🚧 Removing nodes.

src/Topologies/Topologies.jl

@@ -115,8 +115,8 @@ function add_edge!(top::Topology, type, source, target)
     i_type = U.edge_type_index(top, type)
     i_source = U.node_index(top, source)
     i_target = U.node_index(top, target)
-    check_live_node(top, i_source)
-    check_live_node(top, i_target)
+    check_live_node(top, i_source, source)
+    check_live_node(top, i_target, target)
     U.has_edge(top, i_type, i_source, i_target) &&
         argerr("There is already an edge of type $(repr(type))
                 betwen nodes $(repr(source)) and $(repr(target)).")
@@ -127,4 +127,42 @@ function add_edge!(top::Topology, type, source, target)
 end
 export add_edge!
 
+# Remove all neighbours of this node and replace it with a tombstone.
+function _remove_node!(top::Topology, i_node::Int, i_type::Int)
+    # Assumes the node is valid and live, and that the type does correspond.
+    ts = Tombstone()
+    top.outgoing[i_node] = ts
+    top.incoming[i_node] = ts
+    for adjacency in (top.outgoing, top.incoming)
+        for other in adjacency
+            other isa Tombstone && continue
+            for neighbours in other
+                pop!(neighbours, i_node, nothing)
+            end
+        end
+    end
+    top.n_nodes[i_type] -= 1
+    top
+end
+# Checked version.
+function remove_node!(top::Topology, node, type)
+    check_node_ref(top, node)
+    check_node_type(top, type)
+    i_node = U.node_index(top, node)
+    check_live_node(top, i_node, node)
+    i_type = U.node_type_index(top, type)
+    U.is_node_of_type(top, i_node, i_type) ||
+        argerr("Node $(repr(node)) is not of type $(repr(type)).")
+    _remove_node!(top, i_node, i_type)
+end
+# Not specifying the type requires a linear search for it.
+function remove_node!(top::Topology, node)
+    check_node_ref(top, node)
+    i_node = U.node_index(top, node)
+    check_live_node(top, i_node, node)
+    i_type = U.type_index_of_node(top, node)
+    _remove_node!(top, i_node, i_type)
+end
+export remove_node!
+
 end

src/Topologies/checks.jl

@@ -27,8 +27,10 @@ check_edge_type(top::Topology, lab::Symbol) =
 check_node_ref(top::Topology, lab::Symbol) = check_label(lab, keys(top.nodes_index), "node")
 
 # Check node liveliness, assuming the reference is valid.
-function check_live_node(top::Topology, node)
+function check_live_node(top::Topology, node, original_ref = node)
+    # (use the original reference to trace back to actual user input
+    # and improve error message)
     U.is_removed(top, node) &&
-        argerr("Node $(repr(node)) has been removed from this topology.")
+        argerr("Node $(repr(original_ref)) has been removed from this topology.")
     node
 end

src/Topologies/unchecked_queries.jl

@@ -35,9 +35,15 @@ node_label(::Topology, lab::Symbol) = lab
 node_index(::Topology, i::Int) = i
 # Querying node type requires a linear search,
 # but it is generally assumed that if you know the node, then you already know its type.
-node_type_index(top::Topology, id) =
+type_index_of_node(top::Topology, id) =
     findfirst(range -> node_index(top, id) in range, top.nodes_types)
-node_type(top::Topology, id) = node_type_label(node_type_index(top, id))
+type_of_node(top::Topology, id) = node_type_label(type_index_of_node(top, id))
+# But it is O(1) to check whether a given node is of the given type.
+function is_node_of_type(top::Topology, node, type)
+    i_node = node_index(top, node)
+    i_type = node_type_index(type)
+    i_node in top.nodes_types[i_type]
+end
 
 is_removed(top::Topology, node) = top.outgoing[node_index(top, node)] isa Tombstone
 is_live(top::Topology, node) = !is_removed(top, node)

test/topologies.jl

@@ -16,6 +16,7 @@ add_edge!(top, :trophic, :d, :u)
 add_edge!(top, :trophic, :b, :v)
 add_edge!(top, :mutualism, :a, :d)
 add_edge!(top, :interference, :a, :c)
+remove_node!(top, :b) #  HERE: fix!
 
 # Having this correct display implies that numerous internals are working correctly.
 @test "$top" == "Topology(2 node types, 3 edge types, 6 nodes, 7 edges)"