Merge pull request #60 from YosefLab/allow-overlap

default allow overlap

Author: colganwi

CHANGELOG.md

@@ -16,6 +16,18 @@ and this project adheres to [Semantic Versioning][].
 
 ### Fixed
 
+## [0.2.2] - 2025-09-18
+
+### Added
+
+-  `tdata.has_overlap` parameter to check whether the `TreeData` object contains overlapping trees (#59)
+
+### Changed
+
+- Default value for `tdata.allow_overlap` is now `True` (#60)
+
+### Fixed
+
 ## [0.2.1] - 2025-07-10
 
 ### Added

docs/notebooks/getting-started.ipynb

@@ -4,7 +4,7 @@ requires = [ "hatchling" ]
 
 [project]
 name = "treedata"
-version = "0.2.1"
+version = "0.2.2"
 description = "anndata with trees"
 readme = "README.md"
 license = { file = "LICENSE" }

pyproject.toml

@@ -76,7 +76,7 @@ class TreeData(ad.AnnData):
         - `nodes`: All leaf and internal node names are present in the observation/variable names.
         - `subset`: A subset of leaf and internal node names are present in the observation/variable names.
     allow_overlap
-        Whether trees containing overlapping sets of leaves or nodes are allowed. Default is False.
+        Whether trees containing overlapping sets of leaves or nodes are allowed. Default is True.
     """
 
     def __init__(
@@ -98,7 +98,7 @@ def __init__(
         asview: bool = False,
         label: str | None = "tree",
         alignment: Literal["leaves", "nodes", "subset"] = "leaves",
-        allow_overlap: bool = False,
+        allow_overlap: bool = True,
         *,
         obsp: np.ndarray | Mapping[str, Sequence[Any]] | None = None,
         varp: np.ndarray | Mapping[str, Sequence[Any]] | None = None,

src/treedata/_core/treedata.py

@@ -51,7 +51,7 @@ def test_attributes(X, tree, axis):
     assert getattr(tdata, f"{dim}t").dim == dim
     assert getattr(tdata, f"{dim}t").parent is tdata
     assert list(getattr(tdata, f"{dim}t").dim_names) == ["0", "1", "2"]
-    assert tdata.allow_overlap is False
+    assert tdata.allow_overlap is True
     assert tdata.has_overlap is False
     assert tdata.label is None
 

tests/test_base.py

@@ -100,7 +100,7 @@ def test_read_anndata(X, tmp_path):
     tdata = td.read_h5td(file_path)
     assert np.array_equal(tdata.X, adata.X)
     assert tdata.label == "tree"
-    assert tdata.allow_overlap is False
+    assert tdata.allow_overlap is True
     assert tdata.alignment == "leaves"
     assert tdata.obst_keys() == []