release: updates for looptrace v0.18.0

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).
 
+## [v0.6.0] - 2026-04-19
+
+### Changed
+* Update expected files and columns list for compatibility with new `looptrace` release, version 0.18.0.
+
 ## [v0.5.8] - 2025-11-04
 
 ### Changed

docs/using-the-plugin.md

@@ -39,7 +39,7 @@ Some spots are labeled:
 ### Necessary data files
 1. 1 ZARR per field of view you wish to view, named like `P0001.zarr`
 1. 0 or 1 files of each of the following types, per field of view, organized into a folder that has the same field of view name as the ZARR, e.g. `P0001`. There must be at least 1 of these 3 files present:
-    - A `*_rois.merge_contributors.csv` file: ROIs initially detected which were then merged together to create a new ROI
+    - A `*_rois.merge_or_discard_contributors.csv` file: ROIs initially detected which were then merged together to create a new ROI
     - A `*_rois.proximity_rejected.csv` file: ROIs which were discarded due to proximity to another ROI
     - A `*_rois.with_trace_ids.csv` file: ROIs after proximity-based filtration and labeling attribution to nuclei
 
@@ -55,10 +55,10 @@ Some spots are labeled:
 * The channel is read from the `channel` column.
 * For the merge contributors file, the `mergeOutput` column is parsed to get the ID of the merge result.
 * For the `*_rois.with_trace_ids.csv` file, the following additional columns are parsed:
-    * `mergePartners` (to tell singleton ROIs from merger output ROIs)
+    * `neighbors` (to tell singleton ROIs from merger output ROIs)
     * `nucleusNumber` (to tell nuclear from non-nuclear ROIs)
     * `traceId` (to label ROIs which participate in a multi-ROI trace)
-    * `tracePartners` (to determine whether a ROI participates in a multi-rOI trace)
+    * `tracePartners` (to determine whether a ROI participates in a multi-ROI trace)
 
 ### Customizability
 * `LOOPTRACE__DISPLAY_SINGLETON_ROI_IDS` can be used to indicate that any singleton ROI should have its ID displayed. 

looptrace_regionals_vis/__init__.py

@@ -10,7 +10,7 @@
 
 from numpydoc_decorator import doc  # type: ignore[import-untyped]
 
-__version__ = "0.5.8"
+__version__ = "0.6.0"
 
 _PACKAGE_NAME = package = Path(__file__).parent.name
 

…amples/P0001_rois.merge_contributors.csv …1_rois.merge_or_discard_contributors.csvlooptrace_regionals_vis/examples/P0001_rois.merge_contributors.csv renamed to looptrace_regionals_vis/examples/P0001_rois.merge_or_discard_contributors.csv looptrace_regionals_vis/examples/P0001_rois.merge_contributors.csv renamed to looptrace_regionals_vis/examples/P0001_rois.merge_or_discard_contributors.csv

@@ -1,4 +1,4 @@
-index,fieldOfView,timepoint,spotChannel,zc,yc,xc,intensityMean,zMin,zMax,yMin,yMax,xMin,xMax,mergePartners,nucleusNumber,traceId,tracePartners
+index,fieldOfView,timepoint,spotChannel,zc,yc,xc,intensityMean,zMin,zMax,yMin,yMax,xMin,xMax,neighbors,nucleusNumber,traceId,tracePartners
 3,P0001.zarr,79,0,16.527137137619988,422.5165732477932,667.2129969610728,157.0530303030303,10.527137137619988,22.527137137619988,410.5165732477932,434.5165732477932,655.2129969610728,679.2129969610728,100 101,3,13,5
 4,P0001.zarr,79,0,16.950424004488077,118.88259896330818,349.6540530977019,161.81065410400436,10.950424004488076,22.95042400448808,106.88259896330818,130.88259896330817,337.6540530977019,361.6540530977019,,2,14,
 5,P0001.zarr,79,0,18.177805530982404,445.4564669785048,607.9657421380375,160.33961681087763,12.177805530982404,24.177805530982404,433.4564669785048,457.4564669785048,595.9657421380375,619.9657421380375,,3,13,3

looptrace_regionals_vis/examples/P0001_rois.with_trace_ids.csv

@@ -7,7 +7,7 @@ contributions:
   readers:
   - command: looptrace-regionals-vis.read_looptrace_regional_points
     filename_patterns:
-    - '*_rois.merge_contributors.csv'
+    - '*_rois.merge_or_discard_contributors.csv'
     - '*_rois.proximity_rejected.csv'
     - '*_rois.with_trace_ids.csv'
     accepts_directories: true

looptrace_regionals_vis/napari.yaml

@@ -43,7 +43,7 @@
 class InputFileContentType(Enum):
     """The processing steps undergone by data in a file or in memory"""
 
-    MergeContributors = ".merge_contributors.csv"
+    MergeContributors = ".merge_or_discard_contributors.csv"
     ProximityRejects = ".proximity_rejected.csv"
     NucleiLabeled = ".with_trace_ids.csv"
 
@@ -435,7 +435,7 @@ def _parse_nucleus_labeled_record(
         None if raw_nuc_num == 0 else NucleusNumber(raw_nuc_num)
     )
 
-    merge_column_name = "mergePartners"
+    merge_column_name = "neighbors"
     id_and_contribs: Optional[IdAndContributors]
     raw_merge_indices = record[merge_column_name]
     if raw_merge_indices is None or raw_merge_indices == "" or pd.isna(raw_merge_indices):

looptrace_regionals_vis/reader.py

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "looptrace-regionals-vis"
-version = "0.5.8"
+version = "0.6.0"
 description = "This project facilitates viewing, in `napari`, regional spots from `looptrace`."
 authors = ["Vince Reuter"]
 license = "MIT"

pyproject.toml

@@ -68,9 +68,11 @@ def test_from_filepath_requires_path(arg):
             ("", ".proximity_rejected.nuclei_labeled.csv", None),
             ("", ".with_trace_ids.csv", None),
             ("", ".merge_contributors.csv", None),
+            ("", ".merge_or_discard_contributors.csv", None),
             ("_rois", "", None),
             ("_rois", ".CSV", None),
-            ("_rois", ".merge_contributors.csv", InputFileContentType.MergeContributors),
+            ("_rois", ".merge_contributors.csv", None),
+            ("_rois", ".merge_or_discard_contributors.csv", InputFileContentType.MergeContributors),
             ("_rois", ".proximity_rejected.csv", InputFileContentType.ProximityRejects),
             ("_rois", ".proximity_accepted.csv", None),
             ("_rois", ".proximity_rejected.nuclei_labeled.csv", None),