Merge branch 'main' into i-am-emmanuel-zipstore-delitem

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+max-line-length = 100

.git-blame-ignore-revs

@@ -0,0 +1,2 @@
+# lint codebase with black and ruff
+4e348d6b80c96da461fd866576c971b8a659ba15

.github/ISSUE_TEMPLATE/bug_report.yml

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

.github/ISSUE_TEMPLATE/config.yml

@@ -3,9 +3,9 @@ contact_links:
   - 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 Zulip
+    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
     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/labeler.yml

@@ -0,0 +1,2 @@
+needs release notes:
+- all: ['!docs/release.rst']

.github/workflows/codeql-analysis.yml

@@ -38,11 +38,11 @@ jobs:
 
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         # If you wish to specify custom queries, you can do so here or in a config file.
@@ -56,7 +56,7 @@ jobs:
     # Autobuild attempts to build any compiled languages  (C/C++, C#, or Java).
     # If this step fails, then you should remove it and run the build manually (see below)
     - name: Autobuild
-      uses: github/codeql-action/autobuild@v2
+      uses: github/codeql-action/autobuild@v3
 
     # ℹ️ Command-line programs to run using the OS shell.
     # 📚 See https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsrun
@@ -69,4 +69,4 @@ jobs:
     #   ./location_of_script_within_repo/buildscript.sh
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3

.github/workflows/minimal.yml

@@ -13,9 +13,9 @@ jobs:
 
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Setup Miniconda
-      uses: conda-incubator/setup-miniconda@v2
+      uses: conda-incubator/setup-miniconda@v3.0.3
       with:
           channels: conda-forge
           environment-file: environment.yml
@@ -24,6 +24,7 @@ jobs:
       shell: "bash -l {0}"
       env:
         ZARR_V3_EXPERIMENTAL_API: 1
+        ZARR_V3_SHARDING: 1
       run: |
         conda activate minimal
         python -m pip install .
@@ -32,6 +33,7 @@ jobs:
       shell: "bash -l {0}"
       env:
         ZARR_V3_EXPERIMENTAL_API: 1
+        ZARR_V3_SHARDING: 1
       run: |
         conda activate minimal
         rm -rf fixture/

.github/workflows/needs_release_notes.yml

@@ -0,0 +1,14 @@
+name: "Pull Request Labeler"
+
+on:
+  - pull_request_target
+
+jobs:
+  triage:
+    if: ${{ github.event.pull_request.user.login != 'dependabot[bot]' }} && ${{ github.event.pull_request.user.login != 'pre-commit-ci[bot]' }}
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/labeler@main
+      with:
+        repo-token: ${{ secrets.GITHUB_TOKEN }}
+        sync-labels: true

.github/workflows/python-package.yml

@@ -15,11 +15,13 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
-        numpy_version: ['>=1.22.0', '==1.20.*']
+        python-version: ['3.9', '3.10', '3.11']
+        numpy_version: ['>=1.22.0', '==1.21.*']
         exclude:
           - python-version: '3.10'
-            numpy_version: '==1.20.*'
+            numpy_version: '==1.21.*'
+          - python-version: '3.11'
+            numpy_version: '==1.21.*'
     services:
       redis:
         image: redis
@@ -36,11 +38,11 @@ jobs:
         ports:
           - 27017:27017
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         fetch-depth: 0
     - name: Setup Miniconda
-      uses: conda-incubator/setup-miniconda@master
+      uses: conda-incubator/setup-miniconda@v3.0.3
       with:
           channels: conda-forge
           python-version: ${{ matrix.python-version }}
@@ -58,7 +60,7 @@ jobs:
       run: |
         conda activate zarr-env
         python -m pip install --upgrade pip
-        python -m pip install -U pip setuptools wheel codecov line_profiler
+        python -m pip install -U pip setuptools wheel line_profiler
         python -m pip install -rrequirements_dev_minimal.txt numpy${{matrix.numpy_version}} -rrequirements_dev_optional.txt pymongo redis
         python -m pip install .
         python -m pip freeze
@@ -70,14 +72,15 @@ jobs:
         ZARR_TEST_MONGO: 1
         ZARR_TEST_REDIS: 1
         ZARR_V3_EXPERIMENTAL_API: 1
+        ZARR_V3_SHARDING: 1
       run: |
         conda activate zarr-env
         mkdir ~/blob_emulator
         azurite -l ~/blob_emulator --debug debug.log 2>&1 > stdouterr.log &
-        pytest --cov=zarr --cov-config=.coveragerc --doctest-plus --cov-report xml --cov=./ --timeout=300
+        pytest --cov=zarr --cov-config=pyproject.toml --doctest-plus --cov-report xml --cov=./ --timeout=300
     - uses: codecov/codecov-action@v3
       with:
-        #token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
+        token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
           #files: ./coverage1.xml,./coverage2.xml # optional
           #flags: unittests # optional
           #name: codecov-umbrella # optional

.github/workflows/releases.yml

@@ -11,15 +11,15 @@ jobs:
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
           fetch-depth: 0
 
-      - uses: actions/setup-python@v4.3.0
+      - uses: actions/setup-python@v5.0.0
         name: Install Python
         with:
-          python-version: '3.8'
+          python-version: '3.9'
 
       - name: Install PyBuild
         run: |
@@ -36,7 +36,7 @@ jobs:
           else
             echo "All seem good"
           fi
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
           name: releases
           path: dist
@@ -45,7 +45,7 @@ jobs:
     needs: [build_artifacts]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: releases
           path: dist
@@ -60,11 +60,11 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: releases
           path: dist
-      - uses: pypa/gh-action-pypi-publish@v1
+      - uses: pypa/gh-action-pypi-publish@v1.8.14
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

.github/workflows/windows-testing.yml

@@ -16,12 +16,12 @@ jobs:
     strategy:
       fail-fast: True
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        python-version: ['3.10', '3.11']
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: conda-incubator/setup-miniconda@v3.0.3
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -52,6 +52,7 @@ jobs:
         env:
           ZARR_TEST_ABS: 1
           ZARR_V3_EXPERIMENTAL_API: 1
+          ZARR_V3_SHARDING: 1
       - name: Conda info
         shell: bash -l {0}
         run: conda info

.gitignore

@@ -8,6 +8,7 @@ __pycache__/
 # Distribution / packaging
 .Python
 env/
+.venv/
 build/
 develop-eggs/
 dist/
@@ -50,6 +51,7 @@ coverage.xml
 
 # Sphinx documentation
 docs/_build/
+docs/_autoapi/
 
 # PyBuilder
 target/
@@ -76,3 +78,5 @@ zarr/version.py
 #doesnotexist
 #test_sync*
 data/*
+
+.DS_Store

.pre-commit-config.yaml

@@ -1,30 +1,30 @@
 ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
   autofix_commit_msg: "style: pre-commit fixes"
+  autofix_prs: false
 default_stages: [commit, push]
 default_language_version:
   python: python3
 repos:
-  - repo: https://github.com/PyCQA/flake8
-    rev: 5.0.4
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: 'v0.2.2'
     hooks:
-    - id: flake8
-      args: [
-        --max-line-length=100
-      ]
-      exclude: ^(venv/|docs/)
-      types: ['python']
+    - id: ruff
+  - repo: https://github.com/psf/black
+    rev: 24.2.0
+    hooks:
+    - id: black
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.2
+    rev: v2.2.6
     hooks:
       - id: codespell
-        args: ["-L", "ba,ihs,kake,nd,noe,nwo,te", "-S", "fixture"]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.5.0
     hooks:
     - id: check-yaml
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.982
+    rev: v1.8.0
     hooks:
       - id: mypy
         files: zarr

.pyup.yml

@@ -13,6 +13,3 @@ requirements:
   - requirements_dev_optional.txt:
       pin: True
       update: all
-  - requirements_rtfd.txt:
-      pin: False
-      update: False

.readthedocs.yaml

@@ -7,9 +7,15 @@ build:
 
 sphinx:
   configuration: docs/conf.py
+  fail_on_warning: true
 
 python:
   install:
-    - requirements: requirements_rtfd.txt
     - method: pip
       path: .
+      extra_requirements:
+        - docs
+
+formats:
+  - htmlzip
+  - pdf

LICENSE → LICENSE.txt

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2015-2022 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