Merge branch 'main' into backend-indexing

* main: (79 commits)
  fix mean for datetime-like using the respective time resolution unit (#9977)
  Add `time_unit` argument to `CFTimeIndex.to_datetimeindex` (#9965)
  remove gate and add a test (#9958)
  Remove repetitive that (replace it with the) (#9994)
  add shxarray to the xarray ecosystem list (#9995)
  Add `shards` to `valid_encodings` to enable sharded Zarr writing (#9948)
  Use flox for grouped first, last (#9986)
  Bump the actions group with 2 updates (#9989)
  Fix some typing (#9988)
  Remove unnecessary a article (#9980)
  Fix test_doc_example on big-endian systems (#9949)
  fix weighted polyfit for arrays with more than 2 dimensions (#9974)
  Use zarr-fixture to prevent thread leakage errors (#9967)
  remove dask-expr from CI runs, fix related tests (#9971)
  Update time coding tests to assert exact equality (#9961)
  cast type to PDDatetimeUnitOptions (#9963)
  Suggest the correct name when no key matches in the dataset (#9943)
  fix upstream dev issues (#9953)
  Relax nanosecond datetime restriction in CF time decoding (#9618)
  Remove outdated quantile test. (#9945)
  ...

Author: dcherian

.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@v5.0.2
+        uses: codecov/codecov-action@v5.3.1
         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@v5.0.2
+        uses: codecov/codecov-action@v5.3.1
         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@v5.0.2
+        uses: codecov/codecov-action@v5.3.1
         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@v5.0.2
+        uses: codecov/codecov-action@v5.3.1
         with:
           file: pyright_report/cobertura.xml
           flags: pyright39

.github/workflows/ci.yaml

@@ -159,7 +159,9 @@ jobs:
           path: pytest.xml
 
       - name: Upload code coverage to Codecov
-        uses: codecov/[email protected]
+        uses: codecov/[email protected]
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
         with:
           file: ./coverage.xml
           flags: unittests

.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].2
+        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].2
+        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@v5.0.2
+        uses: codecov/codecov-action@v5.3.1
         with:
           file: mypy_report/cobertura.xml
           flags: mypy

.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: v0.7.2
+    rev: v0.8.6
     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: v3.3.3
+    rev: v3.4.2
     hooks:
       - id: prettier
         args: [--cache-location=.prettier_cache/cache]
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.13.0
+    rev: v1.14.1
     hooks:
       - id: mypy
         # Copied from setup.cfg
@@ -63,3 +63,13 @@ repos:
     rev: ebf0b5e44d67f8beaa1cd13a0d0393ea04c6058d
     hooks:
       - id: validate-cff
+  - repo: https://github.com/ComPWA/taplo-pre-commit
+    rev: v0.9.3
+    hooks:
+      - id: taplo-format
+        args: ["--option", "array_auto_collapse=false"]
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.23
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]

.readthedocs.yaml

@@ -1,5 +1,9 @@
 version: 2
 
+sphinx:
+  configuration: doc/conf.py
+  fail_on_warning: true
+
 build:
   os: ubuntu-lts-latest
   tools:
@@ -14,7 +18,4 @@ build:
 conda:
   environment: ci/requirements/doc.yml
 
-sphinx:
-  fail_on_warning: true
-
 formats: []

DATATREE_MIGRATION_GUIDE.md

@@ -45,6 +45,7 @@ A number of other API changes have been made, which should only require minor mo
 - The `DataTree.parent` property is now read-only. To assign a ancestral relationships directly you must instead use the `.children` property on the parent node, which remains settable.
 - Similarly the `parent` kwarg has been removed from the `DataTree.__init__` constructor.
 - DataTree objects passed to the `children` kwarg in `DataTree.__init__` are now shallow-copied.
+- `DataTree.map_over_subtree` has been renamed to `DataTree.map_over_datasets`, and changed to no longer work like a decorator. Instead you use it to apply the function and arguments directly, more like how `xarray.apply_ufunc` works.
 - `DataTree.as_array` has been replaced by `DataTree.to_dataarray`.
 - A number of methods which were not well tested have been (temporarily) disabled. In general we have tried to only keep things that are known to work, with the plan to increase API surface incrementally after release.
 

asv_bench/benchmarks/__init__.py

@@ -30,13 +30,13 @@ def requires_sparse():
 
 
 def randn(shape, frac_nan=None, chunks=None, seed=0):
-    rng = np.random.RandomState(seed)
+    rng = np.random.default_rng(seed)
     if chunks is None:
         x = rng.standard_normal(shape)
     else:
         import dask.array as da
 
-        rng = da.random.RandomState(seed)
+        rng = da.random.default_rng(seed)
         x = rng.standard_normal(shape, chunks=chunks)
 
     if frac_nan is not None:
@@ -47,8 +47,8 @@ def randn(shape, frac_nan=None, chunks=None, seed=0):
 
 
 def randint(low, high=None, size=None, frac_minus=None, seed=0):
-    rng = np.random.RandomState(seed)
-    x = rng.randint(low, high, size)
+    rng = np.random.default_rng(seed)
+    x = rng.integers(low, high, size)
     if frac_minus is not None:
         inds = rng.choice(range(x.size), int(x.size * frac_minus))
         x.flat[inds] = -1

asv_bench/benchmarks/dataset_io.py

@@ -305,7 +305,7 @@ def make_ds(self, nfiles=10):
             ds.attrs = {"history": "created for xarray benchmarking"}
 
             self.ds_list.append(ds)
-            self.filenames_list.append("test_netcdf_%i.nc" % i)
+            self.filenames_list.append(f"test_netcdf_{i}.nc")
 
 
 class IOWriteMultipleNetCDF3(IOMultipleNetCDF):

asv_bench/benchmarks/reindexing.py

@@ -11,7 +11,7 @@
 
 class Reindex:
     def setup(self):
-        data = np.random.RandomState(0).randn(ntime, nx, ny)
+        data = np.random.default_rng(0).random((ntime, nx, ny))
         self.ds = xr.Dataset(
             {"temperature": (("time", "x", "y"), data)},
             coords={"time": np.arange(ntime), "x": np.arange(nx), "y": np.arange(ny)},