Cleanup hypergraph methods (#146)

* move isolates() from Hypergraph to NodeView and singletons() from Hypergraph to EdgeView. 
* delete Hypergraph.remove_isolates as it is now equivalent to H.remove_nodes_from(H.nodes.isolates()) and Hypergraph.remove_singletons as it is now equivalent to H.remove_edges_from(H.edges.singletons())

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

@@ -36,8 +36,6 @@
       ~Hypergraph.remove_nodes_from
       ~Hypergraph.remove_edges_from
       ~Hypergraph.remove_node_from_edge
-      ~Hypergraph.remove_isolates
-      ~Hypergraph.remove_singleton_edges
       ~Hypergraph.clear
       ~Hypergraph.clear_edges
 
@@ -56,7 +54,5 @@
    .. autosummary::
       :nosignatures:
 
-      ~Hypergraph.isolates
       ~Hypergraph.duplicate_edges
       ~Hypergraph.has_edge
-      ~Hypergraph.singleton_edges

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

@@ -21,6 +21,7 @@ xgi.classes.reportviews.EdgeView
       :nosignatures:
 
       ~EdgeView.members
+      ~EdgeView.singletons
       ~IDView.neighbors
       ~IDView.filterby
       ~IDView.filterby_attr

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

@@ -21,6 +21,7 @@ xgi.classes.reportviews.NodeView
       :nosignatures:
 
       ~NodeView.memberships
+      ~NodeView.isolates
       ~IDView.neighbors
       ~IDView.filterby
       ~IDView.filterby_attr

docs/source/api/readwrite/xgi.readwrite.xgi_data.rst

@@ -1,10 +1,10 @@
 xgi.readwrite.xgi_data
-==================
+======================
 
 .. currentmodule:: xgi.readwrite.xgi_data
 
 .. automodule:: xgi.readwrite.xgi_data
-   
+
    .. rubric:: Functions
-   
-   .. autofunction:: load_xgi_data
+
+   .. autofunction:: load_xgi_data

tests/classes/test_hypergraph.py

@@ -100,32 +100,15 @@ def test_add_nodes_from(attr1, attr2, attr3):
     assert H.nodes[2]["color"] == attr3["color"]
 
 
-def test_singleton_edges(edgelist1, edgelist2):
-    H1 = xgi.Hypergraph(edgelist1)
-    H2 = xgi.Hypergraph(edgelist2)
-
-    assert len(H1.singleton_edges()) == 1
-    assert 1 in H1.singleton_edges()
-    assert len(H2.singleton_edges()) == 0
-
-
 def test_remove_singleton_edges(edgelist1, edgelist2):
     H1 = xgi.Hypergraph(edgelist1)
     H2 = xgi.Hypergraph(edgelist2)
 
-    H1.remove_singleton_edges()
-    H2.remove_singleton_edges()
-
-    assert H1.singleton_edges() == {}
-    assert H2.singleton_edges() == {}
+    H1.remove_edges_from(H1.edges.singletons())
+    H2.remove_edges_from(H2.edges.singletons())
 
-
-def test_isolates(edgelist1):
-    H = xgi.Hypergraph(edgelist1)
-    assert H.isolates(ignore_singletons=False) == set()
-    assert H.isolates() == {4}
-    H.remove_isolates()
-    assert 4 not in H
+    assert list(H1.edges.singletons()) == []
+    assert list(H2.edges.singletons()) == []
 
 
 def test_add_node_attr(edgelist1):

tests/classes/test_hypergraphviews.py

@@ -52,14 +52,14 @@ def test_subhypergraph(edgelist1):
     new_H = xgi.classes.hypergraphviews.subhypergraph(H, edges=[1, 2])
     assert list(new_H.nodes) == [1, 2, 3, 4, 5, 6, 7, 8]
     assert list(new_H.edges) == [1, 2]
-    assert new_H.isolates(ignore_singletons=False) == {1, 2, 3, 7, 8}
+    assert list(new_H.nodes.isolates(ignore_singletons=False)) == [1, 2, 3, 7, 8]
 
     new_H = xgi.classes.hypergraphviews.subhypergraph(
         H, nodes=[1, 2, 3, 4, 5], edges=[1, 2]
     )
     assert list(new_H.nodes) == [1, 2, 3, 4, 5]
     assert list(new_H.edges) == [1]
-    assert new_H.isolates(ignore_singletons=False) == {1, 2, 3, 5}
+    assert list(new_H.nodes.isolates(ignore_singletons=False)) == [1, 2, 3, 5]
 
     new_H = xgi.classes.hypergraphviews.subhypergraph(H, nodes=[4], edges=[0, 1, 2])
     assert list(new_H.nodes) == [4]
@@ -68,4 +68,4 @@ def test_subhypergraph(edgelist1):
     new_H = xgi.classes.hypergraphviews.subhypergraph(H, nodes=[3, 4, 5, 6], edges=[2])
     assert list(new_H.nodes) == [3, 4, 5, 6]
     assert list(new_H.edges) == [2]
-    assert new_H.isolates(ignore_singletons=False) == {3, 4}
+    assert list(new_H.nodes.isolates(ignore_singletons=False)) == [3, 4]

tests/classes/test_reportviews.py

@@ -205,3 +205,19 @@ def test_call(edgelist1):
     assert len(H.nodes([])) == 0
     assert H.nodes(list(H.nodes)) == H.nodes
     assert H.nodes(H.nodes) == H.nodes
+
+
+def test_isolates(edgelist1):
+    H = xgi.Hypergraph(edgelist1)
+    assert list(H.nodes.isolates(ignore_singletons=False)) == []
+    assert list(H.nodes.isolates()) == [4]
+    H.remove_nodes_from(H.nodes.isolates())
+    assert 4 not in H
+
+
+def test_singletons(edgelist1):
+    H = xgi.Hypergraph(edgelist1)
+    assert list(H.edges.singletons()) == [1]
+    H.remove_edge(1)
+    assert 1 not in H.edges
+    assert list(H.edges.singletons()) == []

xgi/classes/hypergraph.py

@@ -978,73 +978,6 @@ def dual(self):
 
         return dual
 
-    def singleton_edges(self):
-        """Edges with a single member.
-
-        Returns
-        -------
-        EdgeView
-            View of the edges with a single member.
-
-        """
-        return self.edges.filterby("order", 0)
-
-    def remove_singleton_edges(self):
-        """Removes all singletons edges from the hypergraph"""
-        singleton_ids = [
-            id_ for id_, members in self._edge.items() if len(members) == 1
-        ]
-        self.remove_edges_from(singleton_ids)
-
-    def isolates(self, ignore_singletons=True):
-        """Nodes that belong to no edges.
-
-        When ignore_singletons is True (default), a node is considered isolated frmo the
-        rest of the hypergraph when it is included in no edges of size two or more.  In
-        particular, whether the node is part of any singleton edges is irrelevant to
-        determine whether it is isolated.
-
-        When ignore_singletons is False, a node is isolated only when it is a member of
-        exactly zero edges, including singletons.
-
-        Parameters
-        ----------
-        ignore_singletons : bool, default False
-            Whether to consider singleton edges.
-
-        Returns
-        -------
-        set
-            Isolated nodes.
-
-        See Also
-        --------
-        remove_isolates
-
-        """
-        nodes_in_edges = set()
-        for idx in self.edges:
-            edge = self.edges.members(idx)
-            if ignore_singletons and len(edge) == 1:
-                continue
-            nodes_in_edges = nodes_in_edges.union(edge)
-        return set(self.nodes) - nodes_in_edges
-
-    def remove_isolates(self, ignore_singletons=True):
-        """Remove all nodes that belong to no edges.
-
-        Parameters
-        ----------
-        ignore_singletons : bool, default False
-            Whether to consider singleton edges when searching for isolated nodes.
-
-        See Also
-        --------
-        isolates
-
-        """
-        self.remove_nodes_from(self.isolates(ignore_singletons))
-
     def duplicate_edges(self):
         """A list of all duplicate edges.
 
@@ -1053,10 +986,6 @@ def duplicate_edges(self):
         list
             All edges with a duplicate.
 
-        See also
-        --------
-        remove_duplicates
-
         """
         edges = [tuple(e) for e in self._edge.values()]
         edges_unique, counts = np.unique(edges, return_counts=True)

xgi/classes/reportviews.py

@@ -445,6 +445,42 @@ def memberships(self, n=None):
         """
         return self._id_dict.copy() if n is None else self._id_dict[n].copy()
 
+    def isolates(self, ignore_singletons=True):
+        """Nodes that belong to no edges.
+
+        When ignore_singletons is True (default), a node is considered isolated from the
+        rest of the hypergraph when it is included in no edges of size two or more.  In
+        particular, whether the node is part of any singleton edges is irrelevant to
+        determine whether it is isolated.
+
+        When ignore_singletons is False, a node is isolated only when it is a member of
+        exactly zero edges, including singletons.
+
+        Parameters
+        ----------
+        ignore_singletons : bool, default False
+            Whether to consider singleton edges.
+
+        Returns
+        -------
+        NodeView containing the isolated nodes.
+
+        See Also
+        --------
+        :meth:`EdgeView.singletons`
+
+        """
+        if ignore_singletons:
+            nodes_in_edges = set()
+            for members in self._bi_id_dict.values():
+                if len(members) == 1:
+                    continue
+                nodes_in_edges = nodes_in_edges.union(members)
+            isolates = set(self._id_dict) - nodes_in_edges
+            return self.from_view(self, bunch=isolates)
+        else:
+            return self.filterby("degree", 0)
+
 
 class EdgeView(IDView):
     """An IDView that keeps track of edge ids.
@@ -513,3 +549,17 @@ def members(self, e=None, dtype=list):
             raise IDNotFound(f'ID "{e}" not in this view')
 
         return self._id_dict[e].copy()
+
+    def singletons(self):
+        """Edges that contain exactly one node.
+
+        Returns
+        -------
+        EdgeView containing the singleton edges.
+
+        See Also
+        --------
+        :meth:`NodeView.isolates`
+
+        """
+        return self.filterby("size", 1)