Merge branch 'main' into custom-groupers

* main: (85 commits)
  Adds open_datatree and load_datatree to the tutorial module (pydata#10082)
  Fix version in requires_zarr_v3 fixture (pydata#10145)
  Fix `open_datatree` when `decode_cf=False` (pydata#10141)
  [docs] `DataTree` cannot be constructed from `DataArray` (pydata#10142)
  Refactor datetime and timedelta encoding for increased robustness (pydata#9498)
  Fix test_distributed::test_async (pydata#10138)
  Refactor concat / combine / merge into `xarray/structure` (pydata#10134)
  Split `apply_ufunc` out of `computation.py` (pydata#10133)
  Refactor modules from `core` into `xarray.computation` (pydata#10132)
  Refactor compatibility modules into xarray.compat package (pydata#10131)
  Fix type issues from pandas stubs (pydata#10128)
  Don't skip tests when on a `mypy` branch (pydata#10129)
  Change `python_files` in `pyproject.toml` to a list (pydata#10127)
  Better `uv` compatibility (pydata#10124)
  explicitly cast the dtype of `where`'s condition parameter to `bool` (pydata#10087)
  Use `to_numpy` in time decoding (pydata#10081)
  Pin pandas stubs (pydata#10119)
  Fix broken Zarr test (pydata#10109)
  Update asv badge url in README.md (pydata#10113)
  fix and supress some test warnings (pydata#10104)
  ...

Author: dcherian

.github/workflows/ci-additional.yaml

@@ -116,14 +116,14 @@ jobs:
           python xarray/util/print_versions.py
       - name: Install mypy
         run: |
-          python -m pip install "mypy==1.13" --force-reinstall
+          python -m pip install "mypy==1.15" --force-reinstall
 
       - name: Run mypy
         run: |
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v5.1.2
+        uses: codecov/codecov-action@v5.4.0
         with:
           file: mypy_report/cobertura.xml
           flags: mypy
@@ -167,14 +167,14 @@ jobs:
           python xarray/util/print_versions.py
       - name: Install mypy
         run: |
-          python -m pip install "mypy==1.13" --force-reinstall
+          python -m pip install "mypy==1.15" --force-reinstall
 
       - name: Run mypy
         run: |
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v5.1.2
+        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@v5.1.2
+        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@v5.1.2
+        uses: codecov/codecov-action@v5.4.0
         with:
           file: pyright_report/cobertura.xml
           flags: pyright39

.github/workflows/ci.yaml

@@ -47,7 +47,7 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         # Bookend python versions
-        python-version: ["3.10", "3.12"]
+        python-version: ["3.10", "3.13"]
         env: [""]
         include:
           # Minimum python version:
@@ -59,14 +59,23 @@ jobs:
             os: ubuntu-latest
           # Latest python version:
           - env: "all-but-numba"
-            python-version: "3.12"
+            python-version: "3.13"
             os: ubuntu-latest
           - env: "all-but-dask"
-            # Not 3.12 because of pint
-            python-version: "3.11"
+            python-version: "3.12"
             os: ubuntu-latest
           - env: "flaky"
-            python-version: "3.12"
+            python-version: "3.13"
+            os: ubuntu-latest
+          # The mypy tests must be executed using only 1 process in order to guarantee
+          # predictable mypy output messages for comparison to expectations.
+          - env: "mypy"
+            python-version: "3.10"
+            numprocesses: 1
+            os: ubuntu-latest
+          - env: "mypy"
+            python-version: "3.13"
+            numprocesses: 1
             os: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -78,17 +87,21 @@ jobs:
 
           if [[ ${{ matrix.os }} == windows* ]] ;
           then
-            if [[ ${{ matrix.python-version }} != "3.13" ]]; then
+            if [[ ${{ matrix.python-version }} != "3.14" ]]; then
               echo "CONDA_ENV_FILE=ci/requirements/environment-windows.yml" >> $GITHUB_ENV
             else
-              echo "CONDA_ENV_FILE=ci/requirements/environment-windows-3.13.yml" >> $GITHUB_ENV
+              echo "CONDA_ENV_FILE=ci/requirements/environment-windows-3.14.yml" >> $GITHUB_ENV
             fi
           elif [[ "${{ matrix.env }}" != "" ]] ;
           then
             if [[ "${{ matrix.env }}" == "flaky" ]] ;
             then
               echo "CONDA_ENV_FILE=ci/requirements/environment.yml" >> $GITHUB_ENV
               echo "PYTEST_ADDOPTS=-m 'flaky or network' --run-flaky --run-network-tests -W default" >> $GITHUB_ENV
+            elif [[ "${{ matrix.env }}" == "mypy" ]] ;
+            then
+              echo "CONDA_ENV_FILE=ci/requirements/environment.yml" >> $GITHUB_ENV
+              echo "PYTEST_ADDOPTS=-n 1 -m 'mypy' --run-mypy -W default" >> $GITHUB_ENV
             else
               echo "CONDA_ENV_FILE=ci/requirements/${{ matrix.env }}.yml" >> $GITHUB_ENV
             fi
@@ -98,10 +111,10 @@ jobs:
               echo "PYTEST_ADDOPTS=-W default" >> $GITHUB_ENV
             fi
           else
-            if [[ ${{ matrix.python-version }} != "3.13" ]]; then
+            if [[ ${{ matrix.python-version }} != "3.14" ]]; then
               echo "CONDA_ENV_FILE=ci/requirements/environment.yml" >> $GITHUB_ENV
             else
-              echo "CONDA_ENV_FILE=ci/requirements/environment-3.13.yml" >> $GITHUB_ENV
+              echo "CONDA_ENV_FILE=ci/requirements/environment-3.14.yml" >> $GITHUB_ENV
             fi
           fi
 
@@ -145,7 +158,7 @@ jobs:
           save-always: true
 
       - name: Run tests
-        run: python -m pytest -n 4
+        run: python -m pytest -n ${{ matrix.numprocesses || 4 }}
           --timeout 180
           --cov=xarray
           --cov-report=xml
@@ -159,7 +172,7 @@ jobs:
           path: pytest.xml
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v5.1.2
+        uses: codecov/codecov-action@v5.4.0
         env:
           CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:

.github/workflows/pypi-release.yaml

@@ -88,7 +88,7 @@ jobs:
           path: dist
       - name: Publish package to TestPyPI
         if: github.event_name == 'push'
-        uses: pypa/[email protected].3
+        uses: pypa/[email protected].4
         with:
           repository_url: https://test.pypi.org/legacy/
           verbose: true
@@ -110,6 +110,6 @@ jobs:
           name: releases
           path: dist
       - name: Publish package to PyPI
-        uses: pypa/[email protected].3
+        uses: pypa/[email protected].4
         with:
           verbose: true

.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@v5.1.2
+        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: v0.8.6
+    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

README.md

@@ -3,7 +3,7 @@
 [![CI](https://github.com/pydata/xarray/workflows/CI/badge.svg?branch=main)](https://github.com/pydata/xarray/actions?query=workflow%3ACI)
 [![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/)

ci/minimum_versions.py

@@ -26,8 +26,9 @@
     "pytest",
     "pytest-cov",
     "pytest-env",
-    "pytest-xdist",
+    "pytest-mypy-plugins",
     "pytest-timeout",
+    "pytest-xdist",
     "hypothesis",
 ]
 

ci/requirements/all-but-dask.yml

@@ -30,8 +30,9 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-env
-  - pytest-xdist
+  - pytest-mypy-plugins
   - pytest-timeout
+  - pytest-xdist
   - rasterio
   - scipy
   - seaborn

ci/requirements/all-but-numba.yml

@@ -12,7 +12,6 @@ dependencies:
   - cartopy
   - cftime
   - dask-core
-  - dask-expr # dask raises a deprecation warning without this, breaking doctests
   - distributed
   - flox
   - fsspec
@@ -44,8 +43,9 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-env
-  - pytest-xdist
+  - pytest-mypy-plugins
   - pytest-timeout
+  - pytest-xdist
   - rasterio
   - scipy
   - seaborn

ci/requirements/bare-minimum.yml

@@ -9,8 +9,9 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-env
-  - pytest-xdist
+  - pytest-mypy-plugins
   - pytest-timeout
+  - pytest-xdist
   - numpy=1.24
   - packaging=23.1
   - pandas=2.1

ci/requirements/doc.yml

@@ -10,7 +10,6 @@ dependencies:
   - cfgrib
   - kerchunk
   - dask-core>=2022.1
-  - dask-expr
   - hypothesis>=6.75.8
   - h5netcdf>=0.13
   - ipykernel
@@ -31,6 +30,7 @@ dependencies:
   - pre-commit
   - pyarrow
   - pyproj
+  - rich # for Zarr tree()
   - scipy!=1.10.0
   - seaborn
   - setuptools

ci/requirements/environment-3.13.yml ci/requirements/environment-3.14.yml

@@ -10,7 +10,6 @@ dependencies:
   - cartopy
   - cftime
   - dask-core
-  - dask-expr
   - distributed
   - flox
   - fsspec
@@ -30,22 +29,35 @@ dependencies:
   - opt_einsum
   - packaging
   - pandas
+  - pandas-stubs<=2.2.3.241126 # https://github.com/pydata/xarray/issues/10110
   # - pint>=0.22
   - pip
   - pooch
   - pre-commit
+  - pyarrow # pandas raises a deprecation warning without this, breaking doctests
   - pydap
   - pytest
   - pytest-cov
   - pytest-env
-  - pytest-xdist
+  - pytest-mypy-plugins
   - pytest-timeout
+  - pytest-xdist
   - rasterio
   - scipy
   - seaborn
   # - sparse
   - toolz
+  - types-colorama
+  - types-docutils
+  - types-psutil
+  - types-Pygments
+  - types-python-dateutil
+  - types-pytz
+  - types-PyYAML
+  - types-setuptools
   - typing_extensions
   - zarr
   - pip:
       - jax # no way to get cpu-only jaxlib from conda if gpu is present
+      - types-defusedxml
+      - types-pexpect

ci/requirements/environment-windows-3.13.yml ci/requirements/environment-windows-3.14.yml

@@ -8,7 +8,6 @@ dependencies:
   - cartopy
   - cftime
   - dask-core
-  - dask-expr
   - distributed
   - flox
   - fsspec
@@ -26,19 +25,33 @@ dependencies:
   - numpy
   - packaging
   - pandas
+  - pandas-stubs<=2.2.3.241126 # https://github.com/pydata/xarray/issues/10110
   # - pint>=0.22
   - pip
   - pre-commit
+  - pyarrow # importing dask.dataframe raises an ImportError without this
   - pydap
   - pytest
   - pytest-cov
   - pytest-env
-  - pytest-xdist
+  - pytest-mypy-plugins
   - pytest-timeout
+  - pytest-xdist
   - rasterio
   - scipy
   - seaborn
   # - sparse
   - toolz
+  - types-colorama
+  - types-docutils
+  - types-psutil
+  - types-Pygments
+  - types-python-dateutil
+  - types-pytz
+  - types-PyYAML
+  - types-setuptools
   - typing_extensions
   - zarr
+  - pip:
+      - types-defusedxml
+      - types-pexpect