From ef867e5798fe6cb8d9dccc87b0222e104147228d Mon Sep 17 00:00:00 2001
From: richardreeve <richard.reeve@glasgow.ac.uk>
Date: Tue, 21 Nov 2023 19:43:05 +0000
Subject: [PATCH] Fix missing exports and add tests

---
 src/Phylo.jl           | 11 +++++++----
 test/test_Interface.jl | 26 +++++++++++++++++++++++---
 2 files changed, 30 insertions(+), 7 deletions(-)

diff --git a/src/Phylo.jl b/src/Phylo.jl
index 503d1756..5b57b691 100644
--- a/src/Phylo.jl
+++ b/src/Phylo.jl
@@ -34,9 +34,12 @@ export OneTree, ManyTrees
 abstract type AbstractNode{RootType <: Rootedness, NodeLabel} end
 abstract type AbstractBranch{RootType <: Rootedness, NodeLabel} end
 
+using Distances
 abstract type AbstractTree{TT <: TreeType, RT <: Rootedness, NL,
                            N <: AbstractNode{RT, NL},
-                           B <: AbstractBranch{RT, NL}} end
+                           B <: AbstractBranch{RT, NL}} <: Distances.UnionMetric
+end
+
 export AbstractTree
 
 @enum TraversalOrder anyorder preorder inorder postorder breadthfirst
@@ -88,9 +91,9 @@ end
 
 include("Interface.jl")
 # AbstractTree methods
-export ntrees, gettrees, nroots, getroots, getroot
+export ntrees, gettrees, nroots, getroots, getroot, gettree
 export treenametype, gettreenames, gettreename #, getonetree #unimplemented
-export roottype, nodetype, nodedatatype, nodenametype
+export treetype, roottype, nodetype, nodedatatype, nodenametype
 export branchtype, branchdatatype, branchnametype
 export createbranch!, deletebranch!
 export createnode!, createnodes!, deletenode!
@@ -114,7 +117,7 @@ export validate!, traversal, branchdims
 export isleaf, isroot, isinternal, isunattached
 export indegree, outdegree, hasinbound, getinbound, getoutbounds
 export hasoutboundspace, hasinboundspace
-export getleafnames, getleaves, nleaves, nnodes, nbranches
+export getleafnames, getleaves, nleaves, nnodes, ninternal, nbranches
 export getleafinfo, setleafinfo!, leafinfotype
 export getnodedata, setnodedata!
 export hasheight, getheight, setheight!
diff --git a/test/test_Interface.jl b/test/test_Interface.jl
index 2c33d4a5..e454460e 100644
--- a/test/test_Interface.jl
+++ b/test/test_Interface.jl
@@ -10,10 +10,12 @@ using Test
          BinaryTree{ManyRoots, DataFrame, Vector{Float64}},
          RootedTree, ManyRootTree]
 
+        @test treetype(TreeType) == OneTree
         species = ["Dog", "Cat", "Human", "Potato", "Apple"]
         tree = TreeType(species)
         othernodes = ["Some 1", "Some 2"]
         nodes = createnodes!(tree, othernodes)
+        @test !((roottype(TreeType) ≡ ManyRoots) ⊻ validate!(tree))
         @test [getnodename(tree, node) for node in nodes] == othernodes
         extra = [getnodename(tree, node) for node in createnodes!(tree, 1)]
         @test isa(extra[1], String)
@@ -31,13 +33,19 @@ using Test
         allnodes = copy(innodes)
         pop!(innodes)
         @test_throws Exception getroot(tree)
+        matchbranch = true
         branches = map(innodes) do node
             itr = Iterators.filter(name -> hasoutboundspace(tree, name) &&
                                    name != node &&
                                    name ∉ getdescendants(tree, node) &&
                                    name ∉ species, allnodes)
-            getbranch(tree, createbranch!(tree, first(itr), node))
-        end
+            matchbranch = !matchbranch
+            if matchbranch
+                getbranch(tree, createbranch!(tree, getnode(tree, first(itr)), getnode(tree, node)))
+            else
+                getbranch(tree, createbranch!(tree, getnodename(tree, first(itr)), getnodename(tree, node)))
+            end
+            end
         @test_nowarn getroot(tree)
         branchnames = [getbranchname(tree, branch) for branch in branches]
         @test Set(branchnames) == Set(getbranchnames(tree))
@@ -84,6 +92,14 @@ using Test
         @test_nowarn createbranch!(tree, who, species[1])
         @test hasnode(tree, species[1])
         @test validate!(tree)
+        NT = typeof(node1)
+        @test NT ≡ String || nodenametype(NT) ≡ String
+        @test NT ≡ String || branchnametype(NT) ≡ Int
+        @test NT ≡ String || roottype(NT) ≡ roottype(TreeType)
+        BT = typeof(b)
+        @test nodenametype(BT) ≡ String
+        @test branchnametype(BT) ≡ Int
+        @test roottype(BT) ≡ roottype(TreeType)
         @test all(isleaf(tree, node) for node in species)
         @test all((!isroot(tree, node) & !isunattached(tree, node) &
                    !isinternal(tree, node)) for node in species)
@@ -92,7 +108,11 @@ using Test
             Set(getnodename(tree, dst(tree, branch))
                 for branch in getbranches(tree)) == Set(getnodenames(tree))
         createnode!(tree)
-        @test (roottype(TreeType) == OneRoot) ⊻ validate!(tree)
+        @test treenametype(TreeType) ≡ Int ? gettreename(tree) == 1 : gettreename(tree) == "Tree"
+        @test (roottype(TreeType) ≡ OneRoot) ⊻ validate!(tree)
+        @test gettree(tree) ≡ tree
+        @test length(getnodes(tree)) == nnodes(tree)
+        @test ninternal(tree) == nnodes(tree) - nleaves(tree)
     end
 end