ci(pre-commit.ci): autoupdate (#298)

* ci(pre-commit.ci): autoupdate

updates:
- [github.com/adhtruong/mirrors-typos: v1.45.0 → v1.48.0](adhtruong/mirrors-typos@v1.45.0...v1.48.0)
- [github.com/astral-sh/ruff-pre-commit: v0.15.9 → v0.15.20](astral-sh/ruff-pre-commit@v0.15.9...v0.15.20)
- [github.com/pre-commit/mirrors-mypy: v1.20.0 → v2.1.0](pre-commit/mirrors-mypy@v1.20.0...v2.1.0)

* ci: update pre-commit hooks and dependencies; refactor frame handling in ND2File and ModernReader

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Talley Lambert <talley.lambert@gmail.com>

Author: pre-commit-ci[bot]

.pre-commit-config.yaml

@@ -10,19 +10,19 @@ repos:
       - id: validate-pyproject
 
   - repo: https://github.com/adhtruong/mirrors-typos
-    rev: v1.45.0
+    rev: v1.48.0
     hooks:
       - id: typos
         args: [--force-exclude]  # omit --write-changes
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.9
+    rev: v0.16.0
     hooks:
       - id: ruff-check
       - id: ruff-format
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.20.0
+    rev: v2.3.0
     hooks:
       - id: mypy
         files: "^src/"

pyproject.toml

@@ -35,8 +35,8 @@ legacy = [
     "imagecodecs>=2021.2.26",
     "imagecodecs>=2021.8.26; python_version >= '3.10'",
     "imagecodecs>=2022.7.31; python_version >= '3.11'",
-    "imagecodecs>=2023.9.18; python_version >= '3.12'",
-    "imagecodecs>=2024.9.22; python_version >= '3.13'",
+    "imagecodecs>=2024.6.1; python_version >= '3.12'",
+    "imagecodecs>=2024.12.30; python_version >= '3.13'",
 ]
 tiff = ["tifffile>=2021.7.2"]
 ome-zarr = [
@@ -53,6 +53,9 @@ test = [
     "nd2[tiff]",
     "dask[array]>=2023.5.0",
     "imagecodecs>=2023.1.23",
+    # older versions no longer ship wheels for these pythons
+    "imagecodecs>=2024.6.1; python_version >= '3.12'",
+    "imagecodecs>=2024.12.30; python_version >= '3.13'",
     "lxml>=5.3.0",
     "psutil>=5.9.8",
     "pytest-codspeed>=4.1.1",

src/nd2/_nd2file.py

@@ -1252,7 +1252,10 @@ def read_frame(self, frame_index: SupportsInt) -> np.ndarray:
         !!! Tip "new in version 0.8.0"
         """
         frame = self._rdr.read_frame(int(frame_index))
-        frame.shape = self._raw_frame_shape
+        # NOTE: use reshape rather than in-place `frame.shape = ...`,
+        # which numpy deprecated in v2.5.  The reader always returns something
+        # that can be reshaped without a copy.
+        frame = frame.reshape(self._raw_frame_shape)
         return frame.transpose((2, 0, 1, 3)).squeeze()
 
     @cached_property

src/nd2/_parse/_clx_xml.py

@@ -33,7 +33,7 @@ def _float_or_nan(x: str) -> float:
 
 
 # functions to cast CLxvariants to python types
-_XMLCAST: dict[str | None | bytes, Callable[[Any], Scalar]] = {
+_XMLCAST: dict[str | bytes | None, Callable[[Any], Scalar]] = {
     "bool": lambda x: x.lower() in {"true", "1"},
     "CLxByteArray": lambda x: bytearray(x, "utf8"),
     "CLxStringW": str,

src/nd2/_readers/_modern/modern_reader.py

@@ -272,7 +272,7 @@ def _cached_frame_times(self) -> list[float]:
                 warnings.warn(f"Failed to load frame times: {e}", stacklevel=2)
                 self._frame_times = []
 
-        return cast("list[float]", self._frame_times)
+        return self._frame_times
 
     def voxel_size(self) -> tuple[float, float, float]:
         meta = self.metadata()