merge

Author: normanrz

.deepsource.toml

@@ -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
@@ -27,7 +27,7 @@ body:
     attributes:
       label: Python Version
       description: Version of Python interpreter
-      placeholder: 3.8.5, 3.9, 3.10, etc.
+      placeholder: 3.10, 3.11, 3.12 etc.
     validations:
       required: true
   - type: input

.github/ISSUE_TEMPLATE/bug_report.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 gitter
-    url: https://gitter.im/zarr-developers/community
-    about: For questions like "How do I do X with Zarr?", you can move to our Gitter channel.
-  - name: ❓ Discuss something on GitHub Discussions
+  - 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 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/config.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/ISSUE_TEMPLATE/documentation.yml

@@ -1,6 +1,7 @@
 ---
 version: 2
 updates:
+  # Updates for v3 branch (the default branch)
   - package-ecosystem: "pip"
     directory: "/"
     schedule:
@@ -17,3 +18,23 @@ updates:
       actions:
         patterns:
           - "*"
+
+  # Same updates, but for main branch
+  - package-ecosystem: "pip"
+    directory: "/"
+    target-branch: "main"
+    schedule:
+      interval: "daily"
+    groups:
+      requirements:
+        patterns:
+          - "*"
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    target-branch: "main"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/dependabot.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
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  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/[email protected]
+    #   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/gpu_test.yml

@@ -3,11 +3,9 @@ on:
   push:
     branches:
       - "main"
-      - "v3"
   pull_request:
     branches:
       - "main"
-      - "v3"
     types: [opened, reopened, synchronize, labeled]
   schedule:
     - cron: "0 0 * * *" # Daily “At 00:00” UTC

.github/workflows/hypothesis.yaml

@@ -16,7 +16,7 @@ jobs:
           submodules: true
           fetch-depth: 0
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v5.2.0
         name: Install Python
         with:
           python-version: '3.11'
@@ -55,7 +55,7 @@ jobs:
         with:
           name: releases
           path: dist
-      - uses: pypa/gh-action-pypi-publish@v1.9.0
+      - uses: pypa/gh-action-pypi-publish@v1.10.3
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

.github/workflows/releases.yml

@@ -1,13 +1,13 @@
 # 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: Test V3
+name: Test
 
 on:
   push:
-    branches: [ v3 ]
+    branches: [ main ]
   pull_request:
-    branches: [ v3 ]
+    branches: [ main ]
   workflow_dispatch:
 
 concurrency:
@@ -21,8 +21,8 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.10', '3.11', '3.12']
-        numpy-version: ['1.24', '1.26', '2.0']
+        python-version: ['3.11', '3.12', '3.13']
+        numpy-version: ['1.25', '1.26', '2.0']
         dependency-set: ["minimal", "optional"]
 
     steps:

.github/workflows/test.yml

@@ -51,6 +51,7 @@ coverage.xml
 
 # Sphinx documentation
 docs/_build/
+docs/_autoapi
 
 # PyBuilder
 target/
@@ -83,3 +84,5 @@ fixture/
 .DS_Store
 tests/.hypothesis
 .hypothesis/
+
+zarr/version.py