Merge branch 'main' into string-arguments-for-codecs

Author: brokkoli71

.github/workflows/gpu_test.yml

@@ -25,7 +25,7 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.11']
-        numpy-version: ['2.1']
+        numpy-version: ['2.2']
         dependency-set: ["minimal"]
 
     steps:

.github/workflows/hypothesis.yaml

@@ -26,7 +26,7 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.11']
-        numpy-version: ['2.1']
+        numpy-version: ['2.2']
         dependency-set: ["optional"]
 
     steps:

.github/workflows/test.yml

@@ -21,7 +21,7 @@ jobs:
     strategy:
       matrix:
         python-version: ['3.11', '3.12', '3.13']
-        numpy-version: ['1.25', '2.1']
+        numpy-version: ['1.25', '2.2']
         dependency-set: ["minimal", "optional"]
         os: ["ubuntu-latest"]
         include:
@@ -30,15 +30,15 @@ jobs:
             dependency-set: 'optional'
             os: 'macos-latest'
           - python-version: '3.13'
-            numpy-version: '2.1'
+            numpy-version: '2.2'
             dependency-set: 'optional'
             os: 'macos-latest'
           - python-version: '3.11'
             numpy-version: '1.25'
             dependency-set: 'optional'
             os: 'windows-latest'
           - python-version: '3.13'
-            numpy-version: '2.1'
+            numpy-version: '2.2'
             dependency-set: 'optional'
             os: 'windows-latest'
     runs-on: ${{ matrix.os }}

changes/2921.bugfix.rst

@@ -0,0 +1 @@
+Ignore stale child metadata when reconsolidating metadata.

changes/3066.feature.rst

@@ -0,0 +1 @@
+Added `~zarr.errors.GroupNotFoundError`, which is raised when attempting to open a group that does not exist.

changes/3100.bugfix.rst

@@ -0,0 +1,3 @@
+For Zarr format 2, allow fixed-length string arrays to be created without automatically inserting a
+``Vlen-UT8`` codec in the array of filters. Fixed-length string arrays do not need this codec. This
+change fixes a regression where fixed-length string arrays created with Zarr Python 3 could not be read with Zarr Python 2.18.

changes/3103.bugfix.rst

@@ -0,0 +1,7 @@
+When creating arrays without explicitly specifying a chunk size using `zarr.create` and other
+array creation routines, the chunk size will now set automatically instead of defaulting to the data shape.
+For large arrays this will result in smaller default chunk sizes.
+To retain previous behaviour, explicitly set the chunk shape to the data shape.
+
+This fix matches the existing chunking behaviour of
+`zarr.save_array` and `zarr.api.asynchronous.AsyncArray.create`.

docs/conf.py

@@ -105,7 +105,8 @@ def skip_submodules(
      "roadmap": "developers/roadmap.html",
      "installation": "user-guide/installation.html",
      "api": "api/zarr/index",
-     "release": "release-notes"
+     "release": "release-notes.html",
+     "release-notes": "release-notes.html"
 }
 
 # The language for content autogenerated by Sphinx. Refer to documentation

docs/developers/contributing.rst

@@ -251,14 +251,11 @@ See the `towncrier`_ docs for more.
 
 .. _towncrier: https://towncrier.readthedocs.io/en/stable/tutorial.html
 
-Development best practices, policies and procedures
----------------------------------------------------
-
 The following information is mainly for core developers, but may also be of interest to
 contributors.
 
 Merging pull requests
-~~~~~~~~~~~~~~~~~~~~~
+---------------------
 
 Pull requests submitted by an external contributor should be reviewed and approved by at least
 one core developer before being merged. Ideally, pull requests submitted by a core developer
@@ -268,10 +265,10 @@ Pull requests should not be merged until all CI checks have passed (GitHub Actio
 Codecov) against code that has had the latest main merged in.
 
 Compatibility and versioning policies
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+-------------------------------------
 
 Versioning
-""""""""""
+~~~~~~~~~~
 Versions of this library are identified by a triplet of integers with the form
 ``<major>.<minor>.<patch>``, for example ``3.0.4``. A release of ``zarr-python`` is associated with a new
 version identifier. That new identifier is generated by incrementing exactly one of the components of
@@ -323,7 +320,7 @@ backwards-compatible changes wherever possible. When a backwards-incompatible ch
 users should be notified well in advance, e.g. via informative deprecation warnings.
 
 Data format compatibility
-^^^^^^^^^^^^^^^^^^^^^^^^^
+"""""""""""""""""""""""""
 
 The Zarr library is an implementation of a file format standard defined externally --
 see the `Zarr specifications website <https://zarr-specs.readthedocs.io>`_ for the list of
@@ -340,36 +337,28 @@ breaking changes may be more frequent than usual.
 
 
 Release procedure
-~~~~~~~~~~~~~~~~~
-
-.. note::
-
-   Most of the release process is now handled by GitHub workflow which should
-   automatically push a release to PyPI if a tag is pushed.
+-----------------
 
 Pre-release
-"""""""""""
+~~~~~~~~~~~
 1. Make sure that all pull requests which will be included in the release
-   have been properly documented as changelog files in :file:`changes`.
-2. Run ``towncrier build --version x.y.z`` to create the changelog.
+   have been properly documented as changelog files in the :file:`changes/` directory.
+2. Run ``towncrier build --version x.y.z`` to create the changelog, and commit the result
+   to the main branch.
 
 Releasing
-"""""""""
-To make a new release, go to
-https://github.com/zarr-developers/zarr-python/releases and
-click "Draft a new release". Choose a version number prefixed
-with a `v` (e.g. `v0.0.0`). For pre-releases, include the
-appropriate suffix (e.g. `v0.0.0a1` or `v0.0.0rc2`).
-
-
-Set the description of the release to::
+~~~~~~~~~
+1. Go to https://github.com/zarr-developers/zarr-python/releases
+2. Click "Draft a new release".
+3. Choose a version number prefixed with a `v` (e.g. `v0.0.0`).
+   For pre-releases, include the appropriate suffix (e.g. `v0.0.0a1` or `v0.0.0rc2`).
+4. Set the description of the release to::
 
     See release notes https://zarr.readthedocs.io/en/stable/release-notes.html#release-0-0-0
 
-replacing the correct version numbers. For pre-release versions,
-the URL should omit the pre-release suffix, e.g. "a1" or "rc1".
-
-Click on "Generate release notes" to auto-file the description.
+   replacing the correct version numbers. For pre-release versions,
+   the URL should omit the pre-release suffix, e.g. "a1" or "rc1".
+5. Click on "Generate release notes" to auto-fill the description.
 
 After creating the release, the documentation will be built on
 https://readthedocs.io. Full releases will be available under
@@ -378,9 +367,8 @@ pre-releases will be available under
 `/latest <https://zarr.readthedocs.io/en/latest>`_.
 
 Post-release
-""""""""""""
+~~~~~~~~~~~~
 
 - Review and merge the pull request on the
   `conda-forge feedstock <https://github.com/conda-forge/zarr-feedstock>`_ that will be
   automatically generated.
-- Create a new "Unreleased" section in the release notes

pyproject.toml

@@ -72,7 +72,8 @@ gpu = [
 # Development extras
 test = [
     "coverage",
-    "pytest",
+    # Pin possibly due to https://github.com/pytest-dev/pytest-cov/issues/693
+    "pytest<8.4",
     "pytest-asyncio",
     "pytest-cov",
     "pytest-accept",
@@ -111,7 +112,7 @@ docs = [
 
 [project.urls]
 "Bug Tracker" = "https://github.com/zarr-developers/zarr-python/issues"
-Changelog = "https://zarr.readthedocs.io/en/stable/release.html"
+Changelog = "https://zarr.readthedocs.io/en/stable/release-notes.html"
 Discussions = "https://github.com/zarr-developers/zarr-python/discussions"
 Documentation = "https://zarr.readthedocs.io/"
 Homepage = "https://github.com/zarr-developers/zarr-python"
@@ -149,7 +150,7 @@ features = ["test"]
 
 [[tool.hatch.envs.test.matrix]]
 python = ["3.11", "3.12", "3.13"]
-numpy = ["1.25", "2.1"]
+numpy = ["1.25", "2.2"]
 deps = ["minimal", "optional"]
 
 [tool.hatch.envs.test.overrides]
@@ -185,7 +186,7 @@ features = ["test", "gpu"]
 
 [[tool.hatch.envs.gputest.matrix]]
 python = ["3.11", "3.12", "3.13"]
-numpy = ["1.25", "2.1"]
+numpy = ["1.25", "2.2"]
 version = ["minimal"]
 
 [tool.hatch.envs.gputest.scripts]
@@ -209,7 +210,6 @@ dependencies = [
     'packaging @ git+https://github.com/pypa/packaging',
     'numpy',  # from scientific-python-nightly-wheels
     'numcodecs @ git+https://github.com/zarr-developers/numcodecs',
-    'fsspec @ git+https://github.com/fsspec/filesystem_spec',
     's3fs @ git+https://github.com/fsspec/s3fs',
     'universal_pathlib @ git+https://github.com/fsspec/universal_pathlib',
     'typing_extensions @ git+https://github.com/python/typing_extensions',