Cleanup hypergraph methods (#150)

* move convert_labels_to_integers from utils/utilities.py to classes/function.py. The reason is that it was causing aboslute/relative import issues
* implement IDView.duplicates
* remove Hypergraph.has_edge and implement IDView.lookup instead
* remove duplicate_edges in favor of H.edges.duplicates
* change the examples section of the IDView.lookup docstring because it was causing problems during CI (in particular, the output was NodeView(('b', 'a')) instead of NodeView(('a', 'b')). Instead, that particular test was moved to the actual test suite.

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

@@ -33,7 +33,6 @@
       ~Hypergraph.remove_node
       ~Hypergraph.remove_edge
       ~Hypergraph.remove_nodes_from
-      ~Hypergraph.remove_nodes_from
       ~Hypergraph.remove_edges_from
       ~Hypergraph.remove_node_from_edge
       ~Hypergraph.clear
@@ -47,12 +46,3 @@
 
       ~Hypergraph.copy
       ~Hypergraph.dual
-
-
-   .. rubric:: Methods that query nodes and edges
-
-   .. autosummary::
-      :nosignatures:
-
-      ~Hypergraph.duplicate_edges
-      ~Hypergraph.has_edge

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

@@ -23,5 +23,7 @@ xgi.classes.reportviews.EdgeView
       ~EdgeView.members
       ~EdgeView.singletons
       ~IDView.neighbors
+      ~IDView.duplicates
+      ~IDView.lookup
       ~IDView.filterby
       ~IDView.filterby_attr

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

@@ -18,5 +18,7 @@ xgi.classes.reportviews.IDView
 
       ~IDView.from_view
       ~IDView.neighbors
+      ~IDView.duplicates
+      ~IDView.lookup
       ~IDView.filterby
       ~IDView.filterby_attr

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

@@ -23,5 +23,7 @@ xgi.classes.reportviews.NodeView
       ~NodeView.memberships
       ~NodeView.isolates
       ~IDView.neighbors
+      ~IDView.duplicates
+      ~IDView.lookup
       ~IDView.filterby
       ~IDView.filterby_attr

docs/source/api/classes/xgi.utils.utilities.rst

@@ -14,5 +14,4 @@
 
    .. rubric:: Functions
 
-   .. autofunction:: convert_labels_to_integers
    .. autofunction:: dual_dict

tests/classes/test_function.py

@@ -280,3 +280,50 @@ def test_is_empty():
     assert xgi.is_empty(H1)
     assert xgi.is_empty(H2)
     assert not xgi.is_empty(H3)
+
+
+def test_convert_labels_to_integers(hypergraph1, hypergraph2):
+    H1 = xgi.convert_labels_to_integers(hypergraph1)
+    H2 = xgi.convert_labels_to_integers(hypergraph2)
+    H3 = xgi.convert_labels_to_integers(hypergraph1, "old_ids")
+
+    assert set(H1.nodes) == {0, 1, 2}
+    assert set(H1.edges) == {0, 1, 2}
+
+    assert H1.nodes[0]["label"] == "a"
+    assert H1.nodes[1]["label"] == "b"
+    assert H1.nodes[2]["label"] == "c"
+
+    assert H1.edges[0]["label"] == "e1"
+    assert H1.edges[1]["label"] == "e2"
+    assert H1.edges[2]["label"] == "e3"
+
+    assert H1.edges.members(0) == [0, 1]
+    assert H1.edges.members(1) == [0, 1, 2]
+    assert H1.edges.members(2) == [2]
+
+    assert H1.nodes.memberships(0) == [0, 1]
+    assert H1.nodes.memberships(1) == [0, 1]
+    assert H1.nodes.memberships(2) == [1, 2]
+
+    assert set(H2.nodes) == {0, 1, 2}
+    assert set(H2.edges) == {0, 1, 2}
+
+    assert H2.nodes[0]["label"] == "b"
+    assert H2.nodes[1]["label"] == "c"
+    assert H2.nodes[2]["label"] == 0
+
+    assert H2.edges[0]["label"] == "e1"
+    assert H2.edges[1]["label"] == "e2"
+    assert H2.edges[2]["label"] == "e3"
+
+    assert H2.edges.members(0) == [2, 0]
+    assert H2.edges.members(1) == [2, 1]
+    assert H2.edges.members(2) == [2, 0, 1]
+
+    assert H2.nodes.memberships(0) == [0, 2]
+    assert H2.nodes.memberships(1) == [1, 2]
+    assert H2.nodes.memberships(2) == [0, 1, 2]
+
+    assert H3.nodes[0]["old_ids"] == "a"
+    assert H3.edges[0]["old_ids"] == "e1"

tests/classes/test_hypergraph.py

@@ -141,16 +141,6 @@ def test_members(edgelist1):
         H.nodes.memberships(slice(1, 4))
 
 
-def test_has_edge(edgelist1):
-    H = xgi.Hypergraph(edgelist1)
-    assert H.has_edge([1, 2, 3])
-    assert H.has_edge({1, 2, 3})
-    assert H.has_edge({4})
-    assert not H.has_edge([4, 5])
-    assert not H.has_edge([3])
-    assert not H.has_edge([1, 2])
-
-
 def test_add_edge():
     for edge in [[1, 2, 3], {1, 2, 3}, iter([1, 2, 3])]:
         H = xgi.Hypergraph()
@@ -395,3 +385,36 @@ def test_double_edge_swap(edgelist1):
     # loopy swap
     H.double_edge_swap(4, 6, 0, 2)
     assert H.edges.members() == [[6, 2, 6], [3], [5, 4], [1, 7, 8]]
+
+
+def test_duplicate_edges(edgelist1):
+    H = xgi.Hypergraph(edgelist1)
+    assert list(H.edges.duplicates()) == []
+
+    H.add_edge([1, 3, 2])  # same order as existing edge
+    assert list(H.edges.duplicates()) == [0, 4]
+
+    H.add_edge([1, 2, 3])  # different order, same members
+    assert list(H.edges.duplicates()) == [0, 4, 5]
+
+    H = xgi.Hypergraph([[1, 2, 3, 3], [1, 2, 3]])  # repeated nodes
+    assert list(H.edges.duplicates()) == []
+
+    H = xgi.Hypergraph([[1, 2, 3, 3], [3, 1, 2, 3]])  # repeated nodes
+    assert list(H.edges.duplicates()) == [0, 1]
+
+
+def test_duplicate_nodes(edgelist1):
+    H = xgi.Hypergraph(edgelist1)
+    assert list(H.nodes.duplicates()) == [1, 2, 3, 7, 8]
+
+    H.add_edges_from([[1, 4], [2, 6, 7], [6, 8]])
+    assert list(H.nodes.duplicates()) == []
+
+    # this loop makes 1 and 2 belong to the same edges
+    for edgeid, members in H.edges.members(dtype=dict).items():
+        if 1 in members and 2 not in members:
+            H.add_node_to_edge(edgeid, 2)
+        if 1 not in members and 2 in members:
+            H.add_node_to_edge(edgeid, 1)
+    assert list(H.nodes.duplicates()) == [1, 2]

tests/classes/test_reportviews.py

@@ -221,3 +221,24 @@ def test_singletons(edgelist1):
     H.remove_edge(1)
     assert 1 not in H.edges
     assert list(H.edges.singletons()) == []
+
+
+def test_lookup(edgelist1):
+    H = xgi.Hypergraph(edgelist1)
+    assert list(H.edges.lookup([1, 2, 3])) == [0]
+    assert list(H.edges.lookup({1, 2, 3})) == [0]
+    assert list(H.edges.lookup({4})) == [1]
+    assert list(H.edges.lookup([4, 5])) == []
+    assert list(H.edges.lookup([3])) == []
+    assert list(H.edges.lookup([4])) == [1]
+    assert list(H.edges.lookup([1, 2])) == []
+
+    H = xgi.Hypergraph([["a", "b", "c"], ["a", "b", "e"], ["c", "d", "e"]])
+    assert set(H.nodes.lookup([0, 1])) == {"a", "b"}
+
+
+def test_bool(edgelist1):
+    H = xgi.Hypergraph([])
+    assert bool(H.edges) is False
+    H = xgi.Hypergraph(edgelist1)
+    assert bool(H.edges) is True

tests/utils/test_utils.py

@@ -1,8 +1,8 @@
-from xgi.utils import convert_labels_to_integers, dual_dict
+import xgi
 
 
 def test_dual_dict(dict5):
-    dual = dual_dict(dict5)
+    dual = xgi.dual_dict(dict5)
     assert dual[0] == [0]
     assert dual[1] == [0]
     assert dual[2] == [0]
@@ -12,50 +12,3 @@ def test_dual_dict(dict5):
     assert dual[6] == [2, 3]
     assert dual[7] == [3]
     assert dual[8] == [3]
-
-
-def test_convert_labels_to_integers(hypergraph1, hypergraph2):
-    H1 = convert_labels_to_integers(hypergraph1)
-    H2 = convert_labels_to_integers(hypergraph2)
-    H3 = convert_labels_to_integers(hypergraph1, "old_ids")
-
-    assert set(H1.nodes) == {0, 1, 2}
-    assert set(H1.edges) == {0, 1, 2}
-
-    assert H1.nodes[0]["label"] == "a"
-    assert H1.nodes[1]["label"] == "b"
-    assert H1.nodes[2]["label"] == "c"
-
-    assert H1.edges[0]["label"] == "e1"
-    assert H1.edges[1]["label"] == "e2"
-    assert H1.edges[2]["label"] == "e3"
-
-    assert H1.edges.members(0) == [0, 1]
-    assert H1.edges.members(1) == [0, 1, 2]
-    assert H1.edges.members(2) == [2]
-
-    assert H1.nodes.memberships(0) == [0, 1]
-    assert H1.nodes.memberships(1) == [0, 1]
-    assert H1.nodes.memberships(2) == [1, 2]
-
-    assert set(H2.nodes) == {0, 1, 2}
-    assert set(H2.edges) == {0, 1, 2}
-
-    assert H2.nodes[0]["label"] == "b"
-    assert H2.nodes[1]["label"] == "c"
-    assert H2.nodes[2]["label"] == 0
-
-    assert H2.edges[0]["label"] == "e1"
-    assert H2.edges[1]["label"] == "e2"
-    assert H2.edges[2]["label"] == "e3"
-
-    assert H2.edges.members(0) == [2, 0]
-    assert H2.edges.members(1) == [2, 1]
-    assert H2.edges.members(2) == [2, 0, 1]
-
-    assert H2.nodes.memberships(0) == [0, 2]
-    assert H2.nodes.memberships(1) == [1, 2]
-    assert H2.nodes.memberships(2) == [0, 1, 2]
-
-    assert H3.nodes[0]["old_ids"] == "a"
-    assert H3.edges[0]["old_ids"] == "e1"

xgi/__init__.py

@@ -1,24 +1,25 @@
 import pkg_resources
 
 from . import (
-    algorithms,
+    utils,
     classes,
+    algorithms,
     convert,
     drawing,
     generators,
     linalg,
     readwrite,
     stats,
-    utils,
 )
-from .algorithms import *
+from .utils import *
 from .classes import *
+from .algorithms import *
 from .convert import *
 from .drawing import *
 from .generators import *
 from .linalg import *
 from .readwrite import *
 from .stats import *
-from .utils import *
+
 
 __version__ = pkg_resources.require("xgi")[0].version

xgi/algorithms/centrality.py

@@ -5,10 +5,9 @@
 from numpy.linalg import norm
 from scipy.sparse.linalg import eigsh
 
-from ..classes import is_uniform
+from ..classes import is_uniform, convert_labels_to_integers
 from ..exception import XGIError
 from ..linalg import clique_motif_matrix, incidence_matrix
-from ..utils.utilities import convert_labels_to_integers
 
 __all__ = ["CEC_centrality", "HEC_centrality", "ZEC_centrality", "node_edge_centrality"]
 

xgi/classes/__init__.py

@@ -1,4 +1,4 @@
-from .function import *
 from .hypergraph import Hypergraph
+from .function import *
 from .hypergraphviews import subhypergraph
 from .simplicialcomplex import SimplicialComplex

xgi/classes/function.py

@@ -3,6 +3,7 @@
 from collections import Counter
 
 from ..exception import XGIError
+from .hypergraph import Hypergraph
 
 __all__ = [
     "max_edge_order",
@@ -21,6 +22,7 @@
     "get_edge_attributes",
     "is_empty",
     "maximal_simplices",
+    "convert_labels_to_integers",
 ]
 
 
@@ -615,3 +617,44 @@ def maximal_simplices(SC):
         if maximal:
             max_simplices.append(i)
     return max_simplices
+
+
+def convert_labels_to_integers(H, label_attribute="label"):
+    """Relabel node and edge IDs to be sequential integers.
+
+    Parameters
+    ----------
+    H : Hypergraph
+        The hypergraph of interest
+
+    label_attribute : string, default: "label"
+        The attribute name that stores the old node and edge labels
+
+    Returns
+    -------
+    Hypergraph
+        A new hypergraph with nodes and edges with sequential IDs starting at 0.
+        The old IDs are stored in the "label" attribute for both nodes and edges.
+
+    Notes
+    -----
+    The "relabeling" will occur even if the node/edge IDs are sequential.
+    Because the old IDs are stored in the "label" attribute for both nodes and edges,
+    the old "label" values (if they exist) will be overwritten.
+    """
+    node_dict = dict(zip(H.nodes, range(H.num_nodes)))
+    edge_dict = dict(zip(H.edges, range(H.num_edges)))
+    temp_H = Hypergraph()
+    temp_H._hypergraph = H._hypergraph.copy()
+
+    for node, id in node_dict.items():
+        temp_H._node[id] = [edge_dict[e] for e in H._node[node]]
+        temp_H._node_attr[id] = H._node_attr[node].copy()
+        temp_H._node_attr[id][label_attribute] = node
+
+    for edge, id in edge_dict.items():
+        temp_H._edge[id] = [node_dict[n] for n in H._edge[edge]]
+        temp_H._edge_attr[id] = H._edge_attr[edge].copy()
+        temp_H._edge_attr[id][label_attribute] = edge
+
+    return temp_H