Bump the pre-commit-hooks group across 1 directory with 3 updates (#40)

* Bump the pre-commit-hooks group across 1 directory with 3 updates

Bumps the pre-commit-hooks group with 3 updates in the / directory: [https://github.com/tox-dev/pyproject-fmt](https://github.com/tox-dev/pyproject-fmt), [https://github.com/codespell-project/codespell](https://github.com/codespell-project/codespell) and [https://github.com/astral-sh/ruff-pre-commit](https://github.com/astral-sh/ruff-pre-commit).


Updates `https://github.com/tox-dev/pyproject-fmt` from v2.23.0 to 2.25.3
- [Release notes](https://github.com/tox-dev/pyproject-fmt/releases)
- [Commits](tox-dev/pyproject-fmt@v2.23.0...v2.25.3)

Updates `https://github.com/codespell-project/codespell` from v2.4.2 to 2.4.3
- [Release notes](https://github.com/codespell-project/codespell/releases)
- [Commits](codespell-project/codespell@v2.4.2...v2.4.3)

Updates `https://github.com/astral-sh/ruff-pre-commit` from v0.15.16 to 0.16.0
- [Release notes](https://github.com/astral-sh/ruff-pre-commit/releases)
- [Commits](astral-sh/ruff-pre-commit@v0.15.16...v0.16.0)

---
updated-dependencies:
- dependency-name: https://github.com/tox-dev/pyproject-fmt
  dependency-version: 2.25.3
  dependency-type: direct:production
  dependency-group: pre-commit-hooks
- dependency-name: https://github.com/codespell-project/codespell
  dependency-version: 2.4.3
  dependency-type: direct:production
  dependency-group: pre-commit-hooks
- dependency-name: https://github.com/astral-sh/ruff-pre-commit
  dependency-version: 0.16.0
  dependency-type: direct:production
  dependency-group: pre-commit-hooks
...

Signed-off-by: dependabot[bot] <support@github.com>

* Bump the pre-commit-hooks group across 1 directory with 3 updates

Bumps the pre-commit-hooks group with 3 updates in the / directory: [https://github.com/tox-dev/pyproject-fmt](https://github.com/tox-dev/pyproject-fmt), [https://github.com/codespell-project/codespell](https://github.com/codespell-project/codespell) and [https://github.com/astral-sh/ruff-pre-commit](https://github.com/astral-sh/ruff-pre-commit).


Updates `https://github.com/tox-dev/pyproject-fmt` from v2.23.0 to 2.26.0
- [Release notes](https://github.com/tox-dev/pyproject-fmt/releases)
- [Commits](tox-dev/pyproject-fmt@v2.23.0...v2.26.0)

Updates `https://github.com/codespell-project/codespell` from v2.4.2 to 2.4.3
- [Release notes](https://github.com/codespell-project/codespell/releases)
- [Commits](codespell-project/codespell@v2.4.2...v2.4.3)

Updates `https://github.com/astral-sh/ruff-pre-commit` from v0.15.16 to 0.16.0
- [Release notes](https://github.com/astral-sh/ruff-pre-commit/releases)
- [Commits](astral-sh/ruff-pre-commit@v0.15.16...v0.16.0)

---
updated-dependencies:
- dependency-name: https://github.com/astral-sh/ruff-pre-commit
  dependency-version: 0.16.0
  dependency-type: direct:production
  dependency-group: pre-commit-hooks
- dependency-name: https://github.com/codespell-project/codespell
  dependency-version: 2.4.3
  dependency-type: direct:production
  dependency-group: pre-commit-hooks
- dependency-name: https://github.com/tox-dev/pyproject-fmt
  dependency-version: 2.25.3
  dependency-type: direct:production
  dependency-group: pre-commit-hooks
...

Signed-off-by: dependabot[bot] <support@github.com>

* fix positional argument enforcement

---------

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Gregory Way <gregory.way@gmail.com>

Author: dependabot[bot]

.pre-commit-config.yaml

@@ -9,15 +9,15 @@ repos:
     -   id: check-yaml
     -   id: detect-private-key
 -   repo: https://github.com/tox-dev/pyproject-fmt
-    rev: "v2.23.0"
+    rev: "v2.26.0"
     hooks:
     -   id: pyproject-fmt
 -   repo: https://github.com/citation-file-format/cffconvert
     rev: b6045d78aac9e02b039703b030588d54d53262ac
     hooks:
     -   id: validate-cff
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.4.2
+    rev: v2.4.3
     hooks:
     -   id: codespell
         exclude: |
@@ -39,7 +39,7 @@ repos:
     -   id: yamllint
         exclude: pre-commit-config.yaml
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.15.16"
+    rev: "v0.16.0"
     hooks:
     -   id: ruff-format
     -   id: ruff-check

src/zedprofiler/IO/loading_classes.py

@@ -138,6 +138,7 @@ class ImageSetLoader:
 
     def __init__(  # noqa: PLR0913
         self,
+        *,
         anisotropy_spacing: tuple[float, float, float],
         channel_mapping: dict[str, str],
         image_set_path: pathlib.Path | None,

src/zedprofiler/featurization/colocalization.py

@@ -262,6 +262,7 @@ def bisection_costes_threshold_calculation(
 
 
 def prepare_two_images_for_colocalization(  # noqa: PLR0913
+    *,
     label_object1: numpy.ndarray,
     label_object2: numpy.ndarray,
     image_object1: numpy.ndarray,

src/zedprofiler/featurization/granularity.py

@@ -116,6 +116,7 @@ def _upsample_3d(
 
 def compute_granularity(  # noqa: C901, PLR0912, PLR0913, PLR0915
     object_loader: ObjectLoader,
+    *,
     radius: int = 10,
     granular_spectrum_length: int = 16,
     subsample_size: float = 0.25,

tests/featurization/test_colocalization.py

@@ -95,12 +95,12 @@ def test_prepare_two_images_for_colocalization_crops() -> None:
     im2[3, 3, 3] = expected_peak_im2
 
     cropped1, cropped2 = prepare_two_images_for_colocalization(
-        label,
-        label,
-        im1,
-        im2,
-        1,
-        1,
+        label_object1=label,
+        label_object2=label,
+        image_object1=im1,
+        image_object2=im2,
+        object_id1=1,
+        object_id2=1,
     )
 
     assert isinstance(cropped1, np.ndarray) and isinstance(cropped2, np.ndarray)