Merge pull request #10 from YosefLab/unique-names

ensure names unique

src/treedata/_core/aligned_mapping.py

@@ -86,6 +86,15 @@ def _update_tree_labels(self):
                 mapping
             )
 
+    def _check_uniqueness(self):
+        names = "Observation" if self.dim == "obs" else "Variable"
+        if not getattr(self.parent, self.dim).index.is_unique:
+            warnings.warn(
+                f"{names} names must be unique to store a tree. Calling `.{self.dim}_names_make_unique` to make them unique.",
+                stacklevel=2,
+            )
+            getattr(self.parent, self.dim).index = ad.utils.make_index_unique(getattr(self.parent, self.dim).index)
+
     def copy(self):
         d = AxisTrees(self.parent, self._axis)
         for k, v in self.items():
@@ -122,7 +131,7 @@ def dim_names(self) -> pd.Index:
 class AxisTrees(AxisTreesBase):
     def __init__(
         self,
-        parent: ad.AnnData,
+        parent: TreeData,
         axis: int,
         vals: Mapping | None = None,
     ):
@@ -141,6 +150,7 @@ def __getitem__(self, key: str) -> nx.DiGraph:
         return nx.graphviews.generic_graph_view(self._data[key])
 
     def __setitem__(self, key: str, value: nx.DiGraph):
+        self._check_uniqueness()
         value, leaves = self._validate_tree(value, key)
 
         for leaf in leaves:
@@ -194,6 +204,7 @@ def __getitem__(self, key: str) -> nx.DiGraph:
         return subset_tree(self.parent_mapping[key], subset_leaves, asview=True)
 
     def __setitem__(self, key: str, value: nx.DiGraph):
+        self._check_uniqueness()
         value, _ = self._validate_tree(value, key)  # Validate before mutating
         warnings.warn(
             f"Setting element `.{self.attrname}['{key}']` of view, initializing view as actual.", stacklevel=2

src/treedata/_core/treedata.py

@@ -208,7 +208,7 @@ def obst(self) -> AxisTrees:
         return self._obst
 
     @property
-    def vart(self):
+    def vart(self) -> AxisTrees:
         """Tree annotation of variables
 
         Stores for each key a :class:`~networkx.DiGraph` with leaf nodes in
@@ -239,7 +239,7 @@ def obst(self, value):
 
     @vart.setter
     def vart(self, value):
-        vart = AxisTrees(self, 0, vals=dict(value))
+        vart = AxisTrees(self, 1, vals=dict(value))
         self._vart = vart
 
     def _gen_repr(self, n_obs, n_vars) -> str:

tests/test_base.py

@@ -181,3 +181,13 @@ def test_transpose(adata, tree):
     assert treedata.obst["tree"].nodes == treedata_transpose.vart["tree"].nodes
     assert treedata_transpose.obst_keys() == []
     assert np.array_equal(treedata.obs_names, treedata.T.obs_names)
+
+
+@pytest.mark.parametrize("dim", ["obs", "var"])
+def test_not_unique(X, tree, dim):
+    with pytest.warns(UserWarning):
+        tdata = td.TreeData(pd.DataFrame(X, index=["0", "1", "1"], columns=["0", "1", "1"]))
+    assert not getattr(tdata, f"{dim}_names").is_unique
+    with pytest.warns(UserWarning):
+        setattr(tdata, f"{dim}t", {"tree": tree})
+    assert getattr(tdata, f"{dim}_names").is_unique