Merge branch 'main' into fix_1121

.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/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 }}
@@ -80,7 +80,7 @@ jobs:
  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@v4.6.0
+ - 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].7
+ - 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: ['3.10', '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

@@ -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:/PyCQA/flake8
- rev: 6.0.0
+ - repo: https:/astral-sh/ruff-pre-commit
+ # Ruff version.
+ rev: 'v0.1.14'
  hooks:
- - id: flake8
- args: [
- --max-line-length=100
- ]
- exclude: ^(venv/|docs/)
- types: ['python']
+ - id: ruff
+ - repo: https:/psf/black
+ rev: 23.12.1
+ hooks:
+ - id: black
  - repo: https:/codespell-project/codespell
- rev: v2.2.5
+ rev: v2.2.6
  hooks:
  - id: codespell
- args: ["-L", "ba,ihs,kake,nd,noe,nwo,te,fo", "-S", "fixture"]
  - repo: https:/pre-commit/pre-commit-hooks
- rev: v4.4.0
+ rev: v4.5.0
  hooks:
  - id: check-yaml
  - repo: https:/pre-commit/mirrors-mypy
- rev: v1.3.0
+ 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 +7,13 @@ build:
 
 sphinx:
  configuration: docs/conf.py
+ fail_on_warning: true
 
 python:
  install:
- - requirements: requirements_rtfd.txt
  - method: pip
  path: .
+ extra_requirements:
+ - docs
+
+formats: all

LICENSE.txt

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

TEAM.md

@@ -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)

bench/compress_normal.py

@@ -8,37 +8,39 @@
 from zarr import blosc
 
 if __name__ == "__main__":
-
- sys.path.insert(0, '..')
+ sys.path.insert(0, "..")
 
  # setup
- a = np.random.normal(2000, 1000, size=200000000).astype('u2')
- z = zarr.empty_like(a, chunks=1000000,
- compression='blosc',
- compression_opts=dict(cname='lz4', clevel=5, shuffle=2))
+ a = np.random.normal(2000, 1000, size=200000000).astype("u2")
+ z = zarr.empty_like(
+ a,
+ chunks=1000000,
+ compression="blosc",
+ compression_opts=dict(cname="lz4", clevel=5, shuffle=2),
+ )
  print(z)
 
- print('*' * 79)
+ print("*" * 79)
 
  # time
- t = timeit.repeat('z[:] = a', repeat=10, number=1, globals=globals())
+ t = timeit.repeat("z[:] = a", repeat=10, number=1, globals=globals())
  print(t)
  print(min(t))
  print(z)
 
  # profile
  profile = line_profiler.LineProfiler(blosc.compress)
- profile.run('z[:] = a')
+ profile.run("z[:] = a")
  profile.print_stats()
 
- print('*' * 79)
+ print("*" * 79)
 
  # time
- t = timeit.repeat('z[:]', repeat=10, number=1, globals=globals())
+ t = timeit.repeat("z[:]", repeat=10, number=1, globals=globals())
  print(t)
  print(min(t))
 
  # profile
  profile = line_profiler.LineProfiler(blosc.decompress)
- profile.run('z[:]')
+ profile.run("z[:]")
  profile.print_stats()

docs/Makefile

@@ -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/_static/custom.css

@@ -120,4 +120,4 @@ html[data-theme=dark] h1 {
 
 html[data-theme=dark] h3 {
  color: #0a6774;
-}
+}

docs/acknowledgments.rst

@@ -73,4 +73,4 @@ documentation, code reviews, comments and/or ideas:
 * :user:`gsakkis`
 * :user:`hailiangzhang <hailiangzhang>`
 * :user:`pmav99 <pmav99>`
-* :user:`sbalmer <sbalmer>`
+* :user:`sbalmer <sbalmer>`