From 169a834395a974fc6cc7c98aabce2f8789ec54ff Mon Sep 17 00:00:00 2001
From: "Kevin R. Thornton" <krthornt@uci.edu>
Date: Fri, 20 Jun 2025 14:26:08 -0700
Subject: [PATCH 1/4] feat: access nodes in Tree as slice of NodeId

---
 src/sys/tree.rs | 40 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)

diff --git a/src/sys/tree.rs b/src/sys/tree.rs
index e79628214..84b51cf94 100644
--- a/src/sys/tree.rs
+++ b/src/sys/tree.rs
@@ -156,6 +156,46 @@ impl<'treeseq> LLTree<'treeseq> {
         }
     }
 
+    pub fn nodes(&self, order: NodeTraversalOrder) -> Result<Box<[NodeId]>, TskitError> {
+        let mut nodes: Vec<NodeId> = vec![
+            NodeId::NULL;
+            unsafe { super::bindings::tsk_tree_get_size_bound(self.as_ll_ref()) }
+                as usize
+        ];
+
+        let mut num_nodes: super::bindings::tsk_size_t = 0;
+        let ptr = std::ptr::addr_of_mut!(num_nodes);
+        unsafe {
+            super::bindings::tsk_tree_preorder(
+                self.as_ll_ref(),
+                nodes.as_mut_ptr() as *mut super::bindings::tsk_id_t,
+                ptr,
+            );
+        }
+
+        let code = match order {
+            NodeTraversalOrder::Preorder => unsafe {
+                super::bindings::tsk_tree_preorder(
+                    self.as_ll_ref(),
+                    nodes.as_mut_ptr() as *mut super::bindings::tsk_id_t,
+                    ptr,
+                )
+            },
+            NodeTraversalOrder::Postorder => unsafe {
+                super::bindings::tsk_tree_preorder(
+                    self.as_ll_ref(),
+                    nodes.as_mut_ptr() as *mut super::bindings::tsk_id_t,
+                    ptr,
+                )
+            },
+        };
+        if code == 0 {
+            nodes.resize(num_nodes as usize, NodeId::NULL);
+        }
+
+        handle_tsk_return_value!(code, nodes.into_boxed_slice())
+    }
+
     pub fn children(&self, u: NodeId) -> impl Iterator<Item = NodeId> + '_ {
         NodeIteratorAdapter(ChildIterator::new(self, u))
     }

From 20556c581497cee45977c59760bd050887cbbe93 Mon Sep 17 00:00:00 2001
From: "Kevin R. Thornton" <krthornt@uci.edu>
Date: Fri, 20 Jun 2025 16:51:00 -0700
Subject: [PATCH 2/4] pub exposure of fn

---
 src/trees/tree.rs | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/trees/tree.rs b/src/trees/tree.rs
index cbb463f02..93de10250 100644
--- a/src/trees/tree.rs
+++ b/src/trees/tree.rs
@@ -313,6 +313,12 @@ impl<'treeseq> Tree<'treeseq> {
         self.inner.traverse_nodes(order)
     }
 
+    pub fn nodes(
+        &self,
+        order: crate::NodeTraversalOrder,
+    ) -> Result<Box<[NodeId]>, TskitError> {
+    }
+
     /// Return an [`Iterator`] over the children of node `u`.
     /// # Returns
     ///

From 50ec541e2b8282cb2bd1dd3ba1b5f66daf1ca827 Mon Sep 17 00:00:00 2001
From: "Kevin R. Thornton" <krthornt@uci.edu>
Date: Fri, 20 Jun 2025 16:56:30 -0700
Subject: [PATCH 3/4] update example

---
 examples/tree_traversals.rs | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/examples/tree_traversals.rs b/examples/tree_traversals.rs
index 5cd89faa3..1d4c58743 100644
--- a/examples/tree_traversals.rs
+++ b/examples/tree_traversals.rs
@@ -21,7 +21,19 @@ fn traverse_upwards_with_iterator(tree: &tskit::Tree) {
 }
 
 fn preorder_traversal(tree: &tskit::Tree) {
-    for _ in tree.traverse_nodes(tskit::NodeTraversalOrder::Preorder) {}
+    // Iterate over nodes.
+    // For preorder traversal, this avoids allocation.
+    // (But we collect the data for this example, which does allocate.)
+    let nodes_from_iter = tree
+        .traverse_nodes(tskit::NodeTraversalOrder::Preorder)
+        .collect::<Vec<_>>();
+    // Get a COPY of all nodes as a boxed slice
+    let nodes_as_slice = tree.nodes(tskit::NodeTraversalOrder::Preorder).unwrap();
+    assert_eq!(nodes_as_slice.len(), nodes_from_iter.len());
+    nodes_from_iter
+        .iter()
+        .zip(nodes_as_slice.iter())
+        .for_each(|(i, j)| assert_eq!(i, j));
 }
 
 #[derive(clap::Parser)]

From 3eb617a43a1ce46a7d641934967a729b6d2af36b Mon Sep 17 00:00:00 2001
From: "Kevin R. Thornton" <krthornt@uci.edu>
Date: Fri, 20 Jun 2025 16:58:53 -0700
Subject: [PATCH 4/4] todo

---
 tests/test_trees.rs | 1 +
 1 file changed, 1 insertion(+)

diff --git a/tests/test_trees.rs b/tests/test_trees.rs
index 73938176d..0f65a4fec 100644
--- a/tests/test_trees.rs
+++ b/tests/test_trees.rs
@@ -278,6 +278,7 @@ fn test_iterate_samples() {
 #[cfg(feature = "bindings")]
 #[test]
 fn test_iterate_samples_two_trees() {
+    todo!("need a test for the new Tree::nodes function");
     let treeseq = treeseq_from_small_table_collection_two_trees();
     assert_eq!(treeseq.num_trees(), 2);
     let mut tree_iter = treeseq.tree_iterator(TreeFlags::SAMPLE_LISTS).unwrap();