Merge branch 'main' into faster_delitems

Author: d-v-b

.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/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@v2.2.0
+      uses: conda-incubator/setup-miniconda@v3.0.1
       with:
           channels: conda-forge
           environment-file: environment.yml

.github/workflows/python-package.yml

@@ -15,13 +15,13 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
-        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: '==1.20.*'
+            numpy_version: '==1.21.*'
     services:
       redis:
         image: redis
@@ -38,11 +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@v2.2.0
+      uses: conda-incubator/setup-miniconda@v3.0.1
       with:
           channels: conda-forge
           python-version: ${{ matrix.python-version }}

.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@v4.6.0
+      - 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/[email protected].10
+      - uses: pypa/[email protected].11
         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', '3.11']
+        python-version: ['3.9', '3.10', '3.11']
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - uses: conda-incubator/setup-miniconda@v2.2.0
+      - uses: conda-incubator/setup-miniconda@v3.0.1
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}

.gitignore

@@ -51,6 +51,7 @@ coverage.xml
 
 # Sphinx documentation
 docs/_build/
+docs/_autoapi/
 
 # PyBuilder
 target/
@@ -77,3 +78,5 @@ zarr/version.py
 #doesnotexist
 #test_sync*
 data/*
+
+.DS_Store

.pre-commit-config.yaml

@@ -6,29 +6,25 @@ default_stages: [commit, push]
 default_language_version:
   python: python3
 repos:
-  - repo: https://github.com/charliermarsh/ruff-pre-commit
+  - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.0.224'
+    rev: 'v0.1.14'
     hooks:
     - id: ruff
-      # Respect `exclude` and `extend-exclude` settings.
-      args: ["--force-exclude"]
   - repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.12.1
     hooks:
     - id: black
-      language_version: python3.8
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.5
+    rev: v2.2.6
     hooks:
       - 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: v4.4.0
+    rev: v4.5.0
     hooks:
     - id: check-yaml
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.3.0
+    rev: v1.8.0
     hooks:
       - id: mypy
         files: zarr

.readthedocs.yaml

@@ -7,10 +7,13 @@ build:
 
 sphinx:
   configuration: docs/conf.py
+  fail_on_warning: true
 
 python:
   install:
     - method: pip
       path: .
       extra_requirements:
         - docs
+
+formats: all

CODE_OF_CONDUCT.md

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2015-2022 Zarr Developers <https://github.com/zarr-developers>
+Copyright (c) 2015-2023 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

LICENSE.txt

@@ -0,0 +1,26 @@
+## Active core-developers
+- @joshmoore (Josh Moore)
+- @jni (Juan Nunez-Iglesias)
+- @rabernat (Ryan Abernathey)
+- @jhamman (Joe Hamman)
+- @d-v-b (Davis Bennett)
+- @jakirkham (jakirkham)
+- @martindurant (Martin Durant)
+- @normanrz (Norman Rzepka)
+
+## Emeritus core-developers
+- @alimanfoo (Alistair Miles)
+- @shoyer (Stephan Hoyer)
+- @ryan-williams (Ryan Williams)
+- @jrbourbeau (James Bourbeau)
+- @mzjp2 (Zain Patel)
+- @grlee77 (Gregory Lee)
+
+## Former core-developers
+- @jeromekelleher (Jerome Kelleher)
+- @tjcrone (Tim Crone)
+- @funkey (Jan Funke)
+- @shikharsg
+- @Carreau (Matthias Bussonnier)
+- @dazzag24
+- @WardF (Ward Fisher)

TEAM.md

@@ -8,7 +8,6 @@
 from zarr import blosc
 
 if __name__ == "__main__":
-
     sys.path.insert(0, "..")
 
     # setup

bench/compress_normal.py

@@ -2,7 +2,7 @@
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    =
+SPHINXOPTS    = -W --keep-going
 SPHINXBUILD   = sphinx-build
 PAPER         =
 BUILDDIR      = _build

docs/Makefile

@@ -1,24 +1,5 @@
 The Array class (``zarr.core``)
 ===============================
-.. module:: zarr.core
 
-.. autoclass:: Array
-
-    .. automethod:: __getitem__
-    .. automethod:: __setitem__
-    .. automethod:: get_basic_selection
-    .. automethod:: set_basic_selection
-    .. automethod:: get_mask_selection
-    .. automethod:: set_mask_selection
-    .. automethod:: get_block_selection
-    .. automethod:: set_block_selection
-    .. automethod:: get_coordinate_selection
-    .. automethod:: set_coordinate_selection
-    .. automethod:: get_orthogonal_selection
-    .. automethod:: set_orthogonal_selection
-    .. automethod:: digest
-    .. automethod:: hexdigest
-    .. automethod:: resize
-    .. automethod:: append
-    .. automethod:: view
-    .. automethod:: astype
+.. automodapi:: zarr.core
+   :no-heading:

docs/api/core.rst

@@ -42,6 +42,7 @@
     "sphinx.ext.autosummary",
     "sphinx.ext.viewcode",
     "sphinx.ext.intersphinx",
+    "sphinx_automodapi.automodapi",
     "numpydoc",
     "sphinx_issues",
     "sphinx_copybutton",
@@ -52,6 +53,9 @@
 numpydoc_class_members_toctree = False
 issues_github_path = "zarr-developers/zarr-python"
 
+automodapi_inheritance_diagram = False
+automodapi_toctreedirnm = "_autoapi"
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ["_templates"]
 
@@ -68,7 +72,7 @@
 
 # General information about the project.
 project = "zarr"
-copyright = "2022, Zarr Developers"
+copyright = "2023, Zarr Developers"
 author = "Zarr Developers"
 
 version = zarr.__version__
@@ -144,6 +148,7 @@
         },
     ],
     "collapse_navigation": True,
+    "navigation_with_keys": False,
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
@@ -331,6 +336,7 @@ def setup(app):
 intersphinx_mapping = {
     "python": ("https://docs.python.org/", None),
     "numpy": ("https://numpy.org/doc/stable/", None),
+    "numcodecs": ("https://numcodecs.readthedocs.io/en/stable/", None),
 }
 
 

docs/conf.py

@@ -85,9 +85,9 @@ Creating a development environment
 To work with the Zarr source code, it is recommended to set up a Python virtual
 environment and install all Zarr dependencies using the same versions as are used by
 the core developers and continuous integration services. Assuming you have a Python
-3 interpreter already installed, and have also installed the virtualenv package, and
-you have cloned the Zarr source code and your current working directory is the root of
-the repository, you can do something like the following::
+3 interpreter already installed, and you have cloned the Zarr source code and your
+current working directory is the root of the repository, you can do something like
+the following::
 
     $ mkdir -p ~/pyenv/zarr-dev
     $ python -m venv ~/pyenv/zarr-dev