Bump poethepoet from 0.38.0 to 0.40.0

.github/dependabot.yml

@@ -14,6 +14,10 @@ updates:
     schedule:
       # Check for updates to GitHub Actions every week
       interval: "weekly"
+    groups:
+      github-actions:
+        patterns:
+          - "*"
 
   # Perform checks and updates for python uv environment.
   # This depends on changes to dependabot via:
@@ -25,3 +29,7 @@ updates:
     schedule:
       # Check for updates to uv environment files every week
       interval: "weekly"
+    groups:
+      uv:
+        patterns:
+          - "*"

.github/workflows/tests.yml

@@ -21,7 +21,7 @@ jobs:
           python-version: "3.11"
       - name: Install the latest version of uv
         uses: astral-sh/setup-uv@v7
-      - uses: pre-commit/action@v3.0.1
+      - uses: j178/prek-action@v1
       # run pre-commit ci lite for automated fixes
       - uses: pre-commit-ci/lite-action@v1.1.0
         if: ${{ !cancelled() }}

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
     -   id: check-yaml
     -   id: detect-private-key
 -   repo: https://github.com/tox-dev/pyproject-fmt
-    rev: "v2.11.1"
+    rev: "v2.12.1"
     hooks:
     -   id: pyproject-fmt
 -   repo: https://github.com/citation-file-format/cffconvert
@@ -34,12 +34,12 @@ repos:
         additional_dependencies:
         -   mdformat-gfm
 -   repo: https://github.com/adrienverge/yamllint
-    rev: v1.37.1
+    rev: v1.38.0
     hooks:
     -   id: yamllint
         exclude: pre-commit-config.yaml
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.14.11"
+    rev: "v0.15.0"
     hooks:
     -   id: ruff-format
     -   id: ruff-check

pyproject.toml

@@ -40,15 +40,15 @@ dev = [
 [tool.uv]
 package = false
 
-[tool.poe.tasks.setup]
-shell = "uv venv && uv sync"
-
 [tool.poe.tasks.lab]
 shell = "uv venv && uv sync && uv run jupyter lab"
 
 [tool.poe.tasks.run-benchmarks]
 shell = "uv run python src/benchmarks/compare_parquet_vortex_lance.py && uv run python src/benchmarks/compare_parquet_vortex_lance_ome.py && uv run python src/benchmarks/compare_ome_arrow_only.py"
 
+[tool.poe.tasks.setup]
+shell = "uv venv && uv sync"
+
 [tool.jupytext]
 formats = "ipynb,py:light"
 

src/benchmarks/compare_ome_arrow_only.py

@@ -471,8 +471,9 @@ def ome_zarr_random_read_native(indices, base_path=OME_ZARR_DIR):
                     arrays, path
                 ),
                 "read": lambda path=OME_ZARR_DIR: ome_zarr_read_all_native(path),
-                "random_read": lambda path=OME_ZARR_DIR,
-                indices=None: ome_zarr_random_read_native(indices, path),
+                "random_read": lambda path=OME_ZARR_DIR, indices=None: (
+                    ome_zarr_random_read_native(indices, path)
+                ),
                 "table": ome_arrays,  # run_benchmarks passes as cfg_table; here it's a list of numpy arrays
                 "random_repeats": RANDOM_READ_REPEATS,
                 "version": (