Merge branch 'main' into perf-write-shard

Author: d-v-b

.github/CONTRIBUTING.md

@@ -1,4 +1,4 @@
 Contributing
 ============
 
-Please see the [project documentation](https://zarr.readthedocs.io/en/stable/contributing.html) for information about contributing to Zarr.
+Please see the [project documentation](https://zarr.readthedocs.io/en/stable/developers/contributing.html) for information about contributing to Zarr.

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -57,7 +57,22 @@ body:
     id: reproduce
     attributes:
       label: Steps to reproduce
-      description: Minimal, reproducible code sample, a copy-pastable example if possible.
+      description: Minimal, reproducible code sample. Must list dependencies in [inline script metadata](https://packaging.python.org/en/latest/specifications/inline-script-metadata/#example). When put in a file named `issue.py` calling `uv run issue.py` should show the issue.
+      value: |
+        ```python
+        # /// script
+        # requires-python = ">=3.11"
+        # dependencies = [
+        #   "zarr@git+https://github.com/zarr-developers/zarr-python.git@main",
+        # ]
+        # ///
+        #
+        # This script automatically imports the development branch of zarr to check for issues
+
+        import zarr
+        # your reproducer code
+        # zarr.print_debug_info()
+        ```
     validations:
       required: true
   - type: textarea

.github/ISSUE_TEMPLATE/release-checklist.md

@@ -0,0 +1,59 @@
+---
+name: Zarr-Python release checklist
+about: Checklist for a new Zarr-Python release. [For project maintainers only!]
+title: Release Zarr-Python vX.Y.Z
+labels: release-checklist
+assignees: ''
+
+---
+
+**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**
+
+- [ ] Priority pull request #X
+
+**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 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.
+        - Check that the expected version of Zarr-Python was tested using the `Version Info` step of the `upstream-dev` job.
+        - If testing on a branch other than `main` is needed, open a PR modifying https://github.com/pydata/xarray/blob/90ee30943aedba66a37856b2332a41264e288c20/ci/install-upstream-wheels.sh#L56 and add the `run-upstream` label.
+    - [ ] Titiler.Xarray (@maxrjones)
+        - [Modify dependencies](https://github.com/developmentseed/titiler/blob/main/src/titiler/xarray/pyproject.toml) for titiler.xarray.
+        - Modify triggers for running [the test workflow](https://github.com/developmentseed/titiler/blob/61549f2de07b20cca8fb991cfcdc89b23e18ad05/.github/workflows/ci.yml#L5-L7).
+        - Push the branch to the repository and check for the actions for any failures.
+
+**Release**:
+
+- [ ] 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.
+- [ ] Verify that release workflows succeeded.
+  - [ ] The latest version is correct on [PyPI](https://pypi.org/project/zarr/).
+  - [ ] The stable version is correct on [ReadTheDocs](https://zarr.readthedocs.io/en/stable/).
+
+**After release**:
+
+- [ ] Review and merge the pull request on the conda-forge [zarr-feedstock](https://github.com/conda-forge/zarr-feedstock) that will be automatically generated.
+
+---
+
+- [ ] Party :tada:

.github/codecov.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/check_changelogs.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:
@@ -25,11 +25,13 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.11']
-        numpy-version: ['2.1']
+        numpy-version: ['2.2']
         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/gpu_test.yml

@@ -1,11 +1,9 @@
 name: Slow Hypothesis CI
 on:
   push:
-    branches:
-      - "main"
+    branches: [main, 3.1.x]
   pull_request:
-    branches:
-      - "main"
+    branches: [main, 3.1.x]
     types: [opened, reopened, synchronize, labeled]
   schedule:
     - cron: "0 0 * * *" # Daily “At 00:00” UTC
@@ -25,14 +23,21 @@ jobs:
 
     strategy:
       matrix:
-        python-version: ['3.11']
-        numpy-version: ['2.1']
+        python-version: ['3.12']
+        numpy-version: ['2.2']
         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
+          echo "HYPOTHESIS_PROFILE=nightly" >> $GITHUB_ENV
+        else
+          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'
@@ -58,6 +63,7 @@ jobs:
       if: success()
       id: status
       run: |
+        echo "Using Hypothesis profile: $HYPOTHESIS_PROFILE"
         hatch env run --env test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run-hypothesis
 
     # explicitly save the cache so it gets updated, also do this even if it fails.
@@ -81,7 +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/hypothesis.yaml

@@ -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/needs_release_notes.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/nightly_wheels.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 }}