Merge branch 'main' into refactor/upstream-apis

Author: d-v-b

.github/workflows/docs.yml

@@ -0,0 +1,32 @@
+name: Docs
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  docs:
+    name: Check docs
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+        with:
+          persist-credentials: false
+      - uses: astral-sh/setup-uv@f0ec1fc3b38f5e7cd731bb6ce540c5af426746bb # v6.1.0
+      - run: uv sync --group docs
+      - run: uv run mkdocs build
+        env:
+          DISABLE_MKDOCS_2_WARNING: "true"
+          NO_MKDOCS_2_WARNING: "true"
+      - run: uv run python ci/check_unlinked_types.py
+        continue-on-error: true

.github/workflows/releases.yml

@@ -1,6 +1,9 @@
 name: Wheels
 
 on:
+  release:
+    types:
+      - published
   push:
     branches: [main]
   pull_request:
@@ -64,7 +67,7 @@ jobs:
     name: Upload to PyPI
     needs: [build_artifacts, test_dist_pypi]
     runs-on: ubuntu-latest
-    if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
+    if: github.event_name == 'release'
     environment:
       name: releases
       url: https://pypi.org/p/zarr

.github/workflows/test.yml

@@ -155,14 +155,36 @@ jobs:
       run: |
         hatch run doctest:test
 
+  benchmarks:
+    name: Benchmark smoke test
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6.0.2
+      with:
+        fetch-depth: 0
+        persist-credentials: false
+    - name: Set up Python
+      uses: actions/setup-python@a309ff8b426b58ec0e2a45f0f869d46889d02405 # v6.2.0
+      with:
+        python-version: '3.13'
+        cache: 'pip'
+    - name: Install Hatch
+      uses: pypa/hatch@257e27e51a6a5616ed08a39a408a21c35c9931bc
+      with:
+        version: '1.16.5'
+    - name: Run Benchmarks
+      run: |
+        hatch env run --env "test.py3.13-minimal" run-benchmark
+
   test-complete:
     name: Test complete
 
     needs:
       [
         test,
         test-upstream-and-min-deps,
-        doctests
+        doctests,
+        benchmarks
       ]
     if: always()
     runs-on: ubuntu-latest

TEAM.md

@@ -10,6 +10,7 @@
 - @dstansby (David Stansby)
 - @dcherian (Deepak Cherian)
 - @TomAugspurger (Tom Augspurger)
+- @maxrjones (Max Jones)
 
 ## Emeritus core-developers
 - @alimanfoo (Alistair Miles)

changes/3802.feature.md

@@ -0,0 +1,16 @@
+Add support for rectilinear (variable-sized) chunk grids. This feature is experimental and
+must be explicitly enabled via ``zarr.config.set({'array.rectilinear_chunks': True})``.
+
+Rectilinear chunks can be used through:
+
+- **Creating arrays**: Pass nested sequences (e.g., ``[[10, 20, 30], [50, 50]]``) to ``chunks``
+  in ``zarr.create_array``, ``zarr.from_array``, ``zarr.zeros``, ``zarr.ones``, ``zarr.full``,
+  ``zarr.open``, and related functions, or to ``chunk_shape`` in ``zarr.create``.
+- **Opening existing arrays**: Arrays stored with the ``rectilinear`` chunk grid are read
+  transparently via ``zarr.open`` and ``zarr.open_array``.
+- **Rectilinear sharding**: Shard boundaries can be rectilinear while inner chunks remain regular.
+
+**Breaking change**: The ``validate`` method on ``BaseCodec`` and ``CodecPipeline`` now receives
+a ``ChunkGridMetadata`` instance instead of a ``ChunkGrid`` instance for the ``chunk_grid``
+parameter. Third-party codecs that override ``validate`` and inspect the chunk grid will need to
+update their type annotations. No known downstream packages were using this parameter.

ci/check_unlinked_types.py

@@ -0,0 +1,88 @@
+"""Check for unlinked type annotations in built documentation.
+
+mkdocstrings renders resolved types as <a href="..."> links and unresolved
+types as <span title="fully.qualified.Name">Name</span> without an anchor.
+This script finds all such unlinked types in the built HTML and reports them.
+
+Usage:
+    python ci/check_unlinked_types.py [site_dir]
+
+Raises ValueError if unlinked types are found.
+"""
+
+from __future__ import annotations
+
+import re
+import sys
+from pathlib import Path
+
+# Matches the griffe/mkdocstrings pattern for unlinked cross-references:
+# <span class="n"><span title="fully.qualified.Name">Name</span></span>
+UNLINKED_PATTERN = re.compile(
+    r'<span class="n"><span title="(?P<qualname>[^"]+)">(?P<name>[^<]+)</span></span>'
+)
+
+# Patterns to exclude from the report
+EXCLUDE_PATTERNS = [
+    # TypeVars and type parameters (single brackets like Foo[T])
+    re.compile(r"\[.+\]$"),
+    # Dataclass field / namedtuple field references (contain parens)
+    re.compile(r"\("),
+    # Private names
+    re.compile(r"\._"),
+    # Dunder attributes
+    re.compile(r"\.__\w+__$"),
+    # Testing utilities
+    re.compile(r"^zarr\.testing\."),
+    # Third-party types (hypothesis, pytest, etc.)
+    re.compile(r"^(hypothesis|pytest|typing_extensions|builtins|dataclasses)\."),
+]
+
+
+def should_exclude(qualname: str) -> bool:
+    return any(p.search(qualname) for p in EXCLUDE_PATTERNS)
+
+
+def find_unlinked_types(site_dir: Path) -> dict[str, set[str]]:
+    """Find all unlinked types in built HTML files.
+
+    Returns a dict mapping qualified type names to the set of pages where they appear.
+    """
+    api_dir = site_dir / "api"
+    if not api_dir.exists():
+        raise FileNotFoundError(f"{api_dir} does not exist. Run 'mkdocs build' first.")
+
+    unlinked: dict[str, set[str]] = {}
+    for html_file in api_dir.rglob("*.html"):
+        content = html_file.read_text(errors="replace")
+        rel_path = str(html_file.relative_to(site_dir))
+        for match in UNLINKED_PATTERN.finditer(content):
+            qualname = match.group("qualname")
+            if not should_exclude(qualname):
+                unlinked.setdefault(qualname, set()).add(rel_path)
+
+    return unlinked
+
+
+def main() -> None:
+    site_dir = Path(sys.argv[1]) if len(sys.argv) > 1 else Path("site")
+    unlinked = find_unlinked_types(site_dir)
+
+    if not unlinked:
+        print("No unlinked types found.")
+        return
+
+    lines = [f"Found {len(unlinked)} unlinked types:\n"]
+    for qualname in sorted(unlinked):
+        pages = sorted(unlinked[qualname])
+        lines.append(f"  {qualname}")
+        lines.extend(f"    - {page}" for page in pages)
+
+    all_pages = {p for ps in unlinked.values() for p in ps}
+    lines.append(f"\nTotal: {len(unlinked)} unlinked types across {len(all_pages)} pages")
+    report = "\n".join(lines)
+    raise ValueError(report)
+
+
+if __name__ == "__main__":
+    main()