[^_]|has_pandas_ge_|has_numpy_2|has_da
 For each file found:
 
 - Remove imports of deleted decorators
-- Remove `@requires_*` decorators that are always true
-- Remove `if has_*:` conditionals (keep only the true branch)
+- Replace `@requires_*` version decorators with the plain `@requires_<package>`
+  decorator, unless the test or its class already has one. They also skip the
+  test when the package is not installed at all, e.g. `@requires_dask_ge_2024_11_0`
+  in the `bare-minimum` and `no-dask` environments.
+- Remove `if has_*:` conditionals (keep only the true branch), but use
+  `if has_<package>:` instead if the test doesn't require the package already.
 - Remove `if not has_*:` conditionals (delete the code block)
 - Delete tests marked with `@pytest.mark.skipif(has_*, ...)` (always skipped)
 
-### 7. Update whats-new.rst
+Also grep for decorators matching the new minimum exactly (e.g. `has_zarr_v3_dtypes`
+for zarr 3.1) and for version guards defined elsewhere (e.g. `HAS_STRING_DTYPE`
+in `xarray/compat/npcompat.py`).
+
+### 7. Clean Up Version Guards in the Source
+
+The source code has version guards too, which become dead code with the new
+minimums. Search for them, not only for `module_available(..., minversion=...)`:
+
+```bash
+rg -n -i "minversion|__version__|mod_version|NumpyVersion|oldest supported|remove (once|when)|delete when|requires (numpy|dask|pandas|zarr)|numpy ?[<>]=? ?[0-9]" xarray --glob '!xarray/tests/**'
+```
+
+Also go through TODO and compat comments mentioning a dependency version, in
+the source and the tests (e.g. `# use np.cumulative_sum(...) when we support
+numpy>=2`, `# TODO: delete when min dask>=2023.12.1`, or `try: ... except
+ImportError:` fallbacks for old versions):
+
+```bash
+rg -n -i "(TODO|FIXME|NOTE|compat|workaround|legacy|once|when|until|older|drop)[^\n]{0,80}\b(numpy|pandas|scipy|dask|zarr|netcdf4|h5netcdf|flox|numbagg|bottleneck|sparse|pint|matplotlib|cftime|numba)\b[^\n]{0,40}([<>]=?|version|v?[0-9]+\.[0-9]+)" xarray --glob '!xarray/core/_aggregations.py'
+```
+
+- Remove branches for versions older than the new minimum and keep the code for
+  the new versions, e.g. `try: from numpy.exceptions import RankWarning` /
+  `except ImportError:` becomes a plain import at the top of the module.
+- `module_available("flox", minversion=...)` also checks that the package is
+  installed, so replace it with `module_available("flox")`, not `True`.
+- Guards for versions _above_ the new minimum stay (e.g. `flox>=0.10.5`).
+- Leave TODOs that depend on more than the version (e.g. a behavior change or
+  refactor) for a separate PR, and mention them in the PR.
+- Delete compat modules that only re-export something available in all
+  supported versions, and their entries in `pyproject.toml` (e.g. coverage
+  `omit`).
+- The flox checks in `xarray/core/_aggregations.py` are generated: change
+  `min_flox_version` in `xarray/util/generate_aggregations.py` and run
+  `pixi run generate-aggregations`. The generator writes to
+  `../xarray/xarray/...` relative to the current directory, so in a worktree
+  that is not named `xarray` it overwrites the main checkout instead. Run it
+  from a checkout named `xarray`, or check `git status` in both afterwards.
+
+### 8. Update whats-new.rst
 
 Add a table to `doc/whats-new.rst` under "Breaking Changes" documenting the version changes (in alphabetical order):
 
 ```rst
 Breaking Changes
 ~~~~~~~~~~~~~~~~
 
-- The minimum versions of some dependencies were changed:
-
-  ===================== =========  =======
-   Package                    Old      New
-  ===================== =========  =======
-    boto3                  1.34     1.36
-    cartopy                0.23     0.24
-    dask                 2024.6   2025.1
-    distributed          2024.6   2025.1
-    h5netcdf                1.4      1.5
-    iris                    3.9     3.11
-    lxml                    5.1      5.3
-    matplotlib              3.8     3.10
-    numpy                   1.26      2.0
-    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
-  ===================== =========  =======
+- The minimum versions of some dependencies were changed (:pull:`<PR number>`):
+
+  ===========  ======  ======
+  Package         Old     New
+  ===========  ======  ======
+  boto3          1.34    1.36
+  cartopy        0.23    0.24
+  dask         2024.6  2025.1
+  distributed  2024.6  2025.1
+  h5netcdf        1.4     1.5
+  iris            3.9    3.11
+  lxml            5.1     5.3
+  matplotlib      3.8    3.10
+  numpy          1.26     2.0
+  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
+  ===========  ======  ======
 ```
 
+Only edit this entry, older releases contain the same sentence.
+
+Every value must lie within the `=` signs of its column, otherwise the docs
+build fails with "Malformed table". Size the columns to the longest value, e.g.
+`2025.9` for dask.
+
+### 9. Open the PR
+
+Always ask the user before opening the PR, and show them the description first.
+
+Follow `.github/PULL_REQUEST_TEMPLATE.md`: a short description (an intro line
+and a few one-line bullets, e.g. the notable bumps and any policy override),
+the checklist with the relevant items ticked (whats-new) and the AI disclosure
+section filled in. Then add the PR number to the whats-new entry.
+
 ## Common Issues
 
 ### Lock file conflicts
 
 If `pixi lock` fails, check for incompatible version combinations. Some packages (like h5py/hdf5) are noted in comments as prone to conflicts.
 
+A package that is not bumped by the policy can still conflict with the new
+minimums, e.g. netcdf4 1.6 has no builds for numpy 2. Bump it to the oldest
+version that solves, and make sure the policy check still passes.
+
 ### Test failures after cleanup
 
 After removing version guards, some tests may fail if they relied on version-specific behavior. Update the test logic to use only the new minimum version's behavior.
+
+Run the full test suite in an environment with the latest versions (e.g.
+`test-py314`) as well, not only in `test-py312-min-versions`: a workaround whose
+TODO names an old version may still be needed for newer versions.
+
+Run the touched tests not only in `test-py312-min-versions` but also in
+`test-py312-bare-minimum` and `test-py314-no-dask`, which catch removed
+decorators that also skipped tests for missing packages. Run mypy in the CI
+environment, `pixi run -e test-py314-with-typing -- python -m mypy`; the
+`typing` environment lacks optional dependencies and reports false positives.

ci/policy.yaml

@@ -10,7 +10,11 @@ policy:
     numpy: 18
   default: 12
   # overrides for the policy
-  overrides: {}
+  overrides:
+    # conda-forge has no netcdf4 1.7.0 (the series starts at 1.7.1), which the
+    # policy needs to consider 1.7 released. Remove once
+    # https://github.com/xarray-contrib/minimum-dependency-versions/pull/94 is released
+    netcdf4: "1.7"
   # these packages are completely ignored
   exclude:
     - coveralls

doc/whats-new.rst

@@ -58,6 +58,31 @@ Breaking Changes
 - Support for Python 3.11 has been dropped. The minimum required Python version
   is now 3.12, in line with xarray's
   :ref:`minimum dependency policy <mindeps_policy>` (:pull:`11649`).
+  By `Michael Niklas <https://github.com/headtr1ck>`_.
+- The minimum versions of some dependencies were changed (:pull:`11728`):
+
+  ===========  ======  ======
+  Package         Old     New
+  ===========  ======  ======
+  boto3          1.37    1.40
+  bottleneck      1.4     1.6
+  cartopy        0.24    0.25
+  dask         2025.2  2025.9
+  distributed  2025.2  2025.9
+  h5py           3.13    3.14
+  iris           3.11    3.13
+  lxml            5.3     6.0
+  netcdf4         1.6     1.7
+  numba          0.61    0.62
+  numpy          1.26     2.2
+  packaging      24.2    25.0
+  pandas          2.2     2.3
+  pint           0.24    0.25
+  scipy          1.15    1.16
+  sparse         0.15    0.17
+  zarr            3.0     3.1
+  ===========  ======  ======
+
   By `Michael Niklas <https://github.com/headtr1ck>`_.
 - :py:class:`~xarray.NamedArray` is now generic in the type of its dimension
   names, so static type checkers can infer and check them. It takes three type

pixi.toml

@@ -20,7 +20,7 @@ python = "*"
 numpy = "*"
 pandas = "*"
 
-packaging = "24.2.*"
+packaging = "25.0.*"
 git = "*"            # needed for dynamic versioning
 
 [dependencies]
@@ -101,46 +101,46 @@ jax = "*" # no way to get cpu-only jaxlib from conda if gpu is present
 [feature.minimal.dependencies]
 # minimal versions
 python = "3.12.*"
-numpy = "1.26.*"
-pandas = "2.2.*"
+numpy = "2.2.*"
+pandas = "2.3.*"
 
 [feature.minimum-scipy.dependencies]
-scipy = "1.15.*"
+scipy = "1.16.*"
 
 [feature.min-versions.dependencies]
 array-api-strict = "2.4.*" # dependency for testing the array api compat
-boto3 = "1.37.*"
-bottleneck = "1.4.*"
-cartopy = "0.24.*"
+boto3 = "1.40.*"
+bottleneck = "1.6.*"
+cartopy = "0.25.*"
 cftime = "1.6.*"
-dask-core = "2025.2.*"
-distributed = "2025.2.*"
+dask-core = "2025.9.*"
+distributed = "2025.9.*"
 flox = "0.10.*"
 # h5netcdf 1.8.0 introduced a few compatibility features with netcdf4
 # https://github.com/pydata/xarray/issues/10657#issuecomment-3711095986
 h5netcdf = "1.8.*"
 # h5py and hdf5 tend to cause conflicts
 # for e.g. hdf5 1.12 conflicts with h5py=3.1
 # prioritize bumping other packages instead
-h5py = "3.13.*"
+h5py = "3.14.*"
 hdf5 = "1.14.*"
-iris = "3.11.*"
-lxml = "5.3.*"             # Optional dep of pydap
+iris = "3.13.*"
+lxml = "6.0.*"             # 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 = "0.61.*"
+netcdf4 = "1.7.*"
+numba = "0.62.*"
 numbagg = "0.9.*"
-packaging = "24.2.*"
-pint = "0.24.*"
+packaging = "25.0.*"
+pint = "0.25.*"
 pydap = "3.5.*"
 rasterio = "1.4.*"
 seaborn = "0.13.*"
-sparse = "0.15.*"
+sparse = "0.17.*"
 toolz = "1.0.*"
-zarr = "3.0.*"
+zarr = "3.1.*"
 pyarrow = "*"        # required by dask.dataframe
 # numcodecs warns on import when crc32c is used instead of google-crc32c
 google-crc32c = "*"

pyproject.toml

@@ -18,7 +18,7 @@ name = "xarray"
 readme = "README.md"
 requires-python = ">=3.12"
 
-dependencies = ["numpy>=1.26", "packaging>=24.2", "pandas>=2.2"]
+dependencies = ["numpy>=2.2", "packaging>=25.0", "pandas>=2.3"]
 
 # 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
@@ -27,7 +27,7 @@ dependencies = ["numpy>=1.26", "packaging>=24.2", "pandas>=2.2"]
 
 [project.optional-dependencies]
 accel = [
-  "scipy>=1.15",
+  "scipy>=1.16",
   "bottleneck",
   "numbagg>=0.9,!=0.9.5", # 0.9.5 breaks dask.array.nanmedian
   "numba>=0.62",          # numba 0.62 added support for numpy 2.3
@@ -36,21 +36,21 @@ accel = [
 ]
 complete = ["xarray[accel,etc,io,parallel,viz]"]
 io = [
-  "netCDF4>=1.6.0",
+  "netCDF4>=1.7.0",
   # h5netcdf 1.8.0 introduced a few compatibility features with netcdf4
   # https://github.com/pydata/xarray/issues/10657#issuecomment-3711095986
   "h5netcdf[h5py]>=1.8.0",
   "pydap",
-  "scipy>=1.15",
-  "zarr>=3.0",
+  "scipy>=1.16",
+  "zarr>=3.1",
   "fsspec",
   "cftime",
   "pooch",
 ]
 arrow = ["pyarrow"]
-etc = ["sparse>=0.15"]
+etc = ["sparse>=0.17"]
 parallel = ["dask[complete]"]
-viz = ["cartopy>=0.24", "matplotlib>=3.10", "nc-time-axis", "seaborn"]
+viz = ["cartopy>=0.25", "matplotlib>=3.10", "nc-time-axis", "seaborn"]
 types = [
   "pandas-stubs",
   "scipy-stubs",
@@ -118,7 +118,6 @@ fallback_version = "9999"
 omit = [
   "*/xarray/tests/*",
   "*/xarray/compat/dask_array_compat.py",
-  "*/xarray/compat/npcompat.py",
   "*/xarray/compat/pdcompat.py",
   "*/xarray/namedarray/pycompat.py",
   "*/xarray/core/types.py",

xarray/backends/writers.py

@@ -747,9 +747,8 @@ def to_zarr(
     # validate Dataset keys, DataArray names
     _validate_dataset_names(dataset)
 
-    # Load empty arrays to avoid bug saving zero length dimensions (Issue #5741)
-    # TODO: delete when min dask>=2023.12.1
-    # https://github.com/dask/dask/pull/10506
+    # Load empty arrays, otherwise the zero-sized dask chunks become zero-sized
+    # zarr chunks, which zarr rejects (Issue #5741)
     for v in dataset.variables.values():
         if v.size == 0:
             v.load()

xarray/backends/zarr.py

@@ -1931,7 +1931,7 @@ def _get_open_params(
     # TODO: replace AssertionError after https://github.com/zarr-developers/zarr-python/issues/2821 is resolved
     missing_exc = AssertionError
 
-    # zarr 3.0.8 and earlier did not support this property - it was effectively assumed true
+    # store can also be a path or a mapping, which don't have this property
     if not getattr(store, "supports_consolidated_metadata", True):
         consolidated = consolidate_on_close = False
 

xarray/coding/strings.py

@@ -17,13 +17,11 @@
     unpack_for_encoding,
 )
 from xarray.core import indexing
-from xarray.core.utils import emit_user_level_warning, module_available
+from xarray.core.utils import emit_user_level_warning
 from xarray.core.variable import Variable
 from xarray.namedarray.parallelcompat import get_chunked_array_type
 from xarray.namedarray.pycompat import is_chunked_array
 
-HAS_NUMPY_2_0 = module_available("numpy", minversion="2.0.0.dev0")
-
 
 def create_vlen_dtype(element_type):
     if element_type not in (str, bytes):
@@ -199,12 +197,8 @@ def bytes_to_char(arr):
 
 def _numpy_bytes_to_char(arr):
     """Like netCDF4.stringtochar, but faster and more flexible."""
-    # adapt handling of copy-kwarg to numpy 2.0
-    # see https://github.com/numpy/numpy/issues/25916
-    # and https://github.com/numpy/numpy/pull/25922
-    copy = None if HAS_NUMPY_2_0 else False
     # ensure the array is contiguous
-    arr = np.array(arr, copy=copy, order="C", dtype=np.bytes_)
+    arr = np.array(arr, copy=None, order="C", dtype=np.bytes_)
     return arr.reshape(arr.shape + (1,)).view("S1")
 
 
@@ -246,12 +240,8 @@ def char_to_bytes(arr):
 
 def _numpy_char_to_bytes(arr):
     """Like netCDF4.chartostring, but faster and more flexible."""
-    # adapt handling of copy-kwarg to numpy 2.0
-    # see https://github.com/numpy/numpy/issues/25916
-    # and https://github.com/numpy/numpy/pull/25922
-    copy = None if HAS_NUMPY_2_0 else False
     # based on: https://stackoverflow.com/a/10984878/809705
-    arr = np.array(arr, copy=copy, order="C")
+    arr = np.array(arr, copy=None, order="C")
     dtype = "S" + str(arr.shape[-1])
     return arr.view(dtype).reshape(arr.shape[:-1])