Merge branch 'main' into 3_12

.github/workflows/codeql-analysis.yml

@@ -42,7 +42,7 @@ jobs:
 
     # 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

@@ -15,7 +15,7 @@ jobs:
     steps:
     - 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

@@ -42,7 +42,7 @@ jobs:
       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

@@ -16,7 +16,7 @@ jobs:
           submodules: true
           fetch-depth: 0
 
-      - uses: actions/setup-python@v4.7.1
+      - uses: actions/setup-python@v5.0.0
         name: Install Python
         with:
           python-version: '3.9'
@@ -64,7 +64,7 @@ jobs:
         with:
           name: releases
           path: dist
-      - uses: pypa/gh-action-pypi-publish@v1.8.10
+      - uses: pypa/gh-action-pypi-publish@v1.8.11
         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@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/

.pre-commit-config.yaml

@@ -6,28 +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: 'v0.1.9'
     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
   - 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

bench/compress_normal.py

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

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/api/core.rst

@@ -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/conf.py

@@ -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"]
 
@@ -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/contributing.rst

@@ -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

docs/index.rst

@@ -19,7 +19,7 @@ Zarr-Python
 
 **Version**: |version|
 
-**Download documentation**: `Zipped HTML <https://zarr.readthedocs.io/_/downloads/en/stable/htmlzip/>`_
+**Download documentation**: `PDF/Zipped HTML/EPUB <https://readthedocs.org/projects/zarr/downloads/>`_
 
 **Useful links**:
 `Installation <installation.html>`_ |
@@ -60,6 +60,7 @@ Zarr is a file storage format for chunked, compressed, N-dimensional arrays base
         +++
 
         .. button-ref:: tutorial
+            :ref-type: ref
             :expand:
             :color: dark
             :click-parent:

docs/release.rst

@@ -18,9 +18,43 @@ Release notes
 Unreleased
 ----------
 
+Enhancements
+~~~~~~~~~~~~
+
+* Added type hints to ``zarr.creation.create()``.
+  By :user:`David Stansby <dstansby>` :issue:`1536`.
+
+Docs
+~~~~
+
+* Minor correction and changes in documentation.
+  By :user:`Sanket Verma <MSanKeys963>` :issue:`1509`.
+
+* Fix typo in documentation.
+  By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1554`
+
+* The documentation build now fails if there are any warnings.
+  By :user:`David Stansby <dstansby>` :issue:`1548`.
+
+* Add links to ``numcodecs`` docs in the tutorial.
+  By :user:`David Stansby <dstansby>` :issue:`1535`.
+
+* Enable offline formats for documentation builds.
+  By :user:`Sanket Verma <MSanKeys963>` :issue:`1551`.
+
+* Minor tweak to advanced indexing tutorial examples.
+  By :user:`Ross Barnowski <rossbar>` :issue:`1550`.
+
+
 Maintenance
 ~~~~~~~~~~~
 
+* Cache result of ``FSStore._fsspec_installed()``.
+  By :user:`Janick Martinez Esturo <ph03>` :issue:`1581`.
+
+* Extend copyright notice to 2023.
+  By :user:`Jack Kelly <JackKelly>` :issue:`1528`.
+
 * Change occurrence of ``io.open()`` into ``open()``.
   By :user:`Dimitri Papadopoulos Orfanos <DimitriPapadopoulos>` :issue:`1421`.
 
@@ -33,6 +67,10 @@ Maintenance
 * Allow ``black`` code formatter to be run with any Python version.
   By :user:`David Stansby <dstansby>` :issue:`1549`.
 
+* Remove ``sphinx-rtd-theme`` dependency from ``pyproject.toml``.
+  By :user:`Sanket Verma <MSanKeys963>` :issue:`1563`.
+
+
 .. _release_2.16.1:
 
 2.16.1
@@ -161,10 +199,12 @@ Major changes
 
 * Improve Zarr V3 support, adding partial store read/write and storage transformers.
   Add new features from the `v3 spec <https://zarr-specs.readthedocs.io/en/latest/core/v3.0.html>`_:
+
     * storage transformers
     * `get_partial_values` and `set_partial_values`
     * efficient `get_partial_values` implementation for `FSStoreV3`
     * sharding storage transformer
+
   By :user:`Jonathan Striebel <jstriebel>`; :issue:`1096`, :issue:`1111`.
 
 * N5 nows supports Blosc.