Merge branch 'main' into open-typing

Author: d-v-b

.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

@@ -64,7 +64,7 @@ jobs:
         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

@@ -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

@@ -14,14 +14,13 @@ repos:
       # Respect `exclude` and `extend-exclude` settings.
       args: ["--force-exclude"]
   - repo: https://github.com/psf/black
-    rev: 22.12.0
+    rev: 23.10.1
     hooks:
     - id: black
   - repo: https://github.com/codespell-project/codespell
     rev: v2.2.5
     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
     hooks:

CODE_OF_CONDUCT.md

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

bench/compress_normal.py

@@ -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"]
 

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

docs/contributing.rst

@@ -27,15 +27,34 @@ Enhancements
 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`.
 
@@ -48,6 +67,8 @@ 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:

docs/release.rst

@@ -480,17 +480,17 @@ Indexing with coordinate arrays
 Items from a Zarr array can be extracted by providing an integer array of
 coordinates. E.g.::
 
-    >>> z = zarr.array(np.arange(10))
+    >>> z = zarr.array(np.arange(10) ** 2)
     >>> z[:]
-    array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
-    >>> z.get_coordinate_selection([1, 4])
-    array([1, 4])
+    array([ 0,  1,  4,  9, 16, 25, 36, 49, 64, 81])
+    >>> z.get_coordinate_selection([2, 5])
+    array([ 4, 25])
 
 Coordinate arrays can also be used to update data, e.g.::
 
-    >>> z.set_coordinate_selection([1, 4], [-1, -2])
+    >>> z.set_coordinate_selection([2, 5], [-1, -2])
     >>> z[:]
-    array([ 0, -1,  2,  3, -2,  5,  6,  7,  8,  9])
+    array([ 0,  1, -1,  9, 16, -2, 36, 49, 64, 81])
 
 For multidimensional arrays, coordinates must be provided for each dimension,
 e.g.::
@@ -534,17 +534,17 @@ Indexing with a mask array
 
 Items can also be extracted by providing a Boolean mask. E.g.::
 
-    >>> z = zarr.array(np.arange(10))
+    >>> z = zarr.array(np.arange(10) ** 2)
     >>> z[:]
-    array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
+    array([ 0,  1,  4,  9, 16, 25, 36, 49, 64, 81])
     >>> sel = np.zeros_like(z, dtype=bool)
-    >>> sel[1] = True
-    >>> sel[4] = True
+    >>> sel[2] = True
+    >>> sel[5] = True
     >>> z.get_mask_selection(sel)
-    array([1, 4])
+    array([ 4, 25])
     >>> z.set_mask_selection(sel, [-1, -2])
     >>> z[:]
-    array([ 0, -1,  2,  3, -2,  5,  6,  7,  8,  9])
+    array([ 0,  1, -1,  9, 16, -2, 36, 49, 64, 81])
 
 Here's a multidimensional example::
 
@@ -986,7 +986,7 @@ It is also possible to initialize the filesystem outside of Zarr and then pass
 it through. This requires creating an :class:`zarr.storage.FSStore` object
 explicitly. For example::
 
-    >>> import s3fs  * doctest: +SKIP
+    >>> import s3fs  # doctest: +SKIP
     >>> fs = s3fs.S3FileSystem(anon=True)  # doctest: +SKIP
     >>> store = zarr.storage.FSStore('/zarr-demo/store', fs=fs)  # doctest: +SKIP
     >>> g = zarr.open_group(store)  # doctest: +SKIP

docs/tutorial.rst

@@ -45,6 +45,7 @@ jupyter = [
 ]
 docs = [
     'sphinx',
+    'sphinx-automodapi',
     'sphinx_design',
     'sphinx-issues',
     'sphinx-copybutton',
@@ -137,3 +138,8 @@ filterwarnings = [
     "ignore:PY_SSIZE_T_CLEAN will be required.*:DeprecationWarning",
     "ignore:The loop argument is deprecated since Python 3.8.*:DeprecationWarning",
 ]
+
+
+[tool.codespell]
+ignore-words-list = "ba,ihs,kake,nd,noe,nwo,te,fo,zar"
+skip = 'fixture,.git'

pyproject.toml

@@ -1,8 +1,8 @@
 # library requirements
 asciitree==0.3.3
 fasteners==0.19
-numcodecs==0.11.0
+numcodecs==0.12.1
 msgpack-python==0.5.6
 setuptools-scm==8.0.4
 # test requirements
-pytest==7.4.0
+pytest==7.4.3

requirements_dev_minimal.txt

@@ -11,13 +11,13 @@ azure-storage-blob==12.16.0 # pyup: ignore
 redis==5.0.1
 types-redis
 types-setuptools
-pymongo==4.5.0
+pymongo==4.6.1
 # optional test requirements
 coverage
 pytest-cov==4.1.0
 pytest-doctestplus==1.0.0
-pytest-timeout==2.1.0
-h5py==3.9.0
-fsspec==2023.6.0
-s3fs==2023.6.0
+pytest-timeout==2.2.0
+h5py==3.10.0
+fsspec==2023.12.1
+s3fs==2023.12.1
 moto[server]>=4.0.8

requirements_dev_optional.txt

@@ -87,7 +87,7 @@ def __init__(
                 "https://{}.blob.core.windows.net/".format(account_name),
                 container,
                 credential=account_key,
-                **blob_service_kwargs
+                **blob_service_kwargs,
             )
 
         self.client = client
@@ -240,7 +240,6 @@ def __setitem__(self, key, value):
         super().__setitem__(key, value)
 
     def rmdir(self, path=None):
-
         if not path:
             # Currently allowing clear to delete everything as in v2
 

zarr/_storage/absstore.py

@@ -222,9 +222,8 @@ def _validate_key(self, key: str):
             )
 
         if (
-            not key.startswith("data/")
-            and (not key.startswith("meta/"))
-            and (not key == "zarr.json")
+            not key.startswith(("data/", "meta/"))
+            and key != "zarr.json"
             # TODO: Possibly allow key == ".zmetadata" too if we write a
             #       consolidated metadata spec corresponding to this?
         ):
@@ -630,7 +629,6 @@ def _rmdir_from_keys(store: StoreLike, path: Optional[str] = None) -> None:
 
 
 def _rmdir_from_keys_v3(store: StoreV3, path: str = "") -> None:
-
     meta_dir = meta_root + path
     meta_dir = meta_dir.rstrip("/")
     _rmdir_from_keys(store, meta_dir)

zarr/_storage/store.py

@@ -118,7 +118,6 @@ def _get_files_and_dirs_from_path(store, path):
 
 
 class FSStoreV3(FSStore, StoreV3):
-
     # FSStoreV3 doesn't use this (FSStore uses it within _normalize_key)
     _META_KEYS = ()