doc: book chapter on edge differences (#417)

Move some tests from tree.rs to tests/

Author: molpopgen

book/src/SUMMARY.md

@@ -13,6 +13,7 @@
   - [Initialization from a table collection](./tree_sequence_from_table_collection.md)
   - [Iterating over trees](./tree_sequence_iterate_trees.md)
   - [Working with trees](./tree_sequence_tree.md)
+  - [Edge differences](./tree_sequence_edge_diffs.md)
   - [Miscellaneous operations](./tree_sequence_miscellaneous.md)
 
 * [Metadata](./metadata.md)

book/src/tree_sequence_edge_diffs.md

@@ -0,0 +1,19 @@
+## Iterating over edge differences
+
+As with [trees](tree_sequence_iterate_trees.md), the API provides a *lending* iterator over edge differences.
+Each step of the iterator advances to the next tree in the tree sequence.
+For each tree, a standard `Iterator` over removals and insertions is available:
+
+```rust, noplaygound, ignore
+{{#include ../../tests/book_trees.rs:iterate_edge_differences}}
+```
+
+Edge differences are the basis of efficient algorithms based on the incremental updating of summaries of trees.
+The following example co-iterates over edge differences and trees.
+The edge differences are used to calculate the parent array for each tree:
+
+```rust, noplaygound, ignore
+{{#include ../../tests/book_trees.rs:iterate_edge_differences_update_parents}}
+```
+
+

src/trees.rs

@@ -873,56 +873,6 @@ pub(crate) mod test_trees {
             panic!("Expected a tree.");
         }
     }
-
-    // TODO: use trybuild to add tests that the iterator
-    // lifetime is indeed coupled to that of the treeseq
-    #[test]
-    fn test_edge_diffs_lending_iterator_num_trees() {
-        {
-            let treeseq = treeseq_from_small_table_collection_two_trees();
-            let num_nodes: usize = treeseq.nodes().num_rows().try_into().unwrap();
-            let mut parents = vec![NodeId::NULL; num_nodes + 1];
-            if let Ok(mut ediff_iter) = treeseq.edge_differences_iter() {
-                let mut tree_iter = treeseq.tree_iterator(0).unwrap();
-                let mut ntrees = 0;
-                while let Some(diffs) = ediff_iter.next() {
-                    let tree = tree_iter.next().unwrap();
-
-                    for edge_out in diffs.edge_removals() {
-                        let p = edge_out.child();
-                        parents[usize::try_from(p).unwrap()] = NodeId::NULL;
-                    }
-
-                    for edge_in in diffs.edge_insertions() {
-                        let c: usize = edge_in.child().try_into().unwrap();
-                        parents[c] = edge_in.parent();
-                    }
-
-                    assert_eq!(tree.parent_array(), &parents);
-                    ntrees += 1;
-                }
-                assert_eq!(ntrees, 2);
-            } else {
-                panic!("expected an edge differences iterator");
-            }
-        }
-
-        {
-            let treeseq = treeseq_from_small_table_collection_two_trees();
-            let mut ediff_iter = treeseq.edge_differences_iter().unwrap();
-
-            let mut ntrees = 0;
-            while let Some(diffs) = ediff_iter.next() {
-                if ntrees == 0 {
-                    assert_eq!(diffs.interval(), (0.0.into(), 500.0.into()));
-                } else {
-                    assert_eq!(diffs.interval(), (500.0.into(), 1000.0.into()));
-                }
-                ntrees += 1;
-            }
-            assert_eq!(ntrees, 2);
-        }
-    }
 }
 
 #[cfg(test)]

tests/book_trees.rs

@@ -142,4 +142,46 @@ fn initialize_from_table_collection() {
         }
     }
     // ANCHOR_END: iterate_node_siblings_via_array_getters
+
+    // ANCHOR: iterate_edge_differences
+    if let Ok(mut edge_diff_iterator) = treeseq.edge_differences_iter() {
+        while let Some(diffs) = edge_diff_iterator.next() {
+            for edge_removal in diffs.edge_removals() {
+                println!("{}", edge_removal);
+            }
+            for edge_insertion in diffs.edge_insertions() {
+                println!("{}", edge_insertion);
+            }
+        }
+    } else {
+        panic!("creating edge diffs iterator failed");
+    }
+    // ANCHOR_END: iterate_edge_differences
+
+    // ANCHOR: iterate_edge_differences_update_parents
+    let num_nodes: usize = treeseq.nodes().num_rows().try_into().unwrap();
+    // num_nodes + 1 to reflect a "virtual root" present in
+    // the tree arrays
+    let mut parents = vec![NodeId::NULL; num_nodes + 1];
+    match treeseq.edge_differences_iter() {
+        Ok(mut ediff_iter) => match treeseq.tree_iterator(0) {
+            Ok(mut tree_iter) => {
+                while let Some(diffs) = ediff_iter.next() {
+                    let tree = tree_iter.next().unwrap();
+                    for edge_out in diffs.edge_removals() {
+                        let c = edge_out.child();
+                        parents[c.as_usize()] = NodeId::NULL;
+                    }
+                    for edge_in in diffs.edge_insertions() {
+                        let c = edge_in.child();
+                        parents[c.as_usize()] = edge_in.parent();
+                    }
+                    assert_eq!(tree.parent_array(), &parents);
+                }
+            }
+            Err(e) => panic!("error creating tree iter: {:?}", e),
+        },
+        Err(e) => panic!("error creating edge diff iter: {:?}", e),
+    }
+    // ANCHOR_END: iterate_edge_differences_update_parents
 }