Refactor core interface (xgi-org#41)

* fix: node attributes were not being created correctly * chore: whitespace changes * refactor: H[x] now accesses hypergraph attributes * fix: add a way to access hypergraph attributes. fix: a broken test * refactor: now use members to access the nodes of an edge * refactor: use *_attr rather than *_attrs * refactor: use __getitem__ to access attributes, not members * docs: update docs * feat: add H.nodes.memberships, which is the same as H.nodes.members, and add a test for it * Updates * Created a base class for the Node/Edge Views and Degree/Edge Size Views. * Removed the NodeDataView and EdgeDataView. * All unit tests pass * Removed all old references to `.node[id]` and `.edge[id]` * updated list of developers * update hypergraph getitem method * Fixed tests * refactor: use memberships rather than memberships * fix: members associated with edges, memberships associated with nodes * fix: specified that incorrect/missing IDs are KeyError exceptions * docs: added documentation and removed old API references * fix: added correct handling for calling as a slice * tests: added tests for missing or slice ids * BREAKING CHANGE: removed the name attribute and fixed methods and tests to match. Co-authored-by: nwlandry <[email protected]>
arnaudon · Feb 8, 2022 · 99eb038 · 99eb038
1 parent 7b08b6f
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diff --git a/CITATION.cff b/CITATION.cff
@@ -7,6 +7,16 @@ authors:
   -
     family-names: Torres
     given-names: Leo
+  -
+    family-names: Iacopini
+    given-names: Iacopo
+  -
+    family-names: Lucas
+    given-names: Maxime
+  -
+    family-names: Petri
+    given-names: Giovanni
+
 cff-version: "1.1.0"
 license: "BSD-3"
 message: "If you use this software, please cite it using these metadata."

diff --git a/LICENSE.md b/LICENSE.md
@@ -1,8 +1,11 @@
 XGI is distributed with the 3-clause BSD license.
 
-Copyright (C) 2021, Hypergraph Developers
+Copyright (C) 2021, XGI Developers
 Nicholas Landry <[email protected]>
 Leo Torres <[email protected]>
+Iacopo Iacopini <[email protected]>
+Maxime Lucas <[email protected]>
+Giovanni Petri <[email protected]>
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without

diff --git a/tests/classes/test_function.py b/tests/classes/test_function.py
@@ -80,15 +80,15 @@ def test_create_empty_copy(edgelist1):
 
     assert E1.shape == (8, 0)
     for node in E1.nodes:
-        assert len(E1.nodes[node]) == 0
-    assert E1.name == ""
+        assert len(E1.nodes.memberships(node)) == 0
     assert E1._hypergraph == {}
 
     assert E2.shape == (8, 0)
     for node in E2.nodes:
-        assert len(E1.nodes[node]) == 0
+        assert len(E1.nodes.memberships(node)) == 0
     assert E2._hypergraph == {"name": "test", "timestamp": "Nov. 20"}
-    assert dict(E2.nodes.data()) == attr_dict
+    for n in H.nodes:
+        assert H.nodes[n]["name"] == attr_dict[n]["name"]
 
 
 def test_is_empty():

diff --git a/tests/classes/test_hypergraph.py b/tests/classes/test_hypergraph.py
@@ -1,4 +1,6 @@
+import pytest
 import xgi
+from xgi.exception import XGIError
 
 
 def test_constructor(edgelist5, dict5, incidence5, dataframe5):
@@ -21,20 +23,20 @@ def test_constructor(edgelist5, dict5, incidence5, dataframe5):
         == list(H_df.edges)
     )
     assert (
-        list(H_list.edges[0])
-        == list(H_dict.edges[0])
-        == list(H_mat.edges[0])
-        == list(H_df.edges[0])
+        list(H_list.edges.members(0))
+        == list(H_dict.edges.members(0))
+        == list(H_mat.edges.members(0))
+        == list(H_df.edges.members(0))
     )
 
 
-def test_name():
+def test_hypergraph_attrs():
     H = xgi.Hypergraph()
-    assert H.name == ""
-    H.name = "test"
-    assert H.name == "test"
+    assert H._hypergraph == dict()
+    with pytest.raises(XGIError):
+        name = H["name"]
     H = xgi.Hypergraph(name="test")
-    assert H.name == "test"
+    assert H["name"] == "test"
 
 
 def test_contains(edgelist1):
@@ -46,6 +48,12 @@ def test_contains(edgelist1):
 
     assert 0 not in H
 
+def test_string():
+    H1 = xgi.Hypergraph()
+    assert str(H1) == "Unnamed Hypergraph with 0 nodes and 0 hyperedges"
+    H2 = xgi.Hypergraph(name="test")
+    # H2["name"] = "test"
+    assert str(H2) == "Hypergraph named test with 0 nodes and 0 hyperedges"
 
 def test_len(edgelist1, edgelist2):
     el1 = edgelist1
@@ -93,7 +101,7 @@ def test_dual(edgelist1, edgelist2, edgelist4):
     assert D3.shape == (3, 5)
 
 
-def test_max_edge_order(edgelist1, edgelist4,edgelist5):
+def test_max_edge_order(edgelist1, edgelist4, edgelist5):
     H0 = xgi.empty_hypergraph()
     H1 = xgi.empty_hypergraph()
     H1.add_nodes_from(range(5))
@@ -103,7 +111,7 @@ def test_max_edge_order(edgelist1, edgelist4,edgelist5):
 
     assert H0.max_edge_order() == None
     assert H1.max_edge_order() == 0
-    assert H2.max_edge_order() == 2 
+    assert H2.max_edge_order() == 2
     assert H3.max_edge_order() == 3
     assert H4.max_edge_order() == 3
 
@@ -112,7 +120,7 @@ def test_is_possible_order(edgelist1):
     H1 = xgi.Hypergraph(edgelist1)
 
     assert H1.is_possible_order(-1) == False
-    assert H1.is_possible_order(0) == False 
+    assert H1.is_possible_order(0) == False
     assert H1.is_possible_order(1) == True
     assert H1.is_possible_order(2) == True
     assert H1.is_possible_order(3) == False
@@ -122,7 +130,7 @@ def test_singleton_edges(edgelist1, edgelist2):
     H1 = xgi.Hypergraph(edgelist1)
     H2 = xgi.Hypergraph(edgelist2)
 
-    assert H1.singleton_edges() == {1 : [4]}
+    assert H1.singleton_edges() == {1: [4]}
     assert H2.singleton_edges() == {}
 
 
@@ -143,8 +151,8 @@ def test_is_uniform(edgelist1, edgelist6, edgelist7):
     H2 = xgi.Hypergraph(edgelist7)
     H3 = xgi.empty_hypergraph()
 
-    assert H0.is_uniform() == False 
-    assert H1.is_uniform() == 2 
+    assert H0.is_uniform() == False
+    assert H1.is_uniform() == 2
     assert H2.is_uniform() == 2
     assert H3.is_uniform() == False
 
@@ -155,3 +163,33 @@ def test_isolates(edgelist1):
     assert H.isolates() == {4}
     H.remove_isolates()
     assert 4 not in H
+
+
+def test_add_node_attr(edgelist1):
+    H = xgi.Hypergraph(edgelist1)
+    assert "new_node" not in H
+    H.add_node("new_node", color="red")
+    assert "new_node" in H
+    assert "color" in H.nodes["new_node"]
+    assert H.nodes["new_node"]["color"] == "red"
+
+
+def test_hypergraph_attr(edgelist1):
+    H = xgi.Hypergraph(edgelist1)
+    with pytest.raises(XGIError):
+        H["color"]
+    H["color"] = "red"
+    assert H["color"] == "red"
+
+
+def test_members(edgelist1):
+    H = xgi.Hypergraph(edgelist1)
+    assert H.nodes.memberships(1) == [0]
+    assert H.nodes.memberships(2) == [0]
+    assert H.nodes.memberships(3) == [0]
+    assert H.nodes.memberships(4) == [1]
+    assert H.nodes.memberships(6) == [2, 3]
+    with pytest.raises(XGIError):
+        H.nodes.memberships(0)
+    with pytest.raises(XGIError):
+        H.nodes.memberships(slice(1, 4))
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -30,14 +30,16 @@ def edgelist4():
 @pytest.fixture
 def edgelist5():
     return [[0, 1, 2, 3], [4], [5, 6], [6, 7, 8]]
-
+
+
 @pytest.fixture
 def edgelist6():
     return [[0, 1, 2], [1, 2, 3], [2, 3, 4]]
-
+
+
 @pytest.fixture
 def edgelist7():
-    return [[0, 1, 2], [1, 2, 3], [2, 3, 4], [4]]    
+    return [[0, 1, 2], [1, 2, 3], [2, 3, 4], [4]]
 
 
 @pytest.fixture

diff --git a/tests/generators/test_nonuniform.py b/tests/generators/test_nonuniform.py
@@ -13,7 +13,7 @@ def test_erdos_renyi_hypergraph():
     H = xgi.erdos_renyi_hypergraph(10, 20, 0.0)
     assert H.number_of_nodes() == 10
     assert H.number_of_edges() == 0
-    
+
     H = xgi.erdos_renyi_hypergraph(10, 20, 1.0)
     assert H.number_of_nodes() == 10
     assert H.number_of_edges() == 20
@@ -32,4 +32,3 @@ def test_chung_lu_hypergraph():
         k1 = {1: 1, 2: 2}
         k2 = {1: 2, 1: 2}
         H = xgi.chung_lu_hypergraph(k1, k2)
-
diff --git a/xgi/classes/function.py b/xgi/classes/function.py
@@ -64,7 +64,7 @@ def unique_edge_sizes(H, return_counts=False):
     list()
         The unique edge sizes
     """
-    return list({len(H.edges[edge]) for edge in H.edges})
+    return list({len(H.edges.members(edge)) for edge in H.edges})
 
 
 def frozen(*args, **kwargs):
@@ -198,7 +198,7 @@ def create_empty_copy(H, with_data=True):
     H_copy = H.__class__()
     H_copy.add_nodes_from(H.nodes)
     if with_data:
-        xgi.set_node_attributes(H_copy, dict(H.nodes.data()))
+        xgi.set_node_attributes(H_copy, dict(H._node_attr))
         H_copy._hypergraph.update(H._hypergraph)
     return H_copy
 
@@ -251,7 +251,7 @@ def set_node_attributes(H, values, name=None):
         try:  # `values` is a dict
             for n, v in values.items():
                 try:
-                    H._node_attr[n][name] = values[n]
+                    H._node_attr[n][name] = v
                 except KeyError:
                     pass
         except AttributeError:  # `values` is a constant
@@ -362,7 +362,7 @@ def get_edge_attributes(H, name):
     get_node_attributes
     set_edge_attributes
     """
-    edge_data = H.edges.data
+    edge_data = H._edge_attr
     return {id: edge_data[edge][name] for edge in edge_data if name in edge_data[edge]}