Merge branch 'main' into pre-commit-ci-update-config

Author: abkfenris

.github/workflows/main.yaml

@@ -14,16 +14,16 @@ jobs:
       matrix:
         python-version: ["3.11", "3.12", "3.13"]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
           architecture: x64
 
       - name: Setup pip cache
-        uses: actions/cache@v4.2.3
+        uses: actions/cache@v5.0.1
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-${{ matrix.python-version }}-${{ hashFiles('**/dev-requirements.txt') }}
@@ -43,7 +43,7 @@ jobs:
           python -m pytest --cov=./ --cov-report=xml --verbose
 
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v5.4.3
+        uses: codecov/codecov-action@v5.5.2
         with:
           file: ./coverage.xml
           fail_ci_if_error: false
@@ -55,16 +55,16 @@ jobs:
       matrix:
         python-version: ["3.11", "3.12", "3.13"]
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Setup Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: ${{ matrix.python-version }}
           architecture: x64
 
       - name: Setup pip cache
-        uses: actions/cache@v4.2.3
+        uses: actions/cache@v5.0.1
         with:
           path: ~/.cache/pip
           key: ${{ runner.os }}-pip-dev-${{ matrix.python-version }}-${{ hashFiles('**/dev-requirements.txt') }}

.github/workflows/pypipublish.yaml

@@ -16,10 +16,10 @@ jobs:
     permissions:
       id-token: write # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
 
       - name: Set up Python
-        uses: actions/setup-python@v5
+        uses: actions/setup-python@v6
         with:
           python-version: "3.x"
 

docs/requirements.txt

@@ -1,9 +1,8 @@
 sphinx<8.0
-pydantic<2.0
 sphinx-autosummary-accessors
 pydata-sphinx-theme
 sphinx-autodoc-typehints
-autodoc_pydantic==1.9.1
+autodoc_pydantic==2.2.0
 myst-nb
 sphinx-design
 sphinx_github_changelog

noxfile.py

@@ -53,6 +53,8 @@ def docs(session: nox.Session):
     if args.clean:
         session.run('rm', '-rf', f'{BUILDDIR}/*')
 
+    session.run('python', 'source/api/generate_openapi.py')
+
     if args.live:
         session.run('sphinx-autobuild', '-b', 'dirhtml', 'source/', '_build/dirhtml/')
     else:

pyproject.toml

@@ -23,7 +23,7 @@ requires-python = ">=3.11"
 classifiers = [
   "Development Status :: 4 - Beta",
   "Intended Audience :: Science/Research",
-  "License :: OSI Approved :: MIT License",
+  "License :: OSI Approved :: Apache Software License",
   "Operating System :: OS Independent",
   "Programming Language :: Python",
   "Programming Language :: Python :: 3 :: Only",

requirements.txt

@@ -7,5 +7,5 @@ pluggy
 pydantic>=2.5.0
 toolz
 uvicorn
-xarray>=2025.1.0
+xarray>=2025.7.0
 zarr>=3.0.7

tests/test_core.py

@@ -51,7 +51,7 @@ def test_invalid_encoding_chunks_with_dask_raise():
     with pytest.raises(ValueError) as excinfo:
         _ = create_zmetadata(ds)
     excinfo.match(
-        r"Specified zarr chunks encoding\['chunks'\]=\(8, 5, 1\) for variable named None would overlap multiple dask chunks*"
+        r"Specified Zarr chunks encoding\['chunks'\]=\[8, 5, 1\] for variable named 'foo' would overlap multiple Dask chunks.*"
     )
 
 

xpublish/utils/zarr.py

@@ -17,6 +17,7 @@
 import xarray as xr
 from numcodecs.abc import Codec
 from numcodecs.compat import ensure_ndarray
+from xarray.backends.chunks import validate_grid_chunks_alignment
 from xarray.backends.zarr import (
     DIMENSION_KEY,
     encode_zarr_attr_value,
@@ -199,10 +200,18 @@ def create_zmetadata(dataset: xr.Dataset) -> dict:
             dvar = da.variable
 
         encoded_da = encode_zarr_variable(dvar, name=key)
+        if 'chunks' in encoded_da.encoding:
+            validate_grid_chunks_alignment(
+                nd_v_chunks=dvar.chunks,
+                enc_chunks=encoded_da.encoding['chunks'],
+                region=tuple([SimpleNamespace(start=None, stop=None) for _ in da.shape]),
+                allow_partial_chunks=False,
+                name=key,
+                backend_shape=encoded_da.shape,
+            )
         encoding = extract_zarr_variable_encoding(
             dvar,
             zarr_format=ZARR_FORMAT,
-            region=tuple([SimpleNamespace(start=None, stop=None) for _ in da.shape]),
         )
         zattrs = _extract_dataarray_zattrs(encoded_da)
         zattrs = _extract_dataarray_coords(da, zattrs)