added tests

src/treedata/_core/aligned_mapping.py

@@ -53,6 +53,8 @@ def _validate_tree(self, tree: nx.DiGraph, key: str) -> nx.DiGraph:
         for node in tree.nodes:
             if tree.in_degree(node) == 0:
                 root_count += 1
+                if tree.out_degree(node) == 0:
+                    raise ValueError(f"Value for key {key} must be fully connected")
             elif tree.in_degree(node) > 1:
                 raise ValueError(f"Value for key {key} must be a tree")
             if tree.out_degree(node) == 0:
@@ -196,8 +198,6 @@ def __setitem__(self, key: str, value: nx.DiGraph):
         )
         with view_update(self.parent, self.attrname, ()) as new_mapping:
             new_mapping[key] = value
-        print("here2")
-        print(key)
 
     def __delitem__(self, key: str):
         if key not in self:
@@ -222,7 +222,7 @@ def __len__(self) -> int:
 
 @contextmanager
 def view_update(tdata_view: TreeData, attr_name: str, keys: tuple[str, ...]):
-    """Context manager for updating a view of an AnnData object.
+    """Context manager for updating a view of an TreeData object.
 
     Contains logic for "actualizing" a view. Yields the object to be modified in-place.
 
@@ -241,8 +241,6 @@ def view_update(tdata_view: TreeData, attr_name: str, keys: tuple[str, ...]):
     """
     new = tdata_view.copy()
     attr = getattr(new, attr_name)
-    for key in attr:
-        print(key)
     container = reduce(lambda d, k: d[k], keys, attr)
     yield container
     tdata_view._init_as_actual(new)

src/treedata/_core/treedata.py

@@ -182,7 +182,7 @@ def _init_as_actual(
             self._vart = AxisTrees(self, 1, vals=vart)
 
     def _init_as_view(self, tdata_ref: TreeData, oidx: Index, vidx: Index):
-        super()._init_as_view(tdata_ref, oidx, vidx)
+        super()._init_as_view(tdata_ref, oidx=oidx, vidx=vidx)
 
         # view of obst and vart
         self._obst = tdata_ref.obst._view(self, (oidx,))

src/treedata/_utils.py

@@ -3,20 +3,6 @@
 import networkx as nx
 
 
-def get_leaves(tree: nx.DiGraph) -> list[str]:
-    """Get the leaves of a tree."""
-    leaves = [n for n in tree.nodes if tree.out_degree(n) == 0]
-    return leaves
-
-
-def get_root(tree: nx.DiGraph) -> str:
-    """Get the root of a tree."""
-    roots = [n for n in tree.nodes if tree.in_degree(n) == 0]
-    if len(roots) != 1:
-        raise ValueError(f"Tree must have exactly one root, found {len(roots)}.")
-    return roots[0]
-
-
 def subset_tree(tree: nx.DiGraph, leaves: list[str], asview: bool) -> nx.DiGraph:
     """Subset tree."""
     keep_nodes = set(leaves)

tests/test_base.py

@@ -40,10 +40,17 @@ def test_creation(X, adata, tree):
     assert tdata.X is adata.X
 
 
-@pytest.mark.parametrize("dim", ["obs", "var"])
-def test_tree_keys(X, tree, dim):
+@pytest.mark.parametrize("axis", [0, 1])
+def test_attributes(X, tree, axis):
+    dim = ["obs", "var"][axis]
     tdata = td.TreeData(X, obst={"tree": tree}, vart={"tree": tree}, label=None)
-    check_graph_equality(getattr(tdata, f"{dim}t")["tree"], tree)
+    assert getattr(tdata, f"{dim}t").axes == (axis,)
+    assert getattr(tdata, f"{dim}t").attrname == (f"{dim}t")
+    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.label is None
 
 
 @pytest.mark.parametrize("dim", ["obs", "var"])
@@ -131,6 +138,7 @@ def test_bad_tree(X):
     # Has cycle
     has_cycle = nx.DiGraph()
     has_cycle.add_edges_from([("0", "1"), ("1", "0")])
+    has_cycle.add_node("2")
     with pytest.raises(ValueError):
         _ = td.TreeData(X, obst={"tree": has_cycle})
     # Not fully connected
@@ -145,7 +153,7 @@ def test_bad_tree(X):
         _ = td.TreeData(X, obst={"tree": bad_leaves})
     # Multiple roots
     multi_root = nx.DiGraph()
-    multi_root.add_edges_from([("root", "0"), ("bad", "0")])
+    multi_root.add_edges_from([("0", "1"), ("1", "0"), ("2", "3")])
     with pytest.raises(ValueError):
         _ = td.TreeData(X, obst={"tree": multi_root})
 

tests/test_utils.py

@@ -1,43 +1,18 @@
 import networkx as nx
 import pytest
 
-from treedata._utils import get_leaves, get_root, subset_tree
+from treedata._utils import subset_tree
 
 
 @pytest.fixture
 def tree():
     tree = nx.balanced_tree(r=2, h=3, create_using=nx.DiGraph)
-    root = get_root(tree)
+    root = [n for n, d in tree.in_degree() if d == 0][0]
     depths = nx.single_source_shortest_path_length(tree, root)
     nx.set_node_attributes(tree, values=depths, name="depth")
     yield tree
 
 
-def test_get_leaves():
-    tree = nx.DiGraph()
-    tree.add_edges_from([("root", "0"), ("root", "1")])
-    assert get_leaves(tree) == ["0", "1"]
-
-
-def test_get_root():
-    tree = nx.DiGraph()
-    tree.add_edges_from([("root", "0"), ("root", "1")])
-    assert get_root(tree) == "root"
-
-
-def test_get_root_raises():
-    # Has cycle
-    has_cycle = nx.DiGraph()
-    has_cycle.add_edges_from([("root", "0"), ("0", "root")])
-    with pytest.raises(ValueError):
-        get_root(has_cycle)
-    # Multiple roots
-    multi_root = nx.DiGraph()
-    multi_root.add_edges_from([("root", "0"), ("bad", "0")])
-    with pytest.raises(ValueError):
-        get_root(multi_root)
-
-
 def test_subset_tree(tree):
     # copy
     subtree = subset_tree(tree, [7, 8, 9], asview=False)

tests/test_views.py

@@ -4,15 +4,13 @@
 import pytest
 
 import treedata as td
-from treedata._utils import get_root
 
 
 @pytest.fixture
 def tree():
     tree = nx.balanced_tree(r=2, h=3, create_using=nx.DiGraph)
     tree = nx.relabel_nodes(tree, {i: str(i) for i in tree.nodes})
-    root = get_root(tree)
-    depths = nx.single_source_shortest_path_length(tree, root)
+    depths = nx.single_source_shortest_path_length(tree, "0")
     nx.set_node_attributes(tree, values=depths, name="depth")
     yield tree
 
@@ -36,6 +34,16 @@ def test_views(tdata):
     assert tdata_subset.obs["test"].tolist() == list(range(2))
 
 
+# this test should pass once anndata bug is fixed
+# See https://github.com/scverse/anndata/issues/1382
+@pytest.mark.xfail
+def test_views_creation(tdata):
+    tdata_view = td.TreeData(tdata, asview=True)
+    assert tdata_view.is_view
+    with pytest.raises(ValueError):
+        _ = td.TreeData(np.zeros(shape=(3, 3)), asview=False)
+
+
 def test_views_subset_tree(tdata):
     expected_edges = [
         ("0", "1"),
@@ -58,6 +66,7 @@ def test_views_subset_tree(tdata):
     tdata_subset = tdata_subset.copy()
     edges = list(tdata_subset.obst["tree"].edges)
     assert edges == expected_edges
+    assert len(tdata.obst["tree"].edges) == 14
 
 
 def test_views_mutability(tdata):
@@ -76,7 +85,7 @@ def test_views_mutability(tdata):
         tdata_subset.obst["tree"].remove_node("8")
 
 
-def test_set(tdata):
+def test_views_set(tdata):
     tdata_subset = tdata[[0, 1, 4], :]
     # bad assignment
     bad_tree = nx.DiGraph()
@@ -94,7 +103,7 @@ def test_set(tdata):
     assert list(tdata_subset.obst["new_tree"].edges) == [("0", "8")]
 
 
-def test_del(tdata):
+def test_views_del(tdata):
     tdata_subset = tdata[[0, 1, 4], :]
     # bad deletion
     with pytest.raises(KeyError):
@@ -107,12 +116,12 @@ def test_del(tdata):
     assert list(tdata_subset.obst.keys()) == []
 
 
-def test_contains(tdata):
+def test_views_contains(tdata):
     tdata_subset = tdata[[0, 1, 4], :]
     assert "tree" in tdata_subset.obst
     assert "bad" not in tdata_subset.obst
 
 
-def test_len(tdata):
+def test_views_len(tdata):
     tdata_subset = tdata[[0, 1, 4], :]
     assert len(tdata_subset.obst) == 1