Merge branch 'main' into coalesce-shard-reads

Author: aldenks

.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`.

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]

tests/benchmarks/test_indexing.py

@@ -22,18 +22,27 @@
     (slice(None), slice(0, 3, 2), slice(0, 10)),
 )
 
+shards = (
+    None,
+    (50,) * 3,
+)
+
 
-@pytest.mark.parametrize("store", ["memory"], indirect=["store"])
+@pytest.mark.parametrize("store", ["memory", "memory_get_latency"], indirect=["store"])
 @pytest.mark.parametrize("indexer", indexers, ids=str)
+@pytest.mark.parametrize("shards", shards, ids=str)
 def test_slice_indexing(
-    store: Store, indexer: tuple[int | slice], benchmark: BenchmarkFixture
+    store: Store,
+    indexer: tuple[int | slice],
+    shards: tuple[int, ...] | None,
+    benchmark: BenchmarkFixture,
 ) -> None:
     data = create_array(
         store=store,
         shape=(105,) * 3,
         dtype="uint8",
         chunks=(10,) * 3,
-        shards=None,
+        shards=shards,
         compressors=None,
         filters=None,
         fill_value=0,

tests/conftest.py

@@ -40,6 +40,7 @@
 from zarr.core.metadata.v3 import ArrayV3Metadata
 from zarr.core.sync import sync
 from zarr.storage import FsspecStore, LocalStore, MemoryStore, StorePath, ZipStore
+from zarr.testing.store import LatencyStore
 
 if TYPE_CHECKING:
     from collections.abc import Generator
@@ -58,8 +59,8 @@
 
 
 async def parse_store(
-    store: Literal["local", "memory", "fsspec", "zip"], path: str
-) -> LocalStore | MemoryStore | FsspecStore | ZipStore:
+    store: Literal["local", "memory", "fsspec", "zip", "memory_get_latency"], path: str
+) -> LocalStore | MemoryStore | FsspecStore | ZipStore | LatencyStore:
     if store == "local":
         return await LocalStore.open(path)
     if store == "memory":
@@ -68,6 +69,8 @@ async def parse_store(
         return await FsspecStore.open(url=path)
     if store == "zip":
         return await ZipStore.open(path + "/zarr.zip", mode="w")
+    if store == "memory_get_latency":
+        return LatencyStore(MemoryStore(), get_latency=0.0001, set_latency=0)
     raise AssertionError