Sort elements in widgets (#285)

* Sort elements and coordinate systems in widgets

* Sort table names

* fix test, update changelog

---------

Co-authored-by: Luca Marconato <[email protected]>

Author: aeisenbarth

CHANGELOG.md

@@ -8,6 +8,11 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
+## incoming release
+
+- Global setting variables for showing circles as points and point size for scatter widget #309 #334
+- Sorting the element names and coordinate system names alphabetically #285
+
 ## [0.5.4] - 2024-11-26
 
 ### Changed

src/napari_spatialdata/_sdata_widgets.py

@@ -3,6 +3,7 @@
 import platform
 from collections.abc import Iterable
 from importlib.metadata import version
+from operator import itemgetter
 from pathlib import Path
 from typing import TYPE_CHECKING, cast
 
@@ -16,6 +17,7 @@
 from qtpy.QtGui import QIcon
 from qtpy.QtWidgets import QLabel, QListWidget, QListWidgetItem, QProgressBar, QVBoxLayout, QWidget
 from spatialdata import SpatialData
+from spatialdata.models._utils import DEFAULT_COORDINATE_SYSTEM
 
 from napari_spatialdata._viewer import SpatialDataViewer
 from napari_spatialdata.constants.config import N_CIRCLES_WARNING_THRESHOLD, N_SHAPES_WARNING_THRESHOLD
@@ -59,7 +61,7 @@ def _onItemChange(self, selected_coordinate_system: QListWidgetItem | int | Iter
         self._elements = elements
 
     def _set_element_widget_items(self, elements: dict[str, dict[str, str | int]]) -> None:
-        for key, dict_val in elements.items():
+        for key, dict_val in sorted(elements.items(), key=itemgetter(0)):
             sdata = self._sdata[dict_val["sdata_index"]]
             element_type = dict_val["element_type"]
             element_name = dict_val["original_name"]
@@ -95,7 +97,11 @@ def __init__(self, sdata: EventedList):
         self._sdata = sdata
         self._system: None | str = None
 
-        coordinate_systems = {cs for sdata in self._sdata for cs in sdata.coordinate_systems}
+        # Sort alphabetically, but keep default "global" at the top.
+        coordinate_systems = sorted(cs for sdata in self._sdata for cs in sdata.coordinate_systems)
+        if DEFAULT_COORDINATE_SYSTEM in coordinate_systems:
+            coordinate_systems.remove(DEFAULT_COORDINATE_SYSTEM)
+            coordinate_systems.insert(0, DEFAULT_COORDINATE_SYSTEM)
         self.addItems(coordinate_systems)
 
     def _select_coord_sys(self, selected_coordinate_system: QListWidgetItem | int | Iterable[str]) -> None:

src/napari_spatialdata/_viewer.py

@@ -422,7 +422,7 @@ def inherit_metadata(self, layers: list[Layer], ref_layer: Layer) -> None:
     def _get_table_data(
         self, sdata: SpatialData, element_name: str
     ) -> tuple[AnnData | None, str | None, list[str] | None]:
-        table_names: list[str] = list(get_element_annotators(sdata, element_name))
+        table_names: list[str] = sorted(get_element_annotators(sdata, element_name))
         table_name = table_names[0] if len(table_names) > 0 else None
         adata = _get_init_metadata_adata(sdata, table_name, element_name)
         return adata, table_name, table_names

tests/test_viewer.py

@@ -172,8 +172,9 @@ def test_save_layer(qtbot, tmp_path: str, make_napari_viewer: any):
     n = len(widget.elements_widget)
     # I would have expected Shapes to be in position -2 and Points in position -1, but we have the following order
     # because elements of the same type are grouped together
-    assert widget.elements_widget.item(n - 1).text() == "Shapes"
-    assert widget.elements_widget.item(n - 5).text() == "Points"
+    all_elements = [widget.elements_widget.item(i).text() for i in range(n)]
+    assert "Shapes" in all_elements
+    assert "Points" in all_elements
 
     # add a new layer to the viewer with the newly saved shapes element
     widget._onClick("Shapes")