Merge branch 'main' into shards-multiprocessing

Author: d-v-b

.github/ISSUE_TEMPLATE/release-checklist.md

@@ -7,7 +7,7 @@ assignees: ''
 
 ---
 
-**Release**: [v0.x.x](https://github.com/zarr-developers/zarr-python/milestones/?)
+**Release**: [v3.x.x](https://github.com/zarr-developers/zarr-python/milestones/?)
 **Scheduled Date**: 20YY/MM/DD
 
 **Priority PRs/issues to complete prior to release**
@@ -16,15 +16,17 @@ assignees: ''
 
 **Before release**:
 
+- [ ] Make sure the release branch (e.g., `3.1.x`) is up to date with any backports.
 - [ ] Make sure that all pull requests which will be included in the release have been properly documented as changelog files in the [`changes/` directory](https://github.com/zarr-developers/zarr-python/tree/main/changes).
-- [ ] Run ``towncrier build --version x.y.z`` to create the changelog, and commit the result to the main branch.
+- [ ] Run ``towncrier build --version x.y.z`` to create the changelog, and commit the result to the release branch.
 - [ ] Check [SPEC 0](https://scientific-python.org/specs/spec-0000/#support-window) to see if the minimum supported version of Python or NumPy needs bumping.
 - [ ] Check to ensure that:
   - [ ] Deprecated workarounds/codes/tests are removed. Run `grep "# TODO" **/*.py` to find all potential TODOs.
   - [ ] All tests pass in the ["Tests" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/test.yml).
   - [ ] All tests pass in the ["GPU Tests" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/gpu_test.yml).
   - [ ] All tests pass in the ["Hypothesis" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/hypothesis.yaml).
   - [ ] Check that downstream libraries work well (maintainers can make executive decisions about whether all checks are required for this release).
+    - [ ] numcodecs
     - [ ] Xarray (@jhamman @dcherian @TomNicholas)
         - Zarr's upstream compatibility is tested via the [Upstream Dev CI worklow](https://github.com/pydata/xarray/actions/workflows/upstream-dev-ci.yaml).
         - Click on the most recent workflow and check that the `upstream-dev` job has run and passed. `upstream-dev` is not run on all all workflow runs.
@@ -40,6 +42,7 @@ assignees: ''
 - [ ] Go to https://github.com/zarr-developers/zarr-python/releases.
   - [ ] Click "Draft a new release".
   - [ ] Choose a version number prefixed with a `v` (e.g. `v0.0.0`). For pre-releases, include the appropriate suffix (e.g. `v0.0.0a1` or `v0.0.0rc2`).
+  - [ ] Set the target branch to the release branch (e.g., `3.1.x`)
   - [ ] Set the description of the release to: `See release notes https://zarr.readthedocs.io/en/stable/release-notes.html#release-0-0-0`, replacing the correct version numbers. For pre-release versions, the URL should omit the pre-release suffix, e.g. "a1" or "rc1".
   - [ ] Click on "Generate release notes" to auto-fill the description.
   - [ ] Make a release by clicking the 'Publish Release' button, this will automatically create a tag too.

.github/workflows/check_changelogs.yml

@@ -0,0 +1,18 @@
+name: Check changelog entries
+
+on:
+  pull_request:
+
+jobs:
+  check-changelogs:
+    name: Check changelog entries
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@b75a909f75acd358c2196fb9a5f1299a9a8868a4 # v6.7.0
+
+      - name: Check changelog entries
+        run: uv run --no-sync python ci/check_changelog_entries.py

.github/workflows/gpu_test.yml

@@ -5,9 +5,9 @@ name: GPU Test
 
 on:
   push:
-    branches: [ main ]
+    branches: [ main, 3.1.x ]
   pull_request:
-    branches: [ main ]
+    branches: [ main, 3.1.x ]
   workflow_dispatch:
 
 env:
@@ -29,7 +29,9 @@ jobs:
         dependency-set: ["minimal"]
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
+      with:
+        fetch-depth: 0  # grab all branches and tags
     # - name: cuda-toolkit
     #   uses: Jimver/[email protected]
     #   id: cuda-toolkit
@@ -49,7 +51,7 @@ jobs:
         echo $LD_LIBRARY_PATH
         nvcc -V
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
@@ -63,7 +65,7 @@ jobs:
         hatch env run -e gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} list-env
     - name: Run Tests
       run: |
-        hatch env run --env gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run-coverage
+        hatch env run --env gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run-coverage-gpu
 
     - name: Upload coverage
       uses: codecov/codecov-action@13ce06bfc6bbe3ecf90edbbf1bc32fe5978ca1d3  # v5.3.1

.github/workflows/hypothesis.yaml

@@ -1,9 +1,9 @@
 name: Slow Hypothesis CI
 on:
   push:
-    branches: [main, 3.0.x]
+    branches: [main, 3.1.x]
   pull_request:
-    branches: [main, 3.0.x]
+    branches: [main, 3.1.x]
     types: [opened, reopened, synchronize, labeled]
   schedule:
     - cron: "0 0 * * *" # Daily “At 00:00” UTC
@@ -28,7 +28,7 @@ jobs:
         dependency-set: ["optional"]
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
     - name: Set HYPOTHESIS_PROFILE based on trigger
       run: |
         if [[ "${{ github.event_name }}" == "schedule" || "${{ github.event_name }}" == "workflow_dispatch" ]]; then
@@ -37,7 +37,7 @@ jobs:
           echo "HYPOTHESIS_PROFILE=ci" >> $GITHUB_ENV
         fi
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
@@ -87,7 +87,7 @@ jobs:
         && steps.status.outcome == 'failure'
         && github.event_name == 'schedule'
         && github.repository_owner == 'zarr-developers'
-      uses: xarray-contrib/issue-from-pytest-log@v1
+      uses: scientific-python/issue-from-pytest-log-action@v1
       with:
         log-path: output-${{ matrix.python-version }}-log.jsonl
         issue-title: "Nightly Hypothesis tests failed"

.github/workflows/needs_release_notes.yml

@@ -11,7 +11,7 @@ jobs:
       pull-requests: write
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/labeler@8558fd74291d67161a8a78ce36a881fa63b766a9  # v5.0.0
+    - uses: actions/labeler@634933edcd8ababfe52f92936142cc22ac488b1b  # v6.0.1
       with:
         repo-token: ${{ secrets.GITHUB_TOKEN }}
         sync-labels: true

.github/workflows/nightly_wheels.yml

@@ -0,0 +1,37 @@
+name: Nightly Wheels
+
+on:
+  schedule:
+    # Run nightly at 2 AM UTC
+    - cron: '0 2 * * *'
+  workflow_dispatch:
+
+jobs:
+  build_and_upload_nightly:
+    name: Build and upload nightly wheels
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v5
+        with:
+          submodules: true
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v6
+        name: Install Python
+        with:
+          python-version: '3.13'
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install hatch
+
+      - name: Build wheel and sdist
+        run: hatch build
+
+      - name: Upload nightly wheels
+        uses: scientific-python/upload-nightly-action@b36e8c0c10dbcfd2e05bf95f17ef8c14fd708dbf
+        with:
+          artifacts_path: dist
+          anaconda_nightly_upload_token: ${{ secrets.ANACONDA_ORG_UPLOAD_TOKEN }}

.github/workflows/releases.yml

@@ -11,12 +11,12 @@ jobs:
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           submodules: true
           fetch-depth: 0
 
-      - uses: actions/setup-python@v5.2.0
+      - uses: actions/setup-python@v6
         name: Install Python
         with:
           python-version: '3.11'
@@ -36,7 +36,7 @@ jobs:
     needs: [build_artifacts]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v5
         with:
           name: releases
           path: dist
@@ -51,11 +51,11 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
     steps:
-      - uses: actions/download-artifact@v4
+      - uses: actions/download-artifact@v5
         with:
           name: releases
           path: dist
-      - uses: pypa/gh-action-pypi-publish@v1.12.4
+      - uses: pypa/gh-action-pypi-publish@v1.13.0
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

.github/workflows/test.yml

@@ -5,9 +5,9 @@ name: Test
 
 on:
   push:
-    branches: [ main, 3.0.x ]
+    branches: [ main, 3.1.x ]
   pull_request:
-    branches: [ main, 3.0.x ]
+    branches: [ main, 3.1.x ]
   workflow_dispatch:
 
 concurrency:
@@ -21,20 +21,20 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.11', '3.12', '3.13']
-        numpy-version: ['1.25', '2.2']
+        numpy-version: ['1.26', '2.2']
         dependency-set: ["minimal", "optional"]
         os: ["ubuntu-latest"]
         include:
           - python-version: '3.11'
-            numpy-version: '1.25'
+            numpy-version: '1.26'
             dependency-set: 'optional'
             os: 'macos-latest'
           - python-version: '3.13'
             numpy-version: '2.2'
             dependency-set: 'optional'
             os: 'macos-latest'
           - python-version: '3.11'
-            numpy-version: '1.25'
+            numpy-version: '1.26'
             dependency-set: 'optional'
             os: 'windows-latest'
           - python-version: '3.13'
@@ -44,11 +44,11 @@ jobs:
     runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0  # grab all branches and tags
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
@@ -86,11 +86,11 @@ jobs:
           - python-version: "3.11"
             dependency-set: upstream
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: ${{ matrix.python-version }}
         cache: 'pip'
@@ -115,11 +115,11 @@ jobs:
     name: doctests
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0 # required for hatch version discovery, which is needed for numcodecs.zarr3
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
       with:
         python-version: '3.13'
         cache: 'pip'

.pre-commit-config.yaml

@@ -6,7 +6,7 @@ ci:
 default_stages: [pre-commit, pre-push]
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.2
+    rev: v0.12.11
     hooks:
       - id: ruff-check
         args: ["--fix", "--show-fixes"]
@@ -17,12 +17,12 @@ repos:
       - id: codespell
         args: ["-L", "fo,ihs,kake,te", "-S", "fixture"]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
       - id: trailing-whitespace
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.16.1
+    rev: v1.17.1
     hooks:
       - id: mypy
         files: src|tests
@@ -49,10 +49,10 @@ repos:
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
   - repo: https://github.com/numpy/numpydoc
-    rev: v1.8.0
+    rev: v1.9.0
     hooks:
       - id: numpydoc-validation
   - repo: https://github.com/twisted/towncrier
-    rev: 24.8.0
+    rev: 25.8.0
     hooks:
       - id: towncrier-check

LICENSE.txt

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2015-2024 Zarr Developers <https://github.com/zarr-developers>
+Copyright (c) 2015-2025 Zarr Developers <https://github.com/zarr-developers>
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal