[pull] main from pydata:main

.github/workflows/benchmarks-last-release.yml

@@ -37,7 +37,7 @@ jobs:
 
       - name: "Get Previous tag"
         id: previoustag
-        uses: WyriHaximus/github-action-get-previous-tag@61819f33034117e6c686e6a31dba995a85afc9de # v2.0.0
+        uses: WyriHaximus/github-action-get-previous-tag@83f26fea93bc7efcbca2eb5591f5eaaf66b8f206 # v2.1.0
         # with:
         #   fallback: 1.0.0 # Optional fallback tag to use when no tag can be found
 

.github/workflows/ci-additional.yaml

@@ -139,7 +139,7 @@ jobs:
           pixi run -e ${{env.PIXI_ENV}} -- python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
+        uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7.1.1
         with:
           files: mypy_report/cobertura.xml
           flags: mypy
@@ -185,7 +185,7 @@ jobs:
           pixi run -e ${{env.PIXI_ENV}} -- python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
+        uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7.1.1
         with:
           files: mypy_report/cobertura.xml
           flags: mypy-min
@@ -286,7 +286,7 @@ jobs:
           pixi run -e ${{ matrix.pixi-env }} -- python -m pyright xarray/
 
       - name: Upload pyright coverage to Codecov
-        uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
+        uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7.1.1
         with:
           files: pyright_report/cobertura.xml
           flags: pyright
@@ -348,4 +348,4 @@ jobs:
           persist-credentials: false
 
       - name: Run zizmor
-        uses: zizmorcore/zizmor-action@70fb788f84895a7701f5643d103d587e460b5c99 # v0.6.3
+        uses: zizmorcore/zizmor-action@cc914d7f3750a2d13d75c7f184a1060aa0e9d482 # v0.6.4

.github/workflows/ci.yaml

@@ -155,22 +155,36 @@ jobs:
         run: |
           pixi run -e ${{ matrix.pixi-env }} -- python -c "import xarray"
 
+      # caches are immutable, so use a unique key per job and restore the latest cache
+      # https://github.com/actions/cache/blob/main/tips-and-workarounds.md#update-a-cache
       - name: Restore cached hypothesis directory
-        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
+        uses: actions/cache/restore@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
         with:
           path: .hypothesis/
-          key: cache-hypothesis
+          key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }}-${{ github.run_attempt }}-${{ strategy.job-index }}
+          restore-keys: |
+            cache-hypothesis-${{ runner.os }}-
+            cache-hypothesis-
           enableCrossOsArchive: true
-          save-always: true
 
       - name: Run tests
+        id: tests
         run: |
           pixi run -e ${{ matrix.pixi-env }} -- python -m pytest -n ${{ matrix.numprocesses || 4 }} \
             --timeout 180 \
             --cov=xarray \
             --cov-report=xml \
             --junitxml=pytest.xml
 
+      # explicitly save the cache so it gets updated, also do this even if the tests fail
+      - name: Save cached hypothesis directory
+        if: always() && steps.tests.outcome != 'skipped'
+        uses: actions/cache/save@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
+        with:
+          path: .hypothesis/
+          key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }}-${{ github.run_attempt }}-${{ strategy.job-index }}
+          enableCrossOsArchive: true
+
       - name: Upload test results
         if: always()
         uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
@@ -179,7 +193,7 @@ jobs:
           path: pytest.xml
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
+        uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7.1.1
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:

.github/workflows/nightly-wheels.yml

@@ -69,7 +69,7 @@ jobs:
 
       - name: Upload wheel
         id: upload
-        uses: scientific-python/upload-nightly-action@e76cfec8a4611fd02808a801b0ff5a7d7c1b2d99 # 0.6.4
+        uses: scientific-python/upload-nightly-action@16fa02eacee1655195143de09f03676e60ef2bf5 # 0.6.5
         with:
           anaconda_nightly_upload_token: ${{ secrets.ANACONDA_NIGHTLY }}
           artifacts_path: dist

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

@@ -220,7 +220,7 @@ jobs:
         run: |
           pixi run --manifest-path "$MANIFEST_PATH" -e $ENV -- python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
+        uses: codecov/codecov-action@303a32d7a59b442fa8d48b6a1cc6825c09c847a5 # v7.1.1
         with:
           files: mypy_report/cobertura.xml
           flags: mypy

.pre-commit-config.yaml

@@ -24,7 +24,7 @@ repos:
       - id: rst-inline-touching-normal
       - id: text-unicode-replacement-char
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.20
+    rev: v0.16.6
     hooks:
       - id: ruff-check
         args: ["--fix", "--show-fixes"]
@@ -37,12 +37,12 @@ repos:
         # make sure this is the most recent version of black
         additional_dependencies: ["black==25.11.0"]
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: v3.9.4
+    rev: v3.9.6
     hooks:
       - id: prettier
         args: ["--cache-location=.prettier_cache/cache"]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v2.1.0
+    rev: v2.3.1
     hooks:
       - id: mypy
         # Copied from setup.cfg
@@ -71,16 +71,16 @@ repos:
       - id: taplo-lint
         args: ["--no-schema"]
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.25
+    rev: "0.26"
     hooks:
       - id: validate-pyproject
         additional_dependencies: ["validate-pyproject-schema-store[all]"]
   - repo: https://github.com/adhtruong/mirrors-typos
-    rev: v1.48.0
+    rev: v1.50.1
     hooks:
       - id: typos
   - repo: https://github.com/zizmorcore/zizmor-pre-commit
-    rev: v1.26.1
+    rev: v1.30.0
     hooks:
       - id: zizmor
         args: ["--offline"]

ci/requirements/environment.yml

@@ -24,7 +24,7 @@ dependencies:
   - nc-time-axis
   - netcdf4
   - numba
-  - numbagg
+  - numbagg!=0.9.5
   - numexpr
   - numpy>=2.2
   - opt_einsum

doc/conf.py

@@ -177,6 +177,18 @@
 # mermaid config
 mermaid_version = "11.6.0"
 
+# sphinx-llm config
+# the markdown builder used for llms.txt can't render these nodes; they are omitted
+# from the generated markdown, so don't turn the warnings into build errors
+llms_txt_suppress_unknown_node_warnings = [
+    "abbreviation",
+    "classifier",
+    "desc_optional",
+    "label",
+    "mermaid",
+    "PassthroughTextElement",
+]
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates", sphinx_autosummary_accessors.templates_path]
 

pixi.toml

@@ -58,7 +58,7 @@ aiobotocore = "*"
 
 [feature.numba.dependencies]
 numba = "*"
-numbagg = "*"
+numbagg = "!=0.9.5" # 0.9.5 rejects list axes passed by dask.array.nanmedian
 
 [feature.dask.dependencies]
 dask = "*"
@@ -181,11 +181,11 @@ python = "3.12.*"
 kerchunk = "*"
 ipykernel = "*"
 ipywidgets = "*"                   # silence nbsphinx warning
-iris = "!=3.16.0"                  # avoid ncdata failing. See https://github.com/SciTools/ncdata/issues/255
+iris = "*"
 ipython = "*"
 jupyter_client = "*"
 jupyter_sphinx = "*"
-ncdata = "*"
+ncdata = ">=0.4"                   # support for iris>=3.16. See https://github.com/SciTools/ncdata/issues/255
 pydata-sphinx-theme = "*"
 pyproj = "*"
 rich = "*"                         # for Zarr tree()
@@ -194,7 +194,7 @@ sphinx-autosummary-accessors = "*"
 sphinx-copybutton = "*"
 sphinx-design = "*"
 sphinx-inline-tabs = "*"
-sphinx-llm = ">=0.2.1"
+sphinx-llm = ">=1.1"               # for llms_txt_suppress_unknown_node_warnings
 sphinx = ">=8,<9"
 sphinxcontrib-mermaid = "*"
 sphinxcontrib-srclinks = "*"

pyproject.toml

@@ -29,8 +29,8 @@ dependencies = ["numpy>=1.26", "packaging>=24.2", "pandas>=2.2"]
 accel = [
   "scipy>=1.15",
   "bottleneck",
-  "numbagg>=0.9",
-  "numba>=0.62",  # numba 0.62 added support for numpy 2.3
+  "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
   "flox>=0.10",
   "opt_einsum",
 ]
@@ -172,6 +172,14 @@ module = [
   "array_api_strict.*",
 ]
 
+# pint>=0.26's annotations send mypy into infinite recursion (segfault / RecursionError)
+# when optype is installed, so don't analyse pint at all.
+# Fixed upstream in https://github.com/python/mypy/pull/22036; remove this override
+# once we require mypy > 2.3.1.
+[[tool.mypy.overrides]]
+follow_imports = "skip"
+module = ["pint.*"]
+
 # Gradually we want to add more modules to this list, ratcheting up our total
 # coverage. Once a module is here, functions are checked by mypy regardless of
 # whether they have type annotations. It would be especially useful to have test
@@ -290,6 +298,13 @@ ignore = [
   "RUF003",  # comment contains ambiguous no-break space unicode character
   "RUF005",  # consider unpacking operator instead of concatenation
   "RUF012",  # mutable class attributes
+  # rules added to the default set in ruff 0.16
+  "BLE001", # blind `except Exception`: used on purpose, e.g. in print_versions
+  "DTZ001", # `datetime()` without `tzinfo`: xarray works with naive datetimes
+  "N999",   # invalid module name: `netCDF4_`
+  "S110",   # `try`-`except`-`pass`
+  "TRY002", # raising vanilla `Exception`
+  "TRY004", # prefer `TypeError`: switching would change the raised exceptions
 ]
 
 [tool.ruff.lint.per-file-ignores]

xarray/backends/api.py

@@ -1400,7 +1400,7 @@ def open_mfdataset(
     preprocess: Callable[[Dataset], Dataset] | None = None,
     engine: T_Engine = None,
     data_vars: (
-        Literal["all", "minimal", "different"] | None | list[str] | CombineKwargDefault
+        Literal["all", "minimal", "different"] | list[str] | CombineKwargDefault | None
     ) = _DATA_VARS_DEFAULT,
     coords=_COORDS_DEFAULT,
     combine: Literal["by_coords", "nested"] = "by_coords",

xarray/backends/file_manager.py

@@ -89,7 +89,7 @@ def __init__(
         *args: Any,
         mode: Any = _OMIT_MODE,
         kwargs: Mapping[str, Any] | None = None,
-        lock: Lock | None | Literal[False] = None,
+        lock: Lock | Literal[False] | None = None,
         cache: MutableMapping[Any, T_File] | None = None,
         manager_id: Hashable | None = None,
         ref_counts: dict[Any, int] | None = None,
@@ -355,7 +355,7 @@ def __init__(
         opener: Callable[..., T_File],
         *args: Any,
         mode: Any = _OMIT_MODE,
-        lock: Lock | None | Literal[False] = None,
+        lock: Lock | Literal[False] | None = None,
         kwargs: Mapping[str, Any] | None = None,
     ):
         kwargs = {} if kwargs is None else dict(kwargs)
@@ -458,7 +458,7 @@ def __init__(
         value: T_File,
         *,
         close: Callable[[], None] | None = None,
-        lock: Lock | None | Literal[False] = None,
+        lock: Lock | Literal[False] | None = None,
     ):
         if close is None:
             close = value.close

xarray/backends/locks.py

@@ -276,7 +276,7 @@ def combine_locks(locks: Sequence[Lock]) -> Lock:
         return DummyLock()
 
 
-def ensure_lock(lock: Lock | None | Literal[False]) -> Lock:
+def ensure_lock(lock: Lock | Literal[False] | None) -> Lock:
     """Ensure that the given object is a lock."""
     if lock is None or lock is False:
         return DummyLock()

xarray/backends/store.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 from collections.abc import Iterable
-from typing import TYPE_CHECKING
 
 from xarray import conventions
 from xarray.backends.common import (
@@ -13,9 +12,6 @@
 from xarray.core.coordinates import Coordinates
 from xarray.core.dataset import Dataset
 
-if TYPE_CHECKING:
-    pass
-
 
 class StoreBackendEntrypoint(BackendEntrypoint):
     description = "Open AbstractDataStore instances in Xarray"

xarray/backends/writers.py

@@ -429,7 +429,11 @@ def to_netcdf(
         auto_complex=auto_complex,
     )
     if group is not None:
-        store = store.get_child_store(group)
+        try:
+            store = store.get_child_store(group)
+        except Exception:
+            store.close()
+            raise
 
     writer = ArrayWriter()
 
@@ -801,7 +805,7 @@ def _datatree_to_netcdf(
     compute: bool = True,
     invalid_netcdf: bool = False,
     auto_complex: bool | None = None,
-) -> None | memoryview | Delayed:
+) -> memoryview | Delayed | None:
     """Implementation of `DataTree.to_netcdf`."""
 
     if format not in [None, *get_args(T_DataTreeNetcdfTypes)]:

xarray/coding/strings.py

@@ -60,7 +60,7 @@ def encode(self, variable: Variable, name=None) -> Variable:
         # which all backends support natively (GH11199)
         if data.dtype.kind == "T":
             data = np.asarray(data, dtype=object)
-            data[data == None] = ""  # noqa: E711
+            data[data == None] = ""
             data = np.asarray(data, dtype="U")
             variable = Variable(dims, data, attrs, encoding)
 

xarray/coding/times.py

@@ -976,7 +976,7 @@ def _encode_datetime_with_cftime(dates, units: str, calendar: str) -> np.ndarray
     dates = np.atleast_1d(dates)
 
     # Find all the None position
-    none_position = dates == None  # noqa: E711
+    none_position = dates == None
     filtered_dates = dates[~none_position]
 
     # Since netCDF files do not support storing float128 values, we ensure

xarray/core/dataarray.py

@@ -3677,13 +3677,13 @@ def interpolate_na(
         limit: int | None = None,
         use_coordinate: bool | str = True,
         max_gap: (
-            None
-            | int
+            int
             | float
             | str
             | pd.Timedelta
             | np.timedelta64
             | datetime.timedelta
+            | None
         ) = None,
         keep_attrs: bool | None = None,
         **kwargs: Any,

xarray/core/dataset.py

@@ -1491,7 +1491,7 @@ def __setitem__(
                             f" been successfully updated:\n{processed}"
                         ) from e
                     else:
-                        raise e
+                        raise
 
         elif utils.hashable(key):
             if isinstance(value, Dataset):

xarray/core/datatree.py

@@ -1811,7 +1811,7 @@ def map_over_datasets(
 
     def map_over_datasets(
         self,
-        func: Callable[..., Dataset | None | tuple[Dataset | None, ...]],
+        func: Callable[..., Dataset | tuple[Dataset | None, ...] | None],
         *args: Any,
         kwargs: Mapping[str, Any] | None = None,
     ) -> DataTree | tuple[DataTree, ...]:
@@ -2034,7 +2034,7 @@ def to_netcdf(
         write_inherited_coords: bool = False,
         compute: bool = True,
         **kwargs,
-    ) -> None | memoryview | Delayed:
+    ) -> memoryview | Delayed | None:
         """
         Write datatree contents to a netCDF file.