Merge remote-tracking branch 'upstream/main' into gpu-codecs

Author: TomAugspurger

.github/ISSUE_TEMPLATE/config.yml

@@ -1,8 +1,8 @@
 blank_issues_enabled: true
 contact_links:
-  - name: Propose a new major feature
+  - name: Propose a new Zarr specification feature
     url: https://github.com/zarr-developers/zarr-specs
-    about: A new major feature should be discussed in the Zarr specifications repository.
+    about: A new feature for the Zarr storage specification should be opened on the zarr-specs repository.
   - name: Discuss something on ZulipChat
     url: https://ossci.zulipchat.com/
     about: For questions like "How do I do X with Zarr?", consider posting your question to our developer chat.

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,11 @@
+name: Feature Request
+description: Request a new feature for zarr-python
+# labels: []
+body:
+- type: textarea
+  attributes:
+    label: Describe the new feature you'd like
+    description: >
+      Please provide a description of what new feature or functionality you'd like to see in zarr-python.
+  validations:
+    required: true

.github/workflows/check_changelogs.yml

@@ -9,10 +9,10 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
 
       - name: Install uv
-        uses: astral-sh/setup-uv@b75a909f75acd358c2196fb9a5f1299a9a8868a4 # v6.7.0
+        uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7.2.0
 
       - name: Check changelog entries
         run: uv run --no-sync python ci/check_changelog_entries.py

.github/workflows/codspeed.yml

@@ -0,0 +1,41 @@
+name: CodSpeed Benchmarks
+
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    types: [labeled, synchronize]
+  # `workflow_dispatch` allows CodSpeed to trigger backtest
+  # performance analysis in order to generate initial data.
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  benchmarks:
+    name: Run benchmarks
+    runs-on: codspeed-macro
+    # Only run benchmarks for: pushes to main, manual triggers, or PRs with 'benchmark' label
+    if: |
+      github.event_name == 'push' ||
+      github.event_name == 'workflow_dispatch' ||
+      (github.event_name == 'pull_request' && contains(github.event.pull_request.labels.*.name, 'benchmark'))
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0  # grab all branches and tags
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: "3.11"
+    - name: Install Hatch
+      run: |
+        python -m pip install --upgrade pip
+        pip install hatch
+    - name: Run the benchmarks
+      uses: CodSpeedHQ/action@v4
+      with:
+          mode: walltime
+          run: hatch run test.py3.11-minimal:pytest tests/benchmarks --codspeed

.github/workflows/gpu_test.yml

@@ -19,17 +19,16 @@ concurrency:
 
 jobs:
   test:
-    name: py=${{ matrix.python-version }}, np=${{ matrix.numpy-version }}, deps=${{ matrix.dependency-set }}
+    name: py=${{ matrix.python-version }}, deps=${{ matrix.dependency-set }}
 
     runs-on: gpu-runner
     strategy:
       matrix:
         python-version: ['3.11']
-        numpy-version: ['2.2']
         dependency-set: ["minimal"]
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0  # grab all branches and tags
     # - name: cuda-toolkit
@@ -61,11 +60,11 @@ jobs:
         pip install hatch
     - name: Set Up Hatch Env
       run: |
-        hatch env create gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }}
-        hatch env run -e gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} list-env
+        hatch env create gputest.py${{ matrix.python-version }}-${{ matrix.dependency-set }}
+        hatch env run -e gputest.py${{ matrix.python-version }}-${{ matrix.dependency-set }} list-env
     - name: Run Tests
       run: |
-        hatch env run --env gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run-coverage-gpu
+        hatch env run --env gputest.py${{ matrix.python-version }}-${{ matrix.dependency-set }} run-coverage-gpu
 
     - name: Upload coverage
       uses: codecov/codecov-action@13ce06bfc6bbe3ecf90edbbf1bc32fe5978ca1d3  # v5.3.1

.github/workflows/hypothesis.yaml

@@ -24,11 +24,10 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.12']
-        numpy-version: ['2.2']
         dependency-set: ["optional"]
 
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
     - name: Set HYPOTHESIS_PROFILE based on trigger
       run: |
         if [[ "${{ github.event_name }}" == "schedule" || "${{ github.event_name }}" == "workflow_dispatch" ]]; then
@@ -47,12 +46,12 @@ jobs:
         pip install hatch
     - name: Set Up Hatch Env
       run: |
-        hatch env create test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }}
-        hatch env run -e test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} list-env
+        hatch env create test.py${{ matrix.python-version }}-${{ matrix.dependency-set }}
+        hatch env run -e test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} list-env
     # https://github.com/actions/cache/blob/main/tips-and-workarounds.md#update-a-cache
     - name: Restore cached hypothesis directory
       id: restore-hypothesis-cache
-      uses: actions/cache/restore@v4
+      uses: actions/cache/restore@v5
       with:
         path: .hypothesis/
         key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }}
@@ -64,13 +63,13 @@ jobs:
       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
+        hatch env run --env test.py${{ matrix.python-version }}-${{ matrix.dependency-set }} run-hypothesis
 
     # explicitly save the cache so it gets updated, also do this even if it fails.
     - name: Save cached hypothesis directory
       id: save-hypothesis-cache
       if: always() && steps.status.outcome != 'skipped'
-      uses: actions/cache/save@v4
+      uses: actions/cache/save@v5
       with:
         path: .hypothesis/
         key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }}

.github/workflows/issue-metrics.yml

@@ -35,7 +35,7 @@ jobs:
         SEARCH_QUERY: 'repo:zarr-developers/zarr-python is:issue created:${{ env.last_month }} -reason:"not planned"'
 
     - name: Create issue
-      uses: peter-evans/create-issue-from-file@v5
+      uses: peter-evans/create-issue-from-file@v6
       with:
         title: Monthly issue metrics report
         token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/lint.yml

@@ -0,0 +1,25 @@
+name: Lint
+
+on:
+  push:
+    branches: [main, 3.1.x]
+  pull_request:
+    branches: [main, 3.1.x]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - name: Install uv
+        uses: astral-sh/setup-uv@v7
+      - name: Install prek
+        run: uv tool install prek
+      - name: Run prek
+        run: prek run --all-files

.github/workflows/nightly_wheels.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: true
           fetch-depth: 0
@@ -31,7 +31,7 @@ jobs:
         run: hatch build
 
       - name: Upload nightly wheels
-        uses: scientific-python/upload-nightly-action@b36e8c0c10dbcfd2e05bf95f17ef8c14fd708dbf
+        uses: scientific-python/upload-nightly-action@5748273c71e2d8d3a61f3a11a16421c8954f9ecf
         with:
           artifacts_path: dist
           anaconda_nightly_upload_token: ${{ secrets.ANACONDA_ORG_UPLOAD_TOKEN }}

.github/workflows/releases.yml

@@ -11,7 +11,7 @@ jobs:
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v5
+      - uses: actions/checkout@v6
         with:
           submodules: true
           fetch-depth: 0
@@ -27,7 +27,7 @@ jobs:
           pip install hatch
       - name: Build wheel and sdist
         run: hatch build
-      - uses: actions/upload-artifact@v4
+      - uses: actions/upload-artifact@v6
         with:
           name: releases
           path: dist
@@ -36,7 +36,7 @@ jobs:
     needs: [build_artifacts]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v5
+      - uses: actions/download-artifact@v7
         with:
           name: releases
           path: dist
@@ -51,7 +51,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
     steps:
-      - uses: actions/download-artifact@v5
+      - uses: actions/download-artifact@v7
         with:
           name: releases
           path: dist