Remove id variable from XGI (#620)

* Remove `id` from tests

* remove `id` from core data structures

* Remove `id` from all other files

* Fix failing test

* Fix failing notebook

* response to review

tests/core/test_dihypergraph.py

@@ -210,8 +210,8 @@ def test_add_edge_rejects_set():
 
 def test_add_edge_handles_uid_correctly():
     H1 = xgi.DiHypergraph()
-    H1.add_edge(([1, 2], [3]), id=0)
-    H1.add_edge(([3, 4], [4, 5]), id=2)
+    H1.add_edge(([1, 2], [3]), idx=0)
+    H1.add_edge(([3, 4], [4, 5]), idx=2)
     H1.add_edge([[5, 6], [2, 3]])
     assert H1.edges.dimembers(dtype=dict) == {
         0: ({1, 2}, {3}),
@@ -225,13 +225,13 @@ def test_add_edge_warns_when_overwriting_edge_id():
     H2.add_edge(([1, 2], [3]))
     H2.add_edge(([3, 4], [5, 6, 7]))
     with pytest.warns(Warning):
-        H2.add_edge(([5, 6], [8]), id=0)
+        H2.add_edge(([5, 6], [8]), idx=0)
     assert {i: e["in"] for i, e in H2._edge.items()} == {0: {1, 2}, 1: {3, 4}}
 
 
 def test_add_edge_with_id():
     H = xgi.DiHypergraph()
-    H.add_edge(([1, 2, 3], [3, 4]), id="myedge")
+    H.add_edge(([1, 2, 3], [3, 4]), idx="myedge")
     assert (1 in H) and (2 in H) and (3 in H) and (4 in H)
     assert "myedge" in H.edges
     assert {1, 2, 3, 4} in H.edges.members()
@@ -432,7 +432,7 @@ def test_copy(diedgelist1):
     assert H._net_attr == copy._net_attr
 
     H1 = xgi.DiHypergraph()
-    H1.add_edge(([1, 2], [3]), id="x")
+    H1.add_edge(([1, 2], [3]), idx="x")
     copy2 = H1.copy()  # does not throw error because of str id
     assert list(copy2.nodes) == list(H1.nodes)
     assert list(copy2.edges) == list(H1.edges)
@@ -563,8 +563,8 @@ def test_pickle(diedgelist1):
 
     assert H1.nodes == H2.nodes
     assert H1.edges == H2.edges
-    assert [H1.edges.members(id) for id in H1.edges] == [
-        H2.edges.members(id) for id in H2.edges
+    assert [H1.edges.members(e) for e in H1.edges] == [
+        H2.edges.members(e) for e in H2.edges
     ]
 
 

tests/core/test_hypergraph.py

@@ -190,8 +190,8 @@ def test_add_edge():
 
     # check that uid works correctly
     H1 = xgi.Hypergraph()
-    H1.add_edge([1, 2], id=0)
-    H1.add_edge([3, 4], id=2)
+    H1.add_edge([1, 2], idx=0)
+    H1.add_edge([3, 4], idx=2)
     H1.add_edge([5, 6])
     assert H1._edge == {0: {1, 2}, 2: {3, 4}, 3: {5, 6}}
 
@@ -201,14 +201,14 @@ def test_add_edge():
     with pytest.warns(
         UserWarning, match="uid 0 already exists, cannot add edge {5, 6}"
     ):
-        H2.add_edge([5, 6], id=0)
+        H2.add_edge([5, 6], idx=0)
 
     assert H2._edge == {0: {1, 2}, 1: {3, 4}}
 
 
 def test_add_edge_with_id():
     H = xgi.Hypergraph()
-    H.add_edge([1, 2, 3], id="myedge")
+    H.add_edge([1, 2, 3], idx="myedge")
     assert (1 in H) and (2 in H) and (3 in H)
     assert "myedge" in H.edges
     assert {1, 2, 3} in H.edges.members()
@@ -472,7 +472,7 @@ def test_copy(edgelist1):
     assert H._net_attr == copy._net_attr
 
     H1 = xgi.Hypergraph()
-    H1.add_edge((1, 2), id="x")
+    H1.add_edge((1, 2), idx="x")
     copy2 = H1.copy()  # does not throw error because of str id
     assert list(copy2.nodes) == list(H1.nodes)
     assert list(copy2.edges) == list(H1.edges)
@@ -738,8 +738,8 @@ def test_pickle(edgelist1):
 
     assert H1.nodes == H2.nodes
     assert H1.edges == H2.edges
-    assert [H1.edges.members(id) for id in H1.edges] == [
-        H2.edges.members(id) for id in H2.edges
+    assert [H1.edges.members(e) for e in H1.edges] == [
+        H2.edges.members(e) for e in H2.edges
     ]
 
 

tests/core/test_simplicialcomplex.py

@@ -65,7 +65,7 @@ def test_add_simplex():
     S2.add_simplex([1, 2])
     S2.add_simplex([3, 4])
     with pytest.warns(UserWarning, match="uid 1 already exists, cannot add simplex"):
-        S2.add_simplex([5, 6], id=1)
+        S2.add_simplex([5, 6], idx=1)
     assert S2._edge == {0: frozenset({1, 2}), 1: frozenset({3, 4})}
 
 
@@ -410,7 +410,7 @@ def test_copy(edgelist1):
     assert H._net_attr == copy._net_attr
 
     H1 = xgi.SimplicialComplex()
-    H1.add_simplex((1, 2), id="x")
+    H1.add_simplex((1, 2), idx="x")
     copy2 = H1.copy()  # does not throw error because of str id
     assert list(copy2.nodes) == list(H1.nodes)
     assert list(copy2.edges) == list(H1.edges)
@@ -448,8 +448,8 @@ def test_remove_simplex_id(edgelist6):
     S.add_simplices_from(edgelist6)
 
     # remove simplex and others it belongs to
-    id = list(S._edge.values()).index(frozenset({2, 3}))
-    S.remove_simplex_id(id)  # simplex {2, 3}
+    idx = list(S._edge.values()).index(frozenset({2, 3}))
+    S.remove_simplex_id(idx)  # simplex {2, 3}
     edges = [
         frozenset({0, 1, 2}),
         frozenset({0, 1}),

tests/drawing/test_layout.py

@@ -250,6 +250,6 @@ def test_edge_positions_from_barycenters(edgelist1):
     edge_pos = xgi.edge_positions_from_barycenters(H, node_pos)
 
     assert len(edge_pos) == H.num_edges
-    for id, e in H.edges.members(dtype=dict).items():
+    for idx, e in H.edges.members(dtype=dict).items():
         mean_pos = np.mean([node_pos[n] for n in e], axis=0)
-        assert np.allclose(edge_pos[id], mean_pos)
+        assert np.allclose(edge_pos[idx], mean_pos)

tests/readwrite/test_bipartite_edgelist.py

@@ -48,10 +48,10 @@ def test_read_bipartite_edgelist(file_string, extra_kwargs):
 
     H = xgi.read_bipartite_edgelist(filename, nodetype=int, **extra_kwargs)
     int_edgelist = [{0, 1, 2, 3}, {4}, {5, 6}, {6, 7, 8}]
-    assert [H.edges.members(id) for id in H.edges] == int_edgelist
+    assert [H.edges.members(eid) for eid in H.edges] == int_edgelist
     H = xgi.read_bipartite_edgelist(filename, nodetype=str, **extra_kwargs)
     str_edgelist = [{"0", "1", "2", "3"}, {"4"}, {"5", "6"}, {"6", "7", "8"}]
-    assert [H.edges.members(id) for id in H.edges] == str_edgelist
+    assert [H.edges.members(eid) for eid in H.edges] == str_edgelist
 
 
 def test_parse_bipartite_edgelist():
@@ -92,28 +92,15 @@ def test_parse_bipartite_edgelist():
     H = xgi.parse_bipartite_edgelist(lines, nodetype=int, edgetype=int)
     assert list(H.nodes) == [0, 1, 2, 3, 4, 5, 6, 7, 8]
     assert list(H.edges) == [0, 1, 2, 3]
-    assert [H.edges.members(id) for id in H.edges] == [
-        {0, 1, 2, 3},
-        {4},
-        {5, 6},
-        {6, 7, 8},
-    ]
+    edges = [{0, 1, 2, 3}, {4}, {5, 6}, {6, 7, 8}]
+    assert [H.edges.members(eid) for eid in H.edges] == edges
 
     H = xgi.parse_bipartite_edgelist(lines, nodetype=int, edgetype=int, dual=True)
     assert list(H.nodes) == [0, 1, 2, 3]
     assert list(H.edges) == [0, 1, 2, 3, 4, 5, 6, 7, 8]
-    print([H.edges.members(id) for id in H.edges])
-    assert [H.edges.members(id) for id in H.edges] == [
-        {0},
-        {0},
-        {0},
-        {0},
-        {1},
-        {2},
-        {2, 3},
-        {3},
-        {3},
-    ]
+    print([H.edges.members(eid) for eid in H.edges])
+    edges = [{0}, {0}, {0}, {0}, {1}, {2}, {2, 3}, {3}, {3}]
+    assert [H.edges.members(eid) for eid in H.edges] == edges
 
     # test less than two entries per line
     with pytest.raises(XGIError):
@@ -135,6 +122,6 @@ def test_write_bipartite_edgelist(edgelist1):
     H2 = xgi.read_bipartite_edgelist(filename, nodetype=int, edgetype=int)
     assert H1.nodes == H2.nodes
     assert H1.edges == H2.edges
-    assert [H1.edges.members(id) for id in H1.edges] == [
-        H2.edges.members(id) for id in H2.edges
+    assert [H1.edges.members(e) for e in H1.edges] == [
+        H2.edges.members(e) for e in H2.edges
     ]

tests/readwrite/test_edgelist.py

@@ -34,22 +34,18 @@ def test_read_edgelist(file_string, extra_kwargs):
 
     H = xgi.read_edgelist(filename, nodetype=int, **extra_kwargs)
     int_edgelist = [{1, 2}, {2, 3, 4}, {1, 4, 7, 8}, {2, 3}]
-    assert [H.edges.members(id) for id in H.edges] == int_edgelist
+    assert [H.edges.members(eid) for eid in H.edges] == int_edgelist
     H = xgi.read_edgelist(filename, nodetype=str, **extra_kwargs)
     str_edgelist = [{"1", "2"}, {"2", "3", "4"}, {"1", "4", "7", "8"}, {"2", "3"}]
-    assert [H.edges.members(id) for id in H.edges] == str_edgelist
+    assert [H.edges.members(eid) for eid in H.edges] == str_edgelist
 
 
 def test_parse_edgelist():
     H = xgi.parse_edgelist(["1 2", "2 3 4", "1 4 7 8", "2 3"], nodetype=int)
     assert set(H.nodes) == {1, 2, 3, 4, 7, 8}
     assert set(H.edges) == {0, 1, 2, 3}
-    assert [H.edges.members(id) for id in H.edges] == [
-        {1, 2},
-        {2, 3, 4},
-        {1, 4, 7, 8},
-        {2, 3},
-    ]
+    edges = [{1, 2}, {2, 3, 4}, {1, 4, 7, 8}, {2, 3}]
+    assert [H.edges.members(eid) for eid in H.edges] == edges
 
     # This will fail because the "test" node ID can't be converted to int
     with pytest.raises(TypeError):
@@ -63,6 +59,6 @@ def test_write_edgelist(edgelist1):
     H2 = xgi.read_edgelist(filename, nodetype=int)
     assert H1.nodes == H2.nodes
     assert H1.edges == H2.edges
-    assert [H1.edges.members(id) for id in H1.edges] == [
-        H2.edges.members(id) for id in H2.edges
+    assert [H1.edges.members(e) for e in H1.edges] == [
+        H2.edges.members(e) for e in H2.edges
     ]

tests/readwrite/test_incidence_matrix.py

@@ -45,7 +45,7 @@ def test_read_incidence_matrix(file_string, extra_kwargs):
 
     H = xgi.read_incidence_matrix(filename, **extra_kwargs)
     int_edgelist = [{0, 1, 2, 3}, {4}, {5, 6}, {6, 7, 8}]
-    assert [H.edges.members(id) for id in H.edges] == int_edgelist
+    assert [H.edges.members(eid) for eid in H.edges] == int_edgelist
 
 
 def test_write_incidence_matrix(edgelist5):
@@ -55,6 +55,6 @@ def test_write_incidence_matrix(edgelist5):
     H2 = xgi.read_incidence_matrix(fname)
     assert H1.nodes == H2.nodes
     assert H1.edges == H2.edges
-    assert [H1.edges.members(id) for id in H1.edges] == [
-        H2.edges.members(id) for id in H2.edges
+    assert [H1.edges.members(e) for e in H1.edges] == [
+        H2.edges.members(e) for e in H2.edges
     ]

tests/readwrite/test_json.py

@@ -158,8 +158,8 @@ def test_read_json():
     assert list(H2.nodes) == ["1", "2", "3", "4"]
     assert H1["name"] == "test"
     assert H1["author"] == "Nicholas Landry"
-    assert [H1.edges.members(id) for id in H1.edges] == [{1, 2}, {2, 3, 4}, {1, 4}]
-    assert [H2.edges.members(id) for id in H2.edges] == [
+    assert [H1.edges.members(e) for e in H1.edges] == [{1, 2}, {2, 3, 4}, {1, 4}]
+    assert [H2.edges.members(e) for e in H2.edges] == [
         {"1", "2"},
         {"2", "3", "4"},
         {"1", "4"},
@@ -246,8 +246,8 @@ def test_write_json(edgelist1, edgelist2):
 
     assert set(H1.nodes) == set(H2.nodes)
     assert set(H1.edges) == set(H2.edges)
-    assert {frozenset(H1.edges.members(id)) for id in H1.edges} == {
-        frozenset(H2.edges.members(id)) for id in H2.edges
+    assert {frozenset(H1.edges.members(e)) for e in H1.edges} == {
+        frozenset(H2.edges.members(e)) for e in H2.edges
     }
     assert H2.nodes[2] == {"name": "Ilya"}
     assert H2.edges[1] == {"weight": 2}

xgi/convert/bipartite_graph.py

@@ -80,7 +80,7 @@ def from_bipartite_graph(G, create_using=None, dual=False):
     H.add_nodes_from(nodes)
     for edge in edges:
         nodes_in_edge = list(G.neighbors(edge))
-        H.add_edge(nodes_in_edge, id=edge)
+        H.add_edge(nodes_in_edge, idx=edge)
     return H.dual() if dual else H
 
 

xgi/convert/hypergraph_dict.py

@@ -110,28 +110,28 @@ def from_hypergraph_dict(data, nodetype=None, edgetype=None, max_order=None):
         raise XGIError("Failed to get hypergraph data attributes.")
 
     try:
-        for id, dd in data["node-data"].items():
+        for idx, dd in data["node-data"].items():
             if nodetype is not None:
                 try:
-                    id = nodetype(id)
+                    idx = nodetype(idx)
                 except ValueError as e:
                     raise TypeError(
                         f"Failed to convert edge IDs to type {nodetype}."
                     ) from e
-            H.add_node(id, **dd)
+            H.add_node(idx, **dd)
     except KeyError:
         raise XGIError("Failed to import node attributes.")
 
     try:
-        for id, edge in data["edge-dict"].items():
+        for idx, edge in data["edge-dict"].items():
             if max_order and len(edge) > max_order + 1:
                 continue
             if edgetype is not None:
                 try:
-                    id = edgetype(id)
+                    idx = edgetype(idx)
                 except ValueError as e:
                     raise TypeError(
-                        f"Failed to convert the edge with ID {id} to type {edgetype}."
+                        f"Failed to convert the edge with ID {idx} to type {edgetype}."
                     ) from e
 
             if nodetype is not None:
@@ -141,7 +141,7 @@ def from_hypergraph_dict(data, nodetype=None, edgetype=None, max_order=None):
                     raise TypeError(
                         f"Failed to convert nodes to type {nodetype}."
                     ) from e
-            H.add_edge(edge, id)
+            H.add_edge(edge, idx)
 
     except KeyError as e:
         raise XGIError("Failed to import edge dictionary.") from e