Merge branch 'main' into contrib-docs

.github/ISSUE_TEMPLATE/bug_report.yml

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

.github/dependabot.yml

@@ -5,6 +5,10 @@ updates:
     directory: "/"
     schedule:
       interval: "daily"
+    groups:
+      requirements:
+        patterns:
+          - "*"
   - package-ecosystem: "github-actions"
     directory: "/"
     schedule:

.github/workflows/minimal.yml

@@ -15,7 +15,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Setup Miniconda
-      uses: conda-incubator/setup-miniconda@v3.0.3
+      uses: conda-incubator/setup-miniconda@v3.0.4
       with:
           channels: conda-forge
           environment-file: environment.yml

.github/workflows/python-package.yml

@@ -15,13 +15,11 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
-        numpy_version: ['>=1.22.0', '==1.21.*']
+        python-version: ['3.10', '3.11', '3.12']
+        numpy_version: ['>=2.1', '==1.24.*']
         exclude:
-          - python-version: '3.10'
-            numpy_version: '==1.21.*'
-          - python-version: '3.11'
-            numpy_version: '==1.21.*'
+          - python-version: '3.12'
+            numpy_version: '==1.24.*'
     services:
       redis:
         image: redis
@@ -42,7 +40,7 @@ jobs:
       with:
         fetch-depth: 0
     - name: Setup Miniconda
-      uses: conda-incubator/setup-miniconda@v3.0.3
+      uses: conda-incubator/setup-miniconda@v3.0.4
       with:
           channels: conda-forge
           python-version: ${{ matrix.python-version }}
@@ -52,17 +50,16 @@ jobs:
     - name: Create Conda environment with the rights deps
       shell: "bash -l {0}"
       run: |
-        conda create -n zarr-env python==${{matrix.python-version}} bsddb3 numcodecs lmdb pip nodejs flake8 mypy
+        conda create -n zarr-env python==${{matrix.python-version}} bsddb3 pip nodejs
         conda activate zarr-env
         npm install -g azurite
     - name: Install dependencies
       shell: "bash -l {0}"
       run: |
         conda activate zarr-env
         python -m pip install --upgrade pip
-        python -m pip install -U pip setuptools wheel line_profiler
-        python -m pip install -rrequirements_dev_minimal.txt numpy${{matrix.numpy_version}} -rrequirements_dev_optional.txt pymongo redis
-        python -m pip install .
+        python -m pip install -r requirements_dev_minimal.txt numpy${{matrix.numpy_version}} -r requirements_dev_optional.txt line_profiler pymongo redis
+        python -m pip install -e .
         python -m pip freeze
     - name: Tests
       shell: "bash -l {0}"
@@ -78,11 +75,8 @@ jobs:
         mkdir ~/blob_emulator
         azurite -l ~/blob_emulator --debug debug.log 2>&1 > stdouterr.log &
         pytest --cov=zarr --cov-config=pyproject.toml --doctest-plus --cov-report xml --cov=./ --timeout=300
-    - uses: codecov/codecov-action@v3
+    - uses: codecov/codecov-action@v4
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
       with:
-        token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
-          #files: ./coverage1.xml,./coverage2.xml # optional
-          #flags: unittests # optional
-          #name: codecov-umbrella # optional
-          #fail_ci_if_error: true # optional (default = false)
         verbose: true # optional (default = false)

.github/workflows/releases.yml

@@ -16,10 +16,10 @@ jobs:
           submodules: true
           fetch-depth: 0
 
-      - uses: actions/setup-python@v5.0.0
+      - uses: actions/setup-python@v5.2.0
         name: Install Python
         with:
-          python-version: '3.9'
+          python-version: '3.11'
 
       - name: Install PyBuild
         run: |
@@ -64,7 +64,7 @@ jobs:
         with:
           name: releases
           path: dist
-      - uses: pypa/gh-action-pypi-publish@v1.8.14
+      - uses: pypa/gh-action-pypi-publish@v1.10.2
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

.github/workflows/windows-testing.yml

@@ -21,7 +21,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v3.0.3
+      - uses: conda-incubator/setup-miniconda@v3.0.4
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -31,13 +31,12 @@ jobs:
       - name: Create Conda environment with the rights deps
         shell: bash -l {0}
         run: |
-          conda create -n zarr-env python==${{matrix.python-version}} numcodecs pip nodejs
+          conda create -n zarr-env python==${{matrix.python-version}} pip nodejs
       - name: Install dependencies
         shell: bash -l {0}
         run: |
           conda activate zarr-env
           python -m pip install --upgrade pip
-          python -m pip install -U pip setuptools wheel
           python -m pip install -r requirements_dev_numpy.txt -r requirements_dev_minimal.txt -r requirements_dev_optional.txt
           python -m pip install .
           python -m pip freeze

.pre-commit-config.yaml

@@ -8,23 +8,23 @@ default_language_version:
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.2.2'
+    rev: 'v0.4.4'
     hooks:
     - id: ruff
   - repo: https://github.com/psf/black
-    rev: 24.2.0
+    rev: 24.4.2
     hooks:
     - id: black
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.6
     hooks:
       - id: codespell
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     - id: check-yaml
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
+    rev: v1.10.0
     hooks:
       - id: mypy
         files: zarr

.readthedocs.yaml

@@ -3,7 +3,7 @@ version: 2
 build:
   os: ubuntu-20.04
   tools:
-    python: "3.9"
+    python: "3.11"
 
 sphinx:
   configuration: docs/conf.py

TEAM.md

@@ -7,6 +7,9 @@
 - @jakirkham (jakirkham)
 - @martindurant (Martin Durant)
 - @normanrz (Norman Rzepka)
+- @dstansby (David Stansby)
+- @dcherian (Deepak Cherian)
+- @TomAugspurger (Tom Augspurger)
 
 ## Emeritus core-developers
 - @alimanfoo (Alistair Miles)

docs/api/v3.rst

@@ -1,13 +1,12 @@
 V3 Specification Implementation(``zarr._storage.v3``)
 =====================================================
 
-This module contains the implementation of the `Zarr V3 Specification <https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html>`_.
+This module contains an experimental implementation of the `Zarr V3 Specification <https://zarr-specs.readthedocs.io/en/latest/v3/core/v3.0.html>`_.
 
 .. warning::
-    Since Zarr Python 2.12 release, this module provides experimental infrastructure for reading and
-    writing the upcoming V3 spec of the Zarr format. Users wishing to prepare for the migration can set
-    the environment variable ``ZARR_V3_EXPERIMENTAL_API=1`` to begin experimenting, however data
-    written with this API should be expected to become stale, as the implementation will still change.
+    The experimental v3 implementation included in Zarr Python >2.12,<3 is not aligned with the final
+    V3 specification. This version is deprecated and will be removed in Zarr Python 3.0 in favor of a
+    spec compliant version.
 
 The new ``zarr._store.v3`` package has the necessary classes and functions for evaluating Zarr V3.
 Since the design is not finalised, the classes and functions are not automatically imported into

docs/conf.py

@@ -16,11 +16,8 @@
 import os
 import sys
 
-# The version info for the project you're documenting, acts as replacement for
-# |version| and |release|, also used in various other places throughout the
-# built documents.
-#
-# The short X.Y version.
+from importlib.metadata import version as get_version
+
 import zarr
 
 # If extensions (or modules to document with autodoc) are in another directory,
@@ -75,9 +72,8 @@
 copyright = "2024, Zarr Developers"
 author = "Zarr Developers"
 
-version = zarr.__version__
-# The full version, including alpha/beta/rc tags.
-release = zarr.__version__
+version = get_version("zarr")
+release = get_version("zarr")
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
@@ -199,7 +195,7 @@ def setup(app):
 # html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-# html_sidebars = {}
+html_sidebars = {"tutorial": []}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.