Rename egonet and move the neighbors method to the IDView class (#129)

Changed name from `egonet` to `edge_neighborhood` and moved `neighbors()` to the `IDView` class

docs/source/api/classes/xgi.classes.function.rst

@@ -10,7 +10,7 @@
    .. autofunction:: create_empty_copy
    .. autofunction:: degree_counts
    .. autofunction:: degree_histogram
-   .. autofunction:: egonet
+   .. autofunction:: edge_neighborhood
    .. autofunction:: freeze
    .. autofunction:: frozen
    .. autofunction:: get_edge_attributes

docs/source/api/classes/xgi.classes.hypergraph.Hypergraph.rst

@@ -59,5 +59,4 @@
       ~Hypergraph.isolates
       ~Hypergraph.duplicate_edges
       ~Hypergraph.has_edge
-      ~Hypergraph.neighbors
       ~Hypergraph.singleton_edges

docs/source/api/classes/xgi.classes.reportviews.EdgeView.rst

@@ -21,5 +21,6 @@ xgi.classes.reportviews.EdgeView
       :nosignatures:
 
       ~EdgeView.members
+      ~IDView.neighbors
       ~IDView.filterby
       ~IDView.filterby_attr

docs/source/api/classes/xgi.classes.reportviews.IDView.rst

@@ -17,5 +17,6 @@ xgi.classes.reportviews.IDView
       :nosignatures:
 
       ~IDView.from_view
+      ~IDView.neighbors
       ~IDView.filterby
       ~IDView.filterby_attr

docs/source/api/classes/xgi.classes.reportviews.NodeView.rst

@@ -21,5 +21,6 @@ xgi.classes.reportviews.NodeView
       :nosignatures:
 
       ~NodeView.memberships
+      ~IDView.neighbors
       ~IDView.filterby
       ~IDView.filterby_attr

tests/classes/test_function.py

@@ -41,13 +41,13 @@ def test_is_uniform(edgelist1, edgelist6, edgelist7):
     assert xgi.is_uniform(H3) == False
 
 
-def test_egonet(edgelist3):
+def test_edge_neighborhood(edgelist3):
     H = xgi.Hypergraph(edgelist3)
-    assert H.neighbors(3) == {1, 2, 4}
-    assert xgi.egonet(H, 3) == [[1, 2], [4]]
-    assert xgi.egonet(H, 3, include_self=True) == [[1, 2, 3], [3, 4]]
+    assert H.nodes.neighbors(3) == {1, 2, 4}
+    assert xgi.edge_neighborhood(H, 3) == [[1, 2], [4]]
+    assert xgi.edge_neighborhood(H, 3, include_self=True) == [[1, 2, 3], [3, 4]]
     with pytest.raises(IDNotFound):
-        xgi.egonet(H, 7)
+        xgi.edge_neighborhood(H, 7)
 
 
 def test_degree_counts(edgelist1, edgelist2, edgelist3):

tests/classes/test_hypergraph.py

@@ -69,18 +69,6 @@ def test_len(edgelist1, edgelist2):
     assert len(H2) == 6
 
 
-def test_neighbors(edgelist1, edgelist2):
-    el1 = edgelist1
-    el2 = edgelist2
-    H1 = xgi.Hypergraph(el1)
-    H2 = xgi.Hypergraph(el2)
-    assert H1.neighbors(1) == {2, 3}
-    assert H1.neighbors(4) == set()
-    assert H1.neighbors(6) == {5, 7, 8}
-    assert H2.neighbors(4) == {3, 5, 6}
-    assert H2.neighbors(1) == {2}
-
-
 def test_dual(edgelist1, edgelist2, edgelist4):
     el1 = edgelist1
     el2 = edgelist2

tests/classes/test_iddict.py

@@ -21,7 +21,7 @@ def test_iddict(edgelist1):
 def test_neighbors():
     H = xgi.Hypergraph()
     with pytest.raises(IDNotFound):
-        H.neighbors(0)
+        H.nodes.neighbors(0)
     with pytest.raises(IDNotFound):
         H.remove_node(0)
     with pytest.raises(IDNotFound):

tests/classes/test_reportviews.py

@@ -5,6 +5,23 @@
 from xgi.exception import IDNotFound, XGIError
 
 
+def test_neighbors(edgelist1, edgelist2):
+    el1 = edgelist1
+    el2 = edgelist2
+    H1 = xgi.Hypergraph(el1)
+    H2 = xgi.Hypergraph(el2)
+    assert H1.nodes.neighbors(1) == {2, 3}
+    assert H1.nodes.neighbors(4) == set()
+    assert H1.nodes.neighbors(6) == {5, 7, 8}
+    assert H2.nodes.neighbors(4) == {3, 5, 6}
+    assert H2.nodes.neighbors(1) == {2}
+
+    assert H1.edges.neighbors(0) == set()
+    assert H1.edges.neighbors(1) == set()
+    assert H1.edges.neighbors(2) == {3}
+    assert H1.edges.neighbors(3) == {2}
+
+
 def test_edge_order(edgelist3):
     H = xgi.Hypergraph(edgelist3)
 

xgi/algorithms/connected.py

@@ -200,7 +200,7 @@ def _plain_bfs(H, source):
         for v in thislevel:
             if v not in seen:
                 seen.add(v)
-                nextlevel.update(H.neighbors(v))
+                nextlevel.update(H.nodes.neighbors(v))
     return seen
 
 

xgi/classes/function.py

@@ -8,7 +8,7 @@
     "max_edge_order",
     "is_possible_order",
     "is_uniform",
-    "egonet",
+    "edge_neighborhood",
     "degree_counts",
     "degree_histogram",
     "unique_edge_sizes",
@@ -101,27 +101,27 @@ def is_uniform(H):
     return edge_sizes.pop() - 1  # order of all edges
 
 
-def egonet(H, n, include_self=False):
-    """The egonet of the specified node.
+def edge_neighborhood(H, n, include_self=False):
+    """The edge neighborhood of the specified node.
 
-    The egonet of a node `n` in a hypergraph `H` is another hypergraph whose nodes
-    are the neighbors of `n` and its edges are all the edges in `H` that contain
-    `n`.  Usually, the egonet do not include `n` itself.  This can be controlled
+    The edge neighborhood of a node `n` in a hypergraph `H` is an edgelist of all the edges
+    containing `n` and its edges are all the edges in `H` that contain
+    `n`.  Usually, the edge neighborhood does not include `n` itself.  This can be controlled
     with `include_self`.
 
     Parameters
     ----------
     H : Hypergraph
         THe hypergraph of interest
     n : node
-        Node whose egonet is needed.
+        Node whose edge_neighborhood is needed.
     include_self : bool (default False)
-        Whether the egonet contains `n`.
+        Whether the edge_neighborhood contains `n`.
 
     Returns
     -------
     list
-        An edgelist of the egonet of `n`.
+        An edgelist of the edge_neighborhood of `n`.
 
     See Also
     --------
@@ -131,11 +131,11 @@ def egonet(H, n, include_self=False):
     --------
     >>> import xgi
     >>> H = xgi.Hypergraph([[1, 2, 3], [3, 4], [4, 5, 6]])
-    >>> H.neighbors(3)
+    >>> H.nodes.neighbors(3)
     {1, 2, 4}
-    >>> xgi.egonet(H, 3)
+    >>> xgi.edge_neighborhood(H, 3)
     [[1, 2], [4]]
-    >>> xgi.egonet(H, 3, include_self=True)
+    >>> xgi.edge_neighborhood(H, 3, include_self=True)
     [[1, 2, 3], [3, 4]]
 
     """

xgi/classes/hypergraph.py

@@ -265,33 +265,6 @@ def num_edges(self):
         """
         return len(self._edge)
 
-    def neighbors(self, n):
-        """Find the neighbors of a node.
-        The neighbors of a node are those nodes that appear in at least one edge with
-        said node.
-        Parameters
-        ----------
-        n : node
-            Node to find neighbors of.
-        Returns
-        -------
-        set
-            A set of the neighboring nodes
-        See Also
-        --------
-        egonet
-        Examples
-        --------
-        >>> import xgi
-        >>> hyperedge_list = [[1, 2], [2, 3, 4]]
-        >>> H = xgi.Hypergraph(hyperedge_list)
-        >>> H.neighbors(1)
-        {2}
-        >>> H.neighbors(2)
-        {1, 3, 4}
-        """
-        return {i for e in self._node[n] for i in self._edge[e]}.difference({n})
-
     def add_node(self, node, **attr):
         """Add one node with optional attributes.
 

xgi/classes/reportviews.py

@@ -38,7 +38,14 @@ class IDView(Mapping, Set):
 
     """
 
-    __slots__ = ("_dispatcher", "_id_dict", "_id_attr", "_ids")
+    __slots__ = (
+        "_dispatcher",
+        "_id_dict",
+        "_id_attr",
+        "_bi_id_dict",
+        "_bi_id_attr",
+        "_ids",
+    )
 
     def __getstate__(self):
         """Function that allows pickling.
@@ -53,6 +60,8 @@ def __getstate__(self):
         return {
             "_id_dict": self._id_dict,
             "_id_attr": self._id_attr,
+            "_bi_id_dict": self._bi_id_dict,
+            "_bi_id_attr": self._bi_id_attr,
             "_ids": self._ids,
         }
 
@@ -68,12 +77,16 @@ def __setstate__(self, state):
         """
         self._id_dict = state["_id_dict"]
         self._id_attr = state["_id_attr"]
+        self._bi_id_dict = state["_bi_id_dict"]
+        self._bi_id_attr = state["_bi_id_attr"]
         self._ids = state["_ids"]
 
-    def __init__(self, H, id_dict, id_attr, dispatcher, ids=None):
+    def __init__(self, id_dict, id_attr, bi_id_dict, bi_id_attr, dispatcher, ids=None):
         self._dispatcher = dispatcher
         self._id_dict = id_dict
         self._id_attr = id_attr
+        self._bi_id_dict = bi_id_dict
+        self._bi_id_attr = bi_id_attr
 
         if ids is None:
             self._ids = self._id_dict
@@ -297,6 +310,38 @@ def filterby_attr(self, attr, val, mode="eq", missing=None):
             )
         return type(self).from_view(self, bunch)
 
+    def neighbors(self, id):
+        """Find the neighbors of an ID.
+
+        The neighbors of an ID are those IDs that share at least one bipartite ID.
+
+        Parameters
+        ----------
+        id : hashable
+            ID to find neighbors of.
+        Returns
+        -------
+        set
+            A set of the neighboring IDs
+
+        See Also
+        --------
+        edge_neighborhood
+
+        Examples
+        --------
+        >>> import xgi
+        >>> hyperedge_list = [[1, 2], [2, 3, 4]]
+        >>> H = xgi.Hypergraph(hyperedge_list)
+        >>> H.nodes.neighbors(1)
+        {2}
+        >>> H.nodes.neighbors(2)
+        {1, 3, 4}
+        """
+        return {i for n in self._id_dict[id] for i in self._bi_id_dict[n]}.difference(
+            {id}
+        )
+
     @classmethod
     def from_view(cls, view, bunch=None):
         """Create a view from another view.
@@ -321,6 +366,8 @@ def from_view(cls, view, bunch=None):
         newview._dispatcher = view._dispatcher.__class__(view._dispatcher.net, newview)
         newview._id_dict = view._id_dict
         newview._id_attr = view._id_attr
+        newview._bi_id_dict = view._bi_id_dict
+        newview._bi_id_attr = view._bi_id_attr
         all_ids = set(view._id_dict.keys())
         if bunch is None:
             newview._ids = all_ids
@@ -355,9 +402,11 @@ class NodeView(IDView):
     def __init__(self, H, bunch=None):
         dispatcher = NodeStatDispatcher(H, self)
         if H is None:
-            super().__init__(None, None, None, dispatcher, bunch)
+            super().__init__(None, None, None, None, dispatcher, bunch)
         else:
-            super().__init__(H, H._node, H._node_attr, dispatcher, bunch)
+            super().__init__(
+                H._node, H._node_attr, H._edge, H._edge_attr, dispatcher, bunch
+            )
 
     def memberships(self, n=None):
         """Get the edge ids of which a node is a member.
@@ -403,9 +452,11 @@ class EdgeView(IDView):
     def __init__(self, H, bunch=None):
         dispatcher = EdgeStatDispatcher(H, self)
         if H is None:
-            super().__init__(None, None, None, dispatcher, bunch)
+            super().__init__(None, None, None, None, dispatcher, bunch)
         else:
-            super().__init__(H, H._edge, H._edge_attr, dispatcher, bunch)
+            super().__init__(
+                H._edge, H._edge_attr, H._node, H._node_attr, dispatcher, bunch
+            )
 
     def members(self, e=None, dtype=list):
         """Get the node ids that are members of an edge.

xgi/stats/nodestats.py

@@ -177,7 +177,7 @@ def average_neighbor_degree(net, bunch):
     """
     result = {}
     for n in bunch:
-        neighbors = net.neighbors(n)
+        neighbors = net.nodes.neighbors(n)
         result[n] = sum(len(net._node[nbr]) for nbr in neighbors)
         result[n] = result[n] / len(neighbors) if neighbors else 0
     return result