Move V3 development to main

.git-blame-ignore-revs

@@ -1,2 +1,4 @@
 # lint codebase with black and ruff
 4e348d6b80c96da461fd866576c971b8a659ba15
+# migrate from black to ruff format
+22cea005629913208a85799372e045f353744add

.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

.gitattributes

@@ -1,2 +1,3 @@
 *.py linguist-language=python
 *.ipynb linguist-documentation
+.git_archival.txt export-subst

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -1,5 +1,5 @@
-name: 🐛 File a bug report
-description: X's behavior is deviating from its documented behavior.
+name: Bug Report
+description: Report incorrect behaviour in the library.
 labels: ["bug"]
 body:
   - type: markdown

.github/ISSUE_TEMPLATE/config.yml

@@ -1,11 +1,11 @@
 blank_issues_enabled: true
 contact_links:
-  - name: ✨ Propose a new major feature
+  - name: Propose a new major feature
     url: https://github.com/zarr-developers/zarr-specs
     about: A new major feature should be discussed in the Zarr specifications repository.
-  - name: ❓ Discuss something on Zulip
+  - name: Discuss something on ZulipChat
     url: https://ossci.zulipchat.com/
-    about: For questions like "How do I do X with Zarr?", you can move to our Zulip Chat.
-  - name: ❓ Discuss something on GitHub Discussions
+    about: For questions like "How do I do X with Zarr?", you can move to our ZulipChat.
+  - name: Discuss something on GitHub Discussions
     url: https://github.com/zarr-developers/zarr-python/discussions
     about: For questions like "How do I do X with Zarr?", you can move to GitHub Discussions.

.github/ISSUE_TEMPLATE/documentation.yml

@@ -0,0 +1,18 @@
+name: Documentation Improvement
+description: Report missing or wrong documentation. Alternatively, you can just open a pull request with the suggested change.
+title: "DOC: "
+labels: [documentation, help wanted]
+
+body:
+- type: textarea
+  attributes:
+    label: Describe the issue linked to the documentation
+    description: >
+      Please provide a description of what documentation you believe needs to be fixed/improved.
+  validations:
+    required: true
+- type: textarea
+  attributes:
+    label: Suggested fix for documentation
+    description: >
+      Please explain the suggested fix and why it's better than the existing documentation.

.github/dependabot.yml

@@ -1,8 +1,28 @@
 ---
 version: 2
 updates:
+  # Updates for v3 branch (the default branch)
   - package-ecosystem: "pip"
     directory: "/"
+    schedule:
+      interval: "daily"
+    groups:
+      actions:
+        patterns:
+          - "*"
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"
+
+  # Same updates, but for main branch
+  - package-ecosystem: "pip"
+    directory: "/"
+    target-branch: "main"
     schedule:
       interval: "daily"
     groups:
@@ -11,5 +31,10 @@ updates:
           - "*"
   - package-ecosystem: "github-actions"
     directory: "/"
+    target-branch: "main"
     schedule:
       interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/workflows/gpu_test.yml

@@ -0,0 +1,66 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: GPU Test V3
+
+on:
+  push:
+    branches: [ v3 ]
+  pull_request:
+    branches: [ v3 ]
+  workflow_dispatch:
+
+env:
+  LD_LIBRARY_PATH: /usr/local/cuda/extras/CUPTI/lib64:/usr/local/cuda/lib64
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: py=${{ matrix.python-version }}, np=${{ matrix.numpy-version }}, deps=${{ matrix.dependency-set }}
+
+    runs-on: gpu-runner
+    strategy:
+      matrix:
+        python-version: ['3.11']
+        numpy-version: ['2.0']
+        dependency-set: ["minimal"]
+
+    steps:
+    - uses: actions/checkout@v4
+    # - name: cuda-toolkit
+    #   uses: Jimver/cuda-toolkit@v0.2.16
+    #   id: cuda-toolkit
+    #   with:
+    #     cuda: '12.4.1'
+    - name: Set up CUDA
+      run: |
+        wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-keyring_1.1-1_all.deb
+        sudo dpkg -i cuda-keyring_1.1-1_all.deb
+        sudo apt-get update
+        sudo apt-get -y install cuda-toolkit-12-6
+        echo "/usr/local/cuda/bin" >> $GITHUB_PATH
+    - name: GPU check
+      run: |
+        nvidia-smi
+        echo $PATH
+        echo $LD_LIBRARY_PATH
+        nvcc -V
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+    - name: Install Hatch and CuPy
+      run: |
+        python -m pip install --upgrade pip 
+        pip install hatch
+    - name: Set Up Hatch Env
+      run: |
+        hatch env create gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }}
+        hatch env run -e gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} list-env
+    - name: Run Tests
+      run: |
+        hatch env run --env gputest.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} run-coverage

.github/workflows/hypothesis.yaml

@@ -0,0 +1,84 @@
+name: Slow Hypothesis CI
+on:
+  push:
+    branches:
+      - "main"
+      - "v3"
+  pull_request:
+    branches:
+      - "main"
+      - "v3"
+    types: [opened, reopened, synchronize, labeled]
+  schedule:
+    - cron: "0 0 * * *" # Daily “At 00:00” UTC
+  workflow_dispatch: # allows you to trigger manually
+
+env:
+  FORCE_COLOR: 3
+
+jobs:
+
+  hypothesis:
+    name: Slow Hypothesis Tests
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    strategy:
+      matrix:
+        python-version: ['3.11']
+        numpy-version: ['1.26']
+        dependency-set: ["optional"]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: 'pip'
+    - name: Install Hatch
+      run: |
+        python -m pip install --upgrade pip
+        pip install hatch
+    - name: Set Up Hatch Env
+      run: |
+        hatch env create test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }}
+        hatch env run -e test.py${{ matrix.python-version }}-${{ matrix.numpy-version }}-${{ matrix.dependency-set }} list-env
+    # https://github.com/actions/cache/blob/main/tips-and-workarounds.md#update-a-cache
+    - name: Restore cached hypothesis directory
+      id: restore-hypothesis-cache
+      uses: actions/cache/restore@v4
+      with:
+        path: .hypothesis/
+        key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }}
+        restore-keys: |
+          cache-hypothesis-
+
+    - name: Run slow Hypothesis tests
+      if: success()
+      id: status
+      run: |
+        hatch env run --env test.py${{ 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.
+    - name: Save cached hypothesis directory
+      id: save-hypothesis-cache
+      if: always() && steps.status.outcome != 'skipped'
+      uses: actions/cache/save@v4
+      with:
+        path: .hypothesis/
+        key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }}
+
+    - name: Generate and publish the report
+      if: |
+        failure()
+        && steps.status.outcome == 'failure'
+        && github.event_name == 'schedule'
+        && github.repository_owner == 'zarr-developers'
+      uses: xarray-contrib/issue-from-pytest-log@v1
+      with:
+        log-path: output-${{ matrix.python-version }}-log.jsonl
+        issue-title: "Nightly Hypothesis tests failed"
+        issue-label: "topic-hypothesis"

.github/workflows/issue-metrics.yml

@@ -0,0 +1,42 @@
+name: Monthly issue metrics
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '3 2 1 * *'
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    name: issue metrics
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: read
+    steps:
+    - name: Get dates for last month
+      shell: bash
+      run: |
+        # Calculate the first day of the previous month
+        first_day=$(date -d "last month" +%Y-%m-01)
+
+        # Calculate the last day of the previous month
+        last_day=$(date -d "$first_day +1 month -1 day" +%Y-%m-%d)
+
+        #Set an environment variable with the date range
+        echo "$first_day..$last_day"
+        echo "last_month=$first_day..$last_day" >> "$GITHUB_ENV"
+
+    - name: Run issue-metrics tool
+      uses: github/issue-metrics@v3
+      env:
+        GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        SEARCH_QUERY: 'repo:zarr-developers/zarr-python is:issue created:${{ env.last_month }} -reason:"not planned"'
+
+    - name: Create issue
+      uses: peter-evans/create-issue-from-file@v5
+      with:
+        title: Monthly issue metrics report
+        token: ${{ secrets.GITHUB_TOKEN }}
+        content-filepath: ./issue_metrics.md