Merge branch 'main' of github.com:zarr-developers/zarr-python into feat/default-buffer

Author: d-v-b

.github/workflows/check_changelogs.yml

@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@1af3b93b6815bc44a9784bd300feb67ff0d1eeb3 # v6.0.0
+      - uses: actions/checkout@8e8c483db84b4bee98b60c0593521ed34d9990e8 # v6.0.1
 
       - name: Install uv
         uses: astral-sh/setup-uv@61cb8a9741eeb8a550a1b8544337180c0fc8476b # v7.2.0

.github/workflows/codspeed.yml

@@ -17,7 +17,7 @@ jobs:
     name: Run benchmarks
     runs-on: codspeed-macro
     steps:
-    - uses: actions/checkout@v5
+    - uses: actions/checkout@v6
       with:
         fetch-depth: 0  # grab all branches and tags
     - name: Set up Python

.github/workflows/lint.yml

@@ -0,0 +1,25 @@
+name: Lint
+
+on:
+  push:
+    branches: [main, 3.1.x]
+  pull_request:
+    branches: [main, 3.1.x]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v6
+      - name: Install uv
+        uses: astral-sh/setup-uv@v5
+      - name: Install prek
+        run: uv tool install prek
+      - name: Run prek
+        run: prek run --all-files

.pre-commit-config.yaml

@@ -1,8 +1,9 @@
 ci:
   autoupdate_commit_msg: "chore: update pre-commit hooks"
   autoupdate_schedule: "monthly"
-  autofix_commit_msg: "style: pre-commit fixes"
   autofix_prs: false
+  skip: []  # pre-commit.ci only checks for updates, prek runs hooks locally
+
 default_stages: [pre-commit, pre-push]
 
 default_language_version:

changes/3658.misc.md

@@ -0,0 +1 @@
+Switch from `pre-commit` to [`prek`](https://github.com/j178/prek) for pre-commit checks.

docs/contributing.md

@@ -109,26 +109,50 @@ All tests are automatically run via GitHub Actions for every pull request and mu
 
 > **Note:** Previous versions of Zarr-Python made extensive use of doctests. These tests were not maintained during the 3.0 refactor but may be brought back in the future. See issue #2614 for more details.
 
-### Code standards - using pre-commit
+### Code standards - using prek
 
 All code must conform to the PEP8 standard. Regarding line length, lines up to 100 characters are allowed, although please try to keep under 90 wherever possible.
 
-`Zarr` uses a set of `pre-commit` hooks and the `pre-commit` bot to format, type-check, and prettify the codebase. `pre-commit` can be installed locally by running:
+`Zarr` uses a set of git hooks managed by [`prek`](https://github.com/j178/prek), a fast, Rust-based pre-commit hook manager that is fully compatible with `.pre-commit-config.yaml` files. `prek` can be installed locally by running:
 
 ```bash
-python -m pip install pre-commit
+uv tool install prek
+```
+
+or:
+
+```bash
+pip install prek
 ```
 
 The hooks can be installed locally by running:
 
 ```bash
-pre-commit install
+prek install
+```
+
+This would run the checks every time a commit is created locally. The checks will by default only run on the files modified by a commit, but the checks can be triggered for all the files by running:
+
+```bash
+prek run --all-files
+```
+
+You can also run hooks only for files in a specific directory:
+
+```bash
+prek run --directory src/zarr
+```
+
+Or run hooks for files changed in the last commit:
+
+```bash
+prek run --last-commit
 ```
 
-This would run the checks every time a commit is created locally. These checks will also run on every commit pushed to an open PR, resulting in some automatic styling fixes by the `pre-commit` bot. The checks will by default only run on the files modified by a commit, but the checks can be triggered for all the files by running:
+To list all available hooks:
 
 ```bash
-pre-commit run --all-files
+prek list
 ```
 
 If you would like to skip the failing checks and push the code for further discussion, use the `--no-verify` option with `git commit`.
@@ -143,7 +167,7 @@ Zarr strives to maintain 100% test coverage under the latest Python stable relea
 hatch env run --env test.py3.12-2.2-optional run-coverage
 ```
 
-will automatically run the test suite with coverage and produce a XML coverage report. This should be 100% before code can be accepted into the main code base.
+will automatically run the test suite with coverage and produce an XML coverage report. This should be 100% before code can be accepted into the main code base.
 
 You can also generate an HTML coverage report by running:
 
@@ -273,4 +297,4 @@ performance benchmarks as part of our test suite. The benchmarks can be are foun
 By default pytest is configured to run these benchmarks as plain tests (i.e., no benchmarking). To run
 a benchmark with timing measurements, use the `--benchmark-enable` when invoking `pytest`.
 
-The benchmarks are run as part of the continuous integration suite through [codspeed](https://codspeed.io/zarr-developers/zarr-python).
+The benchmarks are run as part of the continuous integration suite through [codspeed](https://codspeed.io/zarr-developers/zarr-python).

docs/user-guide/storage.md

@@ -138,7 +138,7 @@ print(group)
 ```
 
 The type of filesystem (e.g. S3, https, etc..) is inferred from the scheme of the url (e.g. s3 for "**s3**://noaa-nwm-retro-v2-zarr-pds").
-In case a specific filesystem is needed, one can explicitly create it. For example to create a S3 filesystem:
+In case a specific filesystem is needed, one can explicitly create it. For example to create an S3 filesystem:
 
 ```python exec="true" session="storage" source="above" result="ansi"
 # Note: requires s3fs to be installed

pyproject.toml

@@ -30,7 +30,7 @@ maintainers = [
     { name = "Deepak Cherian" }
 ]
 requires-python = ">=3.11"
-# If you add a new dependency here, please also add it to .pre-commit-config.yml
+# If you add a new dependency here, please also add it to .pre-commit-config.yaml
 dependencies = [
     'packaging>=22.0',
     'numpy>=2.0',
@@ -428,6 +428,7 @@ markers = [
 ignore = [
 	"PC111",  # fix Python code in documentation - enable later
 	"PC180",  # for JavaScript - not interested
+	"PC902",  # pre-commit.ci custom autofix message - not using autofix
 ]
 
 [tool.numpydoc_validation]

src/zarr/abc/store.py

@@ -221,7 +221,7 @@ async def get(
         """
         ...
 
-    async def get_bytes(
+    async def _get_bytes(
         self,
         key: str,
         *,
@@ -268,7 +268,7 @@ async def get_bytes(
         --------
         >>> store = await MemoryStore.open()
         >>> await store.set("data", Buffer.from_bytes(b"hello world"))
-        >>> data = await store.get_bytes("data", prototype=default_buffer_prototype())
+        >>> data = await store._get_bytes("data", prototype=default_buffer_prototype())
         >>> print(data)
         b'hello world'
         """
@@ -277,7 +277,7 @@ async def get_bytes(
             raise FileNotFoundError(key)
         return buffer.to_bytes()
 
-    def get_bytes_sync(
+    def _get_bytes_sync(
         self,
         key: str = "",
         *,
@@ -329,14 +329,14 @@ def get_bytes_sync(
         --------
         >>> store = MemoryStore()
         >>> await store.set("data", Buffer.from_bytes(b"hello world"))
-        >>> data = store.get_bytes_sync("data", prototype=default_buffer_prototype())
+        >>> data = store._get_bytes_sync("data", prototype=default_buffer_prototype())
         >>> print(data)
         b'hello world'
         """
 
-        return sync(self.get_bytes(key, prototype=prototype, byte_range=byte_range))
+        return sync(self._get_bytes(key, prototype=prototype, byte_range=byte_range))
 
-    async def get_json(
+    async def _get_json(
         self,
         key: str,
         *,
@@ -387,14 +387,14 @@ async def get_json(
         >>> store = await MemoryStore.open()
         >>> metadata = {"zarr_format": 3, "node_type": "array"}
         >>> await store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode()))
-        >>> data = await store.get_json("zarr.json", prototype=default_buffer_prototype())
+        >>> data = await store._get_json("zarr.json", prototype=default_buffer_prototype())
         >>> print(data)
         {'zarr_format': 3, 'node_type': 'array'}
         """
 
-        return json.loads(await self.get_bytes(key, prototype=prototype, byte_range=byte_range))
+        return json.loads(await self._get_bytes(key, prototype=prototype, byte_range=byte_range))
 
-    def get_json_sync(
+    def _get_json_sync(
         self,
         key: str = "",
         *,
@@ -451,12 +451,12 @@ def get_json_sync(
         >>> store = MemoryStore()
         >>> metadata = {"zarr_format": 3, "node_type": "array"}
         >>> store.set("zarr.json", Buffer.from_bytes(json.dumps(metadata).encode()))
-        >>> data = store.get_json_sync("zarr.json", prototype=default_buffer_prototype())
+        >>> data = store._get_json_sync("zarr.json", prototype=default_buffer_prototype())
         >>> print(data)
         {'zarr_format': 3, 'node_type': 'array'}
         """
 
-        return sync(self.get_json(key, prototype=prototype, byte_range=byte_range))
+        return sync(self._get_json(key, prototype=prototype, byte_range=byte_range))
 
     @abstractmethod
     async def get_partial_values(

src/zarr/core/dtype/wrapper.py

@@ -191,7 +191,7 @@ def to_json(self, zarr_format: ZarrFormat) -> DTypeSpec_V2 | DTypeSpec_V3:
     @abstractmethod
     def _check_scalar(self, data: object) -> bool:
         """
-        Check that an python object is a valid scalar value for the wrapped data type.
+        Check that a python object is a valid scalar value for the wrapped data type.
 
         Parameters
         ----------