Merge branch 'main' into concat_default_kwargs

Author: jsignell

.github/workflows/ci-additional.yaml

@@ -123,7 +123,7 @@ jobs:
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v5.3.1
+        uses: codecov/codecov-action@v5.4.0
         with:
           file: mypy_report/cobertura.xml
           flags: mypy
@@ -174,7 +174,7 @@ jobs:
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v5.3.1
+        uses: codecov/codecov-action@v5.4.0
         with:
           file: mypy_report/cobertura.xml
           flags: mypy-min
@@ -230,7 +230,7 @@ jobs:
           python -m pyright xarray/
 
       - name: Upload pyright coverage to Codecov
-        uses: codecov/codecov-action@v5.3.1
+        uses: codecov/codecov-action@v5.4.0
         with:
           file: pyright_report/cobertura.xml
           flags: pyright
@@ -286,7 +286,7 @@ jobs:
           python -m pyright xarray/
 
       - name: Upload pyright coverage to Codecov
-        uses: codecov/codecov-action@v5.3.1
+        uses: codecov/codecov-action@v5.4.0
         with:
           file: pyright_report/cobertura.xml
           flags: pyright39

.github/workflows/ci.yaml

@@ -172,7 +172,7 @@ jobs:
           path: pytest.xml
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v5.3.1
+        uses: codecov/codecov-action@v5.4.0
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:

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

@@ -140,7 +140,7 @@ jobs:
         run: |
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v5.3.1
+        uses: codecov/codecov-action@v5.4.0
         with:
           file: mypy_report/cobertura.xml
           flags: mypy

.gitignore

@@ -81,3 +81,8 @@ doc/team-panel.txt
 doc/external-examples-gallery.txt
 doc/notebooks-examples-gallery.txt
 doc/videos-gallery.txt
+
+# Until we support this properly, excluding from gitignore. (adding it to
+# gitignore to make it _easier_ to work with `uv`, not as an indication that I
+# think we shouldn't...)
+uv.lock

.pre-commit-config.yaml

@@ -25,7 +25,7 @@ repos:
       - id: text-unicode-replacement-char
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.9.4
+    rev: v0.9.9
     hooks:
       - id: ruff-format
       - id: ruff
@@ -37,12 +37,12 @@ repos:
         exclude: "generate_aggregations.py"
         additional_dependencies: ["black==24.8.0"]
   - repo: https://github.com/rbubley/mirrors-prettier
-    rev: v3.4.2
+    rev: v3.5.3
     hooks:
       - id: prettier
         args: [--cache-location=.prettier_cache/cache]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.14.1
+    rev: v1.15.0
     hooks:
       - id: mypy
         # Copied from setup.cfg
@@ -73,3 +73,9 @@ repos:
     hooks:
       - id: validate-pyproject
         additional_dependencies: ["validate-pyproject-schema-store[all]"]
+  - repo: https://github.com/crate-ci/typos
+    rev: dictgen-v0.3.1
+    hooks:
+      - id: typos
+        # https://github.com/crate-ci/typos/issues/347
+        pass_filenames: false

doc/api.rst

@@ -697,6 +697,7 @@ For manipulating, traversing, navigating, or mapping over the tree structure.
    DataTree.pipe
    DataTree.match
    DataTree.filter
+   DataTree.filter_like
 
 Pathlib-like Interface
 ----------------------

doc/whats-new.rst

@@ -21,6 +21,8 @@ v2025.02.0 (unreleased)
 
 New Features
 ~~~~~~~~~~~~
+- Added :py:meth:`DataTree.filter_like` to conveniently restructure a DataTree like another DataTree (:issue:`10096`, :pull:`10097`).
+  By `Kobe Vandelanotte <https://github.com/kobebryant432>`_.
 - Added :py:meth:`Coordinates.from_xindex` as convenience for creating a new :py:class:`Coordinates` object
   directly from an existing Xarray index object if the latter supports it (:pull:`10000`)
   By `Benoit Bovy <https://github.com/benbovy>`_.
@@ -60,9 +62,18 @@ Bug fixes
 - Fix DataArray().drop_attrs(deep=False) and add support for attrs to
   DataArray()._replace(). (:issue:`10027`, :pull:`10030`). By `Jan
   Haacker <https://github.com/j-haacker>`_.
+- Prevent false resolution change warnings from being emitted when decoding
+  timedeltas encoded with floating point values, and make it clearer how to
+  silence this warning message in the case that it is rightfully emitted
+  (:issue:`10071`, :pull:`10072`).  By `Spencer Clark
+  <https://github.com/spencerkclark>`_.
 - Fix ``isel`` for multi-coordinate Xarray indexes (:issue:`10063`, :pull:`10066`).
   By `Benoit Bovy <https://github.com/benbovy>`_.
-
+- Fix dask tokenization when opening each node in :py:func:`xarray.open_datatree`
+  (:issue:`10098`, :pull:`10100`). By `Sam Levang <https://github.com/slevang>`_.
+- Improve handling of dtype and NaT when encoding/decoding masked and packaged
+  datetimes and timedeltas (:issue:`8957`, :pull:`10050`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
 
 Documentation
 ~~~~~~~~~~~~~
@@ -103,7 +114,7 @@ class can be passed through the ``decode_times`` keyword argument (see also
     coder = xr.coders.CFDatetimeCoder(time_unit="s")
     ds = xr.open_dataset(filename, decode_times=coder)
 
-Similar control of the resoution of decoded timedeltas can be achieved through
+Similar control of the resolution of decoded timedeltas can be achieved through
 passing a :py:class:`coders.CFTimedeltaCoder` instance to the
 ``decode_timedelta`` keyword argument:
 

pyproject.toml

@@ -1,7 +1,5 @@
 [project]
-authors = [
-  { name = "xarray Developers", email = "[email protected]" },
-]
+authors = [{ name = "xarray Developers", email = "[email protected]" }]
 classifiers = [
   "Development Status :: 5 - Production/Stable",
   "License :: OSI Approved :: Apache Software License",
@@ -22,11 +20,7 @@ name = "xarray"
 readme = "README.md"
 requires-python = ">=3.10"
 
-dependencies = [
-  "numpy>=1.24",
-  "packaging>=23.2",
-  "pandas>=2.1",
-]
+dependencies = ["numpy>=1.24", "packaging>=23.2", "pandas>=2.1"]
 
 # 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
@@ -70,6 +64,7 @@ types = [
   "types-PyYAML",
   "types-Pygments",
   "types-colorama",
+  "types-decorator",
   "types-defusedxml",
   "types-docutils",
   "types-networkx",
@@ -93,10 +88,7 @@ dask = "xarray.namedarray.daskmanager:DaskManager"
 
 [build-system]
 build-backend = "setuptools.build_meta"
-requires = [
-  "setuptools>=42",
-  "setuptools-scm>=7",
-]
+requires = ["setuptools>=42", "setuptools-scm>=7"]
 
 [tool.setuptools]
 packages = ["xarray"]
@@ -120,10 +112,7 @@ exclude_lines = ["pragma: no cover", "if TYPE_CHECKING"]
 
 [tool.mypy]
 enable_error_code = ["ignore-without-code", "redundant-self", "redundant-expr"]
-exclude = [
-  'build',
-  'xarray/util/generate_.*\.py',
-]
+exclude = ['build', 'xarray/util/generate_.*\.py']
 files = "xarray"
 show_error_context = true
 warn_redundant_casts = true
@@ -254,10 +243,7 @@ module = ["xarray.namedarray.*", "xarray.tests.test_namedarray"]
 # reportMissingTypeStubs = false
 
 [tool.ruff]
-extend-exclude = [
-  "doc",
-  "_typed_ops.pyi",
-]
+extend-exclude = ["doc", "_typed_ops.pyi"]
 
 [tool.ruff.lint]
 extend-select = [
@@ -383,3 +369,64 @@ test = "pytest"
 ignore = [
   "PP308", # This option creates a large amount of log lines.
 ]
+
+[tool.typos]
+
+[tool.typos.default]
+extend-ignore-identifiers-re = [
+  # Variable names
+  "nd_.*",
+  ".*_nd",
+  "ba_.*",
+  ".*_ba",
+  "ser_.*",
+  ".*_ser",
+  # Function/class names
+  "NDArray.*",
+  ".*NDArray.*",
+]
+
+[tool.typos.default.extend-words]
+# NumPy function names
+arange = "arange"
+
+# Technical terms
+nd = "nd"
+nin = "nin"
+
+# Variable names
+ba = "ba"
+ser = "ser"
+fo = "fo"
+iy = "iy"
+vart = "vart"
+ede = "ede"
+
+# Organization/Institution names
+Stichting = "Stichting"
+Mathematisch = "Mathematisch"
+
+# People's names
+Soler = "Soler"
+Bruning = "Bruning"
+Tung = "Tung"
+Claus = "Claus"
+Celles = "Celles"
+slowy = "slowy"
+Commun = "Commun"
+
+# Tests
+Ome = "Ome"
+SUR = "SUR"
+Tio = "Tio"
+Ono = "Ono"
+abl = "abl"
+
+# Technical terms
+splitted = "splitted"
+childs = "childs"
+cutted = "cutted"
+LOCA = "LOCA"
+
+[tool.typos.type.jupyter]
+extend-ignore-re = ["\"id\": \".*\""]

xarray/backends/api.py

@@ -35,13 +35,14 @@
 from xarray.backends.locks import _get_scheduler
 from xarray.coders import CFDatetimeCoder, CFTimedeltaCoder
 from xarray.core import dtypes, indexing
+from xarray.core.chunk import _get_chunk, _maybe_chunk
 from xarray.core.combine import (
     _infer_concat_order_from_positions,
     _nested_combine,
     combine_by_coords,
 )
 from xarray.core.dataarray import DataArray
-from xarray.core.dataset import Dataset, _get_chunk, _maybe_chunk
+from xarray.core.dataset import Dataset
 from xarray.core.datatree import DataTree
 from xarray.core.indexes import Index
 from xarray.core.treenode import group_subtrees
@@ -461,6 +462,7 @@ def _datatree_from_backend_datatree(
                     inline_array,
                     chunked_array_type,
                     from_array_kwargs,
+                    node=path,
                     **extra_tokens,
                 )
                 for path, [node] in group_subtrees(backend_tree)

xarray/backends/zarr.py

@@ -375,6 +375,11 @@ def _get_zarr_dims_and_attrs(zarr_obj, dimension_key, try_nczarr):
         pass
     else:
         attributes = dict(zarr_obj.attrs)
+        if len(zarr_obj.shape) != len(dimensions):
+            raise KeyError(
+                "Zarr object is missing the `dimension_names` metadata which is "
+                "required for xarray to determine variable dimensions."
+            )
         return dimensions, attributes
 
     # Zarr arrays do not have dimensions. To get around this problem, we add
@@ -393,7 +398,13 @@ def _get_zarr_dims_and_attrs(zarr_obj, dimension_key, try_nczarr):
 
         # NCZarr defines dimensions through metadata in .zarray
         zarray_path = os.path.join(zarr_obj.path, ".zarray")
-        zarray = json.loads(zarr_obj.store[zarray_path])
+        if _zarr_v3():
+            import asyncio
+
+            zarray_str = asyncio.run(zarr_obj.store.get(zarray_path)).to_bytes()
+        else:
+            zarray_str = zarr_obj.store.get(zarray_path)
+        zarray = json.loads(zarray_str)
         try:
             # NCZarr uses Fully Qualified Names
             dimensions = [