Merge branch 'main' into fix/consistent-create-array-signature

Author: d-v-b

.github/ISSUE_TEMPLATE/release-checklist.md

@@ -0,0 +1,56 @@
+---
+name: Zarr-Python release checklist
+about: Checklist for a new Zarr-Python release. [For project maintainers only!]
+title: Release Zarr-Python vX.Y.Z
+labels: release-checklist
+assignees: ''
+
+---
+
+**Release**: [v0.x.x](https://github.com/zarr-developers/zarr-python/milestones/?)
+**Scheduled Date**: 20YY/MM/DD
+
+**Priority PRs/issues to complete prior to release**
+
+- [ ] Priority pull request #X
+
+**Before release**:
+
+- [ ] Make sure that all pull requests which will be included in the release have been properly documented as changelog files in the [`changes/` directory](https://github.com/zarr-developers/zarr-python/tree/main/changes).
+- [ ] Run ``towncrier build --version x.y.z`` to create the changelog, and commit the result to the main branch.
+- [ ] Check [SPEC 0](https://scientific-python.org/specs/spec-0000/#support-window) to see if the minimum supported version of Python or NumPy needs bumping.
+- [ ] Check to ensure that:
+  - [ ] Deprecated workarounds/codes/tests are removed. Run `grep "# TODO" **/*.py` to find all potential TODOs.
+  - [ ] All tests pass in the ["Tests" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/test.yml).
+  - [ ] All tests pass in the ["GPU Tests" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/gpu_test.yml).
+  - [ ] All tests pass in the ["Hypothesis" workflow](https://github.com/zarr-developers/zarr-python/actions/workflows/hypothesis.yaml).
+  - [ ] Check that downstream libraries work well (maintainers can make executive decisions about whether all checks are required for this release).
+    - [ ] Xarray (@jhamman @dcherian @TomNicholas)
+        - Zarr's upstream compatibility is tested via the [Upstream Dev CI worklow](https://github.com/pydata/xarray/actions/workflows/upstream-dev-ci.yaml).
+        - Click on the most recent workflow and check that the `upstream-dev` job has run and passed. `upstream-dev` is not run on all all workflow runs.
+        - Check that the expected version of Zarr-Python was tested using the `Version Info` step of the `upstream-dev` job.
+        - If testing on a branch other than `main` is needed, open a PR modifying https://github.com/pydata/xarray/blob/90ee30943aedba66a37856b2332a41264e288c20/ci/install-upstream-wheels.sh#L56 and add the `run-upstream` label.
+    - [ ] Titiler.Xarray (@maxrjones)
+        - [Modify dependencies](https://github.com/developmentseed/titiler/blob/main/src/titiler/xarray/pyproject.toml) for titiler.xarray.
+        - Modify triggers for running [the test workflow](https://github.com/developmentseed/titiler/blob/61549f2de07b20cca8fb991cfcdc89b23e18ad05/.github/workflows/ci.yml#L5-L7).
+        - Push the branch to the repository and check for the actions for any failures.
+
+**Release**:
+
+- [ ] Go to https://github.com/zarr-developers/zarr-python/releases.
+  - [ ] 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: `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-fill the description.
+  - [ ] Make a release by clicking the 'Publish Release' button, this will automatically create a tag too.
+- [ ] Verify that release workflows succeeded.
+  - [ ] The latest version is correct on [PyPI](https://pypi.org/project/zarr/).
+  - [ ] The stable version is correct on [ReadTheDocs](https://zarr.readthedocs.io/en/stable/).
+
+**After release**:
+
+- [ ] Review and merge the pull request on the conda-forge [zarr-feedstock](https://github.com/conda-forge/zarr-feedstock) that will be automatically generated.
+
+---
+
+- [ ] Party :tada:

.github/codecov.yml

@@ -6,9 +6,9 @@ ci:
 default_stages: [pre-commit, pre-push]
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.9
+    rev: v0.12.2
     hooks:
-      - id: ruff
+      - id: ruff-check
         args: ["--fix", "--show-fixes"]
       - id: ruff-format
   - repo: https://github.com/codespell-project/codespell
@@ -22,7 +22,7 @@ repos:
       - id: check-yaml
       - id: trailing-whitespace
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.15.0
+    rev: v1.16.1
     hooks:
       - id: mypy
         files: src|tests

.pre-commit-config.yaml

@@ -1,11 +1,11 @@
 import sys
 import timeit
 
+import blosc
 import line_profiler
 import numpy as np
 
 import zarr
-from zarr import blosc
 
 if __name__ == "__main__":
     sys.path.insert(0, "..")

bench/compress_normal.py

@@ -0,0 +1,8 @@
+Suppress `FileNotFoundError` when deleting non-existent keys in the `obstore` adapter.
+
+When writing empty chunks (i.e. chunks where all values are equal to the array's fill value) to a zarr array, zarr
+will delete those chunks from the underlying store. For zarr arrays backed by the `obstore` adapter, this will potentially
+raise a `FileNotFoundError` if the chunk doesn't already exist.
+Since whether or not a delete of a non-existing object raises an error depends on the behavior of the underlying store,
+suppressing the error in all cases results in consistent behavior across stores, and is also what `zarr` seems to expect
+from the store.

changes/3068.bugfix.rst

@@ -0,0 +1,2 @@
+Fixed an issue preventing correct parsing of NumPy ``int32`` dtypes when constructed via
+``np.dtype('i')``.

changes/3140.bugfix.rst

@@ -0,0 +1 @@
+Trying to open a StorePath/Array with ``mode='r'`` when the store is not read-only creates a read-only copy of the store.

changes/3151.bugfix.rst

@@ -0,0 +1,2 @@
+Add a self-contained example of data type extension to the ``examples`` directory, and expanded
+the documentation for data types.

changes/3156.bugfix.rst

@@ -0,0 +1,6 @@
+Fixes a variety of issues related to string data types.
+
+- Brings the ``VariableLengthUTF8`` data type Zarr V3 identifier in alignment with Zarr Python 3.0.8
+- Disallows creation of 0-length fixed-length data types
+- Adds a regression test for the ``VariableLengthUTF8`` data type that checks against version 3.0.8
+- Allows users to request the ``VariableLengthUTF8`` data type with ``str``, ``"str"``, or ``"string"``.