use newest version (v0.6.1) of gertils

Author: vreuter

CHANGELOG.md

@@ -4,6 +4,11 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [v0.3.5] - 2025-10-30
+
+### Changed
+* Depend on newest version (v0.6.1) of `gertils`, and adapt code accordingly.
+
 ## [v0.3.4] - 2025-04-01
 
 ### Changed

looptrace_loci_vis/point_record.py

@@ -5,7 +5,7 @@
 from typing import Union
 
 import numpy as np
-from gertils.geometry import ImagePoint3D, LocatableXY, LocatableZ, ZCoordinate
+from gertils.geometry import ImagePoint3D
 from gertils.types import TimepointFrom0 as Timepoint
 from gertils.types import TraceIdFrom0 as TraceId
 from numpydoc_decorator import doc  # type: ignore[import-untyped]
@@ -23,7 +23,7 @@
     ),
 )
 @dataclasses.dataclass(frozen=True, kw_only=True)
-class PointRecord(LocatableXY, LocatableZ):  # noqa: D101
+class PointRecord:  # noqa: D101
     trace_id: TraceId
     region_time: Timepoint
     timepoint: Timepoint
@@ -50,23 +50,14 @@ def flatten(self) -> FlatPointRecord:
             self.trace_id.get,
             self.region_time.get,
             self.timepoint.get,
-            self.get_z_coordinate(),
-            self.get_y_coordinate(),
-            self.get_x_coordinate(),
+            self.point.z,
+            self.point.y,
+            self.point.x,
         ]
 
-    def get_x_coordinate(self) -> float:  # noqa: D102
-        return self.point.x
-
-    def get_y_coordinate(self) -> float:  # noqa: D102
-        return self.point.y
-
-    def get_z_coordinate(self) -> ZCoordinate:  # noqa: D102
-        return self.point.z
-
     @doc(summary="Round point position to nearest z-slice")
     def with_truncated_z(self) -> "PointRecord":  # noqa: D102
-        new_z: int = floor(self.get_z_coordinate())
+        new_z: int = floor(self.point.z)
         result: PointRecord = self.with_new_z(new_z)
         return result
 
@@ -98,7 +89,7 @@ def expand_along_z(  # noqa: D103
         raise TypeError(f"Bad type for z_max: {type(z_max).__name__}")
 
     r = r.with_truncated_z()
-    z_center: int = int(r.get_z_coordinate())
+    z_center: int = int(r.point.z)
     z_max: int = floor(z_max)  # type: ignore[no-redef]
     if not isinstance(z_center, int) or not isinstance(z_max, int):
         raise TypeError(

looptrace_loci_vis/reader.py

@@ -187,7 +187,7 @@ def records_to_qcpass_layer_data(
     records: list[PointRecord],
 ) -> tuple[list[PointRecord], list[bool], LayerParams]:
     """Extend the given records partially through a z-stack, designate appropriately as central-plane or not."""
-    max_z = max(r.get_z_coordinate() for r in records)
+    max_z = max(r.point.z for r in records)
     points: list[PointRecord] = []
     center_flags: list[bool] = []
     for rec in records:
@@ -202,7 +202,7 @@ def records_to_qcfail_layer_data(
     record_qc_pairs: list[tuple[PointRecord, QCFailReasons]],
 ) -> tuple[list[PointRecord], list[bool], LayerParams]:
     """Extend the given records partially through a z-stack, designate appropriately as central-plane or not; also set fail codes text."""
-    max_z = max(r.get_z_coordinate() for r, _ in record_qc_pairs)
+    max_z = max(r.point.z for r, _ in record_qc_pairs)
     points: list[PointRecord] = []
     center_flags: list[bool] = []
     codes: list[QCFailReasons] = []

poetry.lock

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "looptrace-loci-vis"
-version = "0.3.4"
+version = "0.3.5"
 description = "This project facilitates viewing, in `napari`, locus-specific spots from `looptrace`."
 authors = ["Vince Reuter"]
 license = "MIT"
@@ -30,7 +30,7 @@ looptrace-loci-vis = "looptrace_loci_vis:napari.yaml"
 [tool.poetry.dependencies]
 python = ">=3.10,<3.13"
 expression = ">=5.0.2"
-gertils = { git = "https://github.com/gerlichlab/gertils.git", tag = "v0.6.0" }
+gertils = { git = "https://github.com/gerlichlab/gertils.git", tag = "v0.6.1" }
 numpy = "*"
 numpydoc_decorator = ">=2.2.1"
 pandas = "*"