For adding only nodes to nodelist. Please check before merging.

share/lib/python/neuron/rxd/nodelist.py

@@ -1,10 +1,19 @@
 from .rxdException import RxDException
+from .node import Node
+import types
+from collections import abc
 
 
 class NodeList(list):
     def __init__(self, items):
         """Constructs a NodeList from items, a python iterable containing Node objects."""
-        list.__init__(self, items)
+        if isinstance(items, abc.Generator) or isinstance(items, abc.Iterator):
+            items = list(items)
+
+        if items == [] or all(isinstance(item, Node) for item in items):
+            list.__init__(self, items)
+        else:
+            raise TypeError("Items must be nodes.")
 
     def __call__(self, restriction):
         """returns a sub-NodeList consisting of nodes satisfying restriction"""
@@ -16,6 +25,30 @@ def __getitem__(self, key):
         else:
             return list.__getitem__(self, key)
 
+    def __setitem__(self, index, value):
+        if not isinstance(value, Node):
+            raise TypeError("Only assign a node to the list")
+        super().__setitem__(index, value)
+
+    def append(self, items):
+        if not isinstance(items, Node):
+            raise TypeError("The append item must be a Node.")
+        super().append(items)
+
+    def extend(self, items):
+        if isinstance(items, abc.Generator) or isinstance(items, abc.Iterator):
+            items = list(items)
+
+        for item in items:
+            if not isinstance(item, Node):
+                raise TypeError("The extended items must all be Nodes.")
+        super().extend(items)
+
+    def insert(self, position, items):
+        if not isinstance(items, Node):
+            raise TypeError("The item inserted must be a Node.")
+        super().insert(position, items)
+
     @property
     def value(self):
         # TODO: change this when not everything is a concentration

test/rxd/test_nodelist.py

@@ -0,0 +1,90 @@
+def test_only_nodes(neuron_instance):
+    """Test to make sure node lists only contain nodes"""
+
+    h, rxd, data, save_path = neuron_instance
+
+    dend = h.Section("dend")
+    r = rxd.Region(h.allsec())
+    hydrogen = rxd.Species(r, initial=1)
+    water = rxd.Species(r, initial=1)
+
+    h.finitialize(-65)
+
+    nodelist = hydrogen.nodes
+
+    # test that should not work, so an append that succeeds is an error
+
+    try:
+        nodelist.append(water.nodes)  # append nodelist
+        raise Exception("should not get here")
+    except TypeError:
+        ...
+
+    try:
+        nodelist.extend([1, 2, 3, water.nodes[0]])  # extend with non-nodes
+        raise Exception("should not get here")
+    except TypeError:
+        ...
+
+    try:
+        nodelist[0] = 17
+        raise Exception("should not get here")
+    except TypeError:
+        ...
+
+    try:
+        nl = rxd.nodelist.NodeList(
+            [1, 2, 3, water.nodes[0]]
+        )  # create NodeList with non-nodes
+        raise Exception("should not get here")
+    except TypeError:
+        ...
+
+    try:
+        nodelist.insert(1, "llama")  # insert non-node into nodelist
+        raise Exception("should not get here")
+    except TypeError:
+        ...
+
+    # test that should work, so getting in the except is an error
+    try:
+        nodelist.append(water.nodes[0])  # append node
+    except TypeError:
+        raise Exception("should not get here")
+
+    try:
+        original_length = len(nodelist)  # extend nodes
+        nodelist.extend(item for item in water.nodes)
+        assert len(nodelist) == original_length + len(water.nodes)
+    except TypeError:
+        raise Exception("should not get here")
+
+    try:
+        nodelist[0] = water.nodes[0]
+    except TypeError:
+        raise Exception("should not get here")
+
+    try:
+        nl = rxd.nodelist.NodeList(
+            [water.nodes[0], water.nodes[0]]
+        )  # create nodelist with nodes
+    except TypeError:
+        raise Exception("should not get here")
+
+    try:
+        nodelist.insert(1, water.nodes[0])  # insert node into nodelist
+    except TypeError:
+        raise Exception("should not get here")
+
+    try:
+        nl = rxd.nodelist.NodeList([])  # create empty nodelist
+    except TypeError:
+        raise Exception("should not get here")
+
+    try:
+        nl = rxd.nodelist.NodeList(
+            item for item in [water.nodes[0], water.nodes[0]]
+        )  # create nodelist with nodes generator
+        assert len(nl) == 2
+    except TypeError:
+        raise Exception("should not get here")