Merge branch 'main' into test-stateful-hierarchy

Author: dcherian

.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
@@ -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/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 ZulipChat
+  - 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
+  - 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/workflows/codeql-analysis.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: GPU Test V3
+name: GPU Test
 
 on:
   push:
-    branches: [ v3 ]
+    branches: [ main ]
   pull_request:
-    branches: [ v3 ]
+    branches: [ main ]
   workflow_dispatch:
 
 env:

.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/[email protected].2
+      - uses: pypa/[email protected].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:
@@ -21,7 +21,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.11', '3.12']
+        python-version: ['3.11', '3.12', '3.13']
         numpy-version: ['1.25', '1.26', '2.0']
         dependency-set: ["minimal", "optional"]
 

.github/workflows/test.yml

@@ -2,12 +2,12 @@ ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
   autofix_commit_msg: "style: pre-commit fixes"
   autofix_prs: false
-default_stages: [commit, push]
+default_stages: [pre-commit, pre-push]
 default_language_version:
   python: python3
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.7
+    rev: v0.6.9
     hooks:
     - id: ruff
       args: ["--fix", "--show-fixes"]
@@ -18,7 +18,7 @@ repos:
       - id: codespell
         args: ["-L", "ba,ihs,kake,nd,noe,nwo,te,fo,zar", "-S", "fixture"]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.6.0
+    rev: v5.0.0
     hooks:
     - id: check-yaml
   - repo: https://github.com/pre-commit/mirrors-mypy
@@ -31,7 +31,6 @@ repos:
           - asciitree
           - crc32c
           - donfig
-          - fasteners
           - numcodecs
           - numpy
           - typing_extensions
@@ -49,3 +48,7 @@ repos:
     hooks:
       - id: rst-directive-colons
       - id: rst-inline-touching-normal
+  - repo: https://github.com/numpy/numpydoc
+    rev: v1.8.0
+    hooks:
+      - id: numpydoc-validation

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2015-2023 Zarr Developers <https://github.com/zarr-developers>
+Copyright (c) 2015-2024 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