Fix add existing tree to annotation (#1201)

* add test and change hash function

* change hash function

* fix typo.

* Use always id for hash value of Group.

* Adapt __eq__ method for group and skeleton.

* Update changelog.

* Adapt equality check.

* Remove __eq__ and __hash__ method in Skeleton class.

* Remove unused import.

* Add eq=False to attr.define to avoid default equal method.

* Run linter.

---------

Co-authored-by: markbader <[email protected]>

Author: MatthisCl

webknossos/Changelog.md

@@ -34,6 +34,7 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 - Refactored the PimsTiffReader to read the data directly from the tiff file without creating a memmap-able copy first. This greatly reduces the time and storage requirements for converting large tiff files. [#1212](https://github.com/scalableminds/webknossos-libs/pull/1212)
 
 ### Fixed
+- Fixed an issue where adding existing trees to an annotation fails. [#1201](https://github.com/scalableminds/webknossos-libs/pull/1201)
 - Fixed unpickling of the SSL_Context to allow for a second or third pickling. [#1223](https://github.com/scalableminds/webknossos-libs/pull/1223)
 - Fixed offset error in upsample_cube job [#1209](https://github.com/scalableminds/webknossos-libs/pull/1209)
 
@@ -50,15 +51,13 @@ For upgrade instructions, please check the respective _Breaking Changes_ section
 - Fixed pickling issue that has been introduced in 0.15.9. [#1218](https://github.com/scalableminds/webknossos-libs/pull/1218)
 
 
-
 ## [0.15.10](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.15.10) - 2024-11-25
 [Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.15.9...v0.15.10)
 
 ### Fixed
 - Fixed pickling issue that has been introduced in 0.15.9. [#1218](https://github.com/scalableminds/webknossos-libs/pull/1218)
 
 
-
 ## [0.15.9](https://github.com/scalableminds/webknossos-libs/releases/tag/v0.15.9) - 2024-11-25
 [Commits](https://github.com/scalableminds/webknossos-libs/compare/v0.15.8...v0.15.9)
 

webknossos/tests/test_skeleton.py

@@ -438,3 +438,15 @@ def test_add_tree_with_obj_and_properties(tmp_path: Path) -> None:
     assert new_tree.color == (1, 2, 3, 1)
 
     skeleton_b.save(output_path)
+
+
+def test_add_tree_with_group() -> None:
+    annotation = wk.Annotation(
+        name="my_annotation", dataset_name="my_dataset", voxel_size=(11, 11, 24)
+    )
+    group = annotation.skeleton.add_group("a group")
+    tree = group.add_tree("a tree")
+
+    skeleton_a = create_dummy_skeleton()
+
+    skeleton_a.add_tree(tree)

webknossos/webknossos/skeleton/group.py

@@ -1,5 +1,5 @@
 import copy
-from typing import TYPE_CHECKING, Iterator, Optional, Set, Tuple, Union, cast
+from typing import TYPE_CHECKING, Any, Iterator, Optional, Set, Tuple, Union, cast
 
 import attr
 from boltons.strutils import unit_len
@@ -220,7 +220,7 @@ def children(self) -> Iterator[GroupOrTree]:
     @property
     def trees(self) -> Iterator[Tree]:
         """Returns all (immediate) tree children as an iterator.
-        Use flattened_trees if you need also need trees within subgroups."""
+        Use flattened_trees if you also need trees within subgroups."""
         return (child for child in self._child_trees)
 
     @property
@@ -430,5 +430,8 @@ def as_nml_group(self) -> wknml.Group:
             children=[g.as_nml_group() for g in self._child_groups],
         )
 
+    def __eq__(self, other: Any) -> bool:
+        return type(other) is type(self) and self._id == other._id
+
     def __hash__(self) -> int:
-        return self._id
+        return id(self)

webknossos/webknossos/skeleton/skeleton.py

@@ -12,7 +12,7 @@
 Vector3 = Tuple[float, float, float]
 
 
-@attr.define
+@attr.define(eq=False)
 class Skeleton(Group):
     """A hierarchical representation of skeleton annotations in WEBKNOSSOS.
 
@@ -281,6 +281,3 @@ def write(self, out_path: PathLike) -> None:
         """Deprecated. Use Skeleton.save instead."""
         warn_deprecated("Skeleton.write", "skeleton.save")
         self.save(out_path)
-
-    def __hash__(self) -> int:
-        return id(self)