Merge branch 'main' into fix-7794

* main: (76 commits)
  Update how-to-add-new-backend.rst (#10240)
  Support extension array indexes (#9671)
  Switch documentation to pydata-sphinx-theme (#8708)
  Bump codecov/codecov-action from 5.4.0 to 5.4.2 in the actions group (#10239)
  Fix mypy, min-versions CI, xfail Zarr tests (#10255)
  Remove `test_dask_layers_and_dependencies` (#10242)
  Fix: Docs generation create temporary files that are not cleaned up. (#10238)
  opendap / dap4 support for pydap backend (#10182)
  Add RangeIndex (#10076)
  Fix mypy (#10232)
  Fix doctests (#10230)
  Fix broken Sphinx Roles (#10225)
  `DatasetView.map` fix `keep_attrs` (#10219)
  Add datatree repr asv (#10214)
  CI: Automatic PR labelling is back (#10201)
  Fixes dimension order in `xarray.Dataset.to_stacked_array` (#10205)
  Fix references to core classes in docs (#10207)
  Update pre-commit hooks (#10208)
  add `scipy-stubs` as extra `[types]` dependency (#10202)
  Fix sparse dask repr test (#10200)
  ...

Author: dcherian

.github/labeler.yml

@@ -0,0 +1,117 @@
+Automation:
+  - changed-files:
+      - any-glob-to-any-file:
+          - .github/**
+
+CI:
+  - changed-files:
+      - any-glob-to-any-file:
+          - ci/**
+
+dependencies:
+  - changed-files:
+      - any-glob-to-any-file:
+          - ci/requirements/*
+
+topic-arrays:
+  - changed-files:
+      - any-glob-to-any-file:
+          - xarray/core/duck_array_ops.py
+
+topic-backends:
+  - changed-files:
+      - any-glob-to-any-file:
+          - xarray/backends/**
+
+topic-cftime:
+  - changed-files:
+      - any-glob-to-any-file:
+          - xarray/coding/*time*
+
+topic-CF conventions:
+  - changed-files:
+      - any-glob-to-any-file:
+          - xarray/conventions.py
+
+topic-dask:
+  - changed-files:
+      - any-glob-to-any-file:
+          - xarray/compat/dask*
+          - xarray/core/parallel.py
+
+topic-DataTree:
+  - changed-files:
+      - any-glob-to-any-file:
+          - xarray/core/datatree*
+
+topic-documentation:
+  - changed-files:
+      - any-glob-to-any-file:
+          - doc/*
+          - "!doc/whats-new.rst"
+          - doc/**/*
+
+topic-groupby:
+  - changed-files:
+      - any-glob-to-any-file:
+          - xarray/core/groupby.py
+
+topic-html-repr:
+  - changed-files:
+      - any-glob-to-any-file:
+          - xarray/core/formatting_html.py
+
+topic-hypothesis:
+  - changed-files:
+      - any-glob-to-any-file:
+          - properties/**
+          - xarray/testing/strategies.py
+
+topic-indexing:
+  - changed-files:
+      - any-glob-to-any-file:
+          - xarray/core/indexes.py
+          - xarray/core/indexing.py
+
+topic-NamedArray:
+  - changed-files:
+      - any-glob-to-any-file:
+          - xarray/namedarray/*
+
+topic-performance:
+  - changed-files:
+      - any-glob-to-any-file:
+          - asv_bench/benchmarks/**
+
+topic-plotting:
+  - changed-files:
+      - any-glob-to-any-file:
+          - xarray/plot/*
+          - xarray/plot/**/*
+
+topic-rolling:
+  - changed-files:
+      - any-glob-to-any-file:
+          - xarray/computation/rolling.py
+          - xarray/computation/rolling_exp.py
+
+topic-testing:
+  - changed-files:
+      - any-glob-to-any-file:
+          - conftest.py
+          - xarray/testing/*
+
+topic-typing:
+  - changed-files:
+      - any-glob-to-any-file:
+          - xarray/core/types.py
+
+topic-zarr:
+  - changed-files:
+      - any-glob-to-any-file:
+          - xarray/backends/zarr.py
+
+io:
+  - changed-files:
+      - any-glob-to-any-file:
+          - xarray/backends/**

.github/workflows/benchmarks.yml

@@ -10,7 +10,7 @@ env:
 
 jobs:
   benchmark:
-    if: ${{ contains( github.event.pull_request.labels.*.name, 'run-benchmark') && github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}
+    if: ${{ contains( github.event.pull_request.labels.*.name, 'run-benchmark') && github.event_name == 'pull_request' || contains( github.event.pull_request.labels.*.name, 'topic-performance') && github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}
     name: Linux
     runs-on: ubuntu-20.04
     env:

.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@v5.4.2
         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@v5.4.2
         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@v5.4.2
         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@v5.4.2
         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@v5.4.2
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:

.github/workflows/label-prs.yml

@@ -0,0 +1,12 @@
+name: "PR Labeler"
+on:
+  - pull_request_target
+
+jobs:
+  label:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/labeler@v5
+        with:
+          repo-token: "${{ secrets.GITHUB_TOKEN }}"
+          sync-labels: false

.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: |
@@ -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@v5.4.2
         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: v0.11.4
     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
@@ -69,7 +69,13 @@ repos:
       - id: taplo-format
         args: ["--option", "array_auto_collapse=false"]
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.23
+    rev: v0.24.1
     hooks:
       - id: validate-pyproject
         additional_dependencies: ["validate-pyproject-schema-store[all]"]
+  - repo: https://github.com/crate-ci/typos
+    rev: v1
+    hooks:
+      - id: typos
+        # https://github.com/crate-ci/typos/issues/347
+        pass_filenames: false

README.md

@@ -1,9 +1,9 @@
 # xarray: N-D labeled arrays and datasets
 
-[![CI](https://github.com/pydata/xarray/workflows/CI/badge.svg?branch=main)](https://github.com/pydata/xarray/actions?query=workflow%3ACI)
+[![CI](https://github.com/pydata/xarray/actions/workflows/ci.yaml/badge.svg?branch=main)](https://github.com/pydata/xarray/actions/workflows/ci.yaml?query=branch%3Amain)
 [![Code coverage](https://codecov.io/gh/pydata/xarray/branch/main/graph/badge.svg?flag=unittests)](https://codecov.io/gh/pydata/xarray)
 [![Docs](https://readthedocs.org/projects/xray/badge/?version=latest)](https://docs.xarray.dev/)
-[![Benchmarked with asv](https://img.shields.io/badge/benchmarked%20by-asv-green.svg?style=flat)](https://pandas.pydata.org/speed/xarray/)
+[![Benchmarked with asv](https://img.shields.io/badge/benchmarked%20by-asv-green.svg?style=flat)](https://asv-runner.github.io/asv-collection/xarray/)
 [![Formatted with black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
 [![Checked with mypy](http://www.mypy-lang.org/static/mypy_badge.svg)](http://mypy-lang.org/)
 [![Available on pypi](https://img.shields.io/pypi/v/xarray.svg)](https://pypi.python.org/pypi/xarray/)

asv_bench/benchmarks/repr.py

@@ -25,6 +25,25 @@ def time_repr_html(self):
         self.ds._repr_html_()
 
 
+class ReprDataTree:
+    def setup(self):
+        # construct a datatree with 500 nodes
+        number_of_files = 20
+        number_of_groups = 25
+        tree_dict = {}
+        for f in range(number_of_files):
+            for g in range(number_of_groups):
+                tree_dict[f"file_{f}/group_{g}"] = xr.Dataset({"g": f * g})
+
+        self.dt = xr.DataTree.from_dict(tree_dict)
+
+    def time_repr(self):
+        repr(self.dt)
+
+    def time_repr_html(self):
+        self.dt._repr_html_()
+
+
 class ReprMultiIndex:
     def setup(self):
         index = pd.MultiIndex.from_product(

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 \

ci/minimum_versions.py

@@ -20,6 +20,12 @@
 
 channels = ["conda-forge"]
 platforms = ["noarch", "linux-64"]
+# these packages don't fail the CI, but will be printed in the report
+ignore_failure_packages = [
+    # remove when we can pin to pydap 3.5.1 without error
+    "pydap",
+]
+# these packages are completely ignored
 ignored_packages = [
     "coveralls",
     "pip",
@@ -171,7 +177,11 @@ def compare_versions(environments, policy_versions):
     status = {}
     for env, specs in environments.items():
         env_status = any(
-            spec.version > policy_versions[spec.name].version for spec in specs
+            (
+                (spec.version > policy_versions[spec.name].version)
+                and (spec.name not in ignore_failure_packages)
+            )
+            for spec in specs
         )
         status[env] = env_status
     return status

ci/requirements/doc.yml

@@ -4,49 +4,50 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python=3.12
+  - python
   - bottleneck
   - cartopy
   - cfgrib
   - kerchunk
-  - dask-core>=2022.1
-  - hypothesis>=6.75.8
-  - h5netcdf>=0.13
+  - dask-core
+  - hypothesis
+  - h5netcdf
   - ipykernel
   - ipywidgets # silence nbsphinx warning
   - ipython
-  - iris>=2.3
+  - iris
   - jupyter_client
+  - jupyter_sphinx
   - matplotlib-base
   - nbsphinx
   - ncdata
-  - netcdf4>=1.5
+  - netcdf4
   - numba
   - numpy>=2
-  - packaging>=23.2
-  - pandas>=1.4,!=2.1.0
+  - packaging
+  - pandas
   - pooch
   - pip
   - pre-commit
   - pyarrow
+  - pydata-sphinx-theme
   - pyproj
   - rich # for Zarr tree()
-  - scipy!=1.10.0
+  - scipy
   - seaborn
   - setuptools
   - sparse
   - sphinx-autosummary-accessors
-  - sphinx-book-theme<=1.0.1
   - sphinx-copybutton
   - sphinx-design
   - sphinx-inline-tabs
-  - sphinx>=5.0,<7.0 # https://github.com/executablebooks/sphinx-book-theme/issues/749
+  - sphinx>=6,<8
+  - sphinxcontrib-mermaid
   - sphinxcontrib-srclinks
   - sphinx-remove-toctrees
   - sphinxext-opengraph
   - sphinxext-rediraffe
-  - zarr>=2.10
+  - zarr
   - pip:
-      - sphinxcontrib-mermaid
       # relative to this file. Needs to be editable to be accepted.
       - -e ../..