Centrality update

docs/source/api/algorithms/xgi.algorithms.centrality.rst

@@ -9,6 +9,5 @@ xgi.algorithms.centrality
 
    .. autofunction:: CEC_centrality
    .. autofunction:: HEC_centrality
-   .. autofunction:: ZEC_centrality
    .. autofunction:: node_edge_centrality
    .. autofunction:: line_vector_centrality

docs/source/api/stats/xgi.stats.nodestats.rst

@@ -13,5 +13,4 @@
    .. autofunction:: clustering
    .. autofunction:: degree
    .. autofunction:: hec_centrality
-   .. autofunction:: node_edge_centrality
-   .. autofunction:: zec_centrality
+   .. autofunction:: node_edge_centrality

tests/algorithms/test_assortativity.py

@@ -7,7 +7,6 @@
 
 
 def test_dynamical_assortativity(edgelist1, edgelist6, edgelist9, edgelist10):
-
     H = xgi.Hypergraph()
     with pytest.raises(XGIError):
         xgi.dynamical_assortativity(H)

tests/algorithms/test_centrality.py

@@ -7,6 +7,16 @@
 
 
 def test_cec_centrality():
+    # test empty hypergraph
+    H = xgi.Hypergraph()
+    assert xgi.CEC_centrality(H) == dict()
+    # Test no edges
+    H.add_nodes_from([0, 1, 2])
+    assert xgi.CEC_centrality(H) == {0: np.NaN, 1: np.NaN, 2: np.NaN}
+    # test disconnected
+    H.add_edge([0, 1])
+    assert xgi.CEC_centrality(H) == {0: np.NaN, 1: np.NaN, 2: np.NaN}
+
     H = xgi.sunflower(3, 1, 3)
     c = H.nodes.cec_centrality.asnumpy()
     assert norm(c[1:] - c[1]) < 1e-4
@@ -20,6 +30,19 @@ def test_cec_centrality():
 
 @pytest.mark.slow
 def test_hec_centrality():
+    # test empty hypergraph
+    H = xgi.Hypergraph()
+    c = xgi.HEC_centrality(H)
+    assert c == dict()
+    # Test no edges
+    H.add_nodes_from([0, 1, 2])
+    c = xgi.HEC_centrality(H)
+    assert c == {0: np.NaN, 1: np.NaN, 2: np.NaN}
+    # test disconnected
+    H.add_edge([0, 1])
+    c = xgi.HEC_centrality(H)
+    assert c == {0: np.NaN, 1: np.NaN, 2: np.NaN}
+
     H = xgi.sunflower(3, 1, 5)
     c = H.nodes.hec_centrality(max_iter=1000).asnumpy()
     assert norm(c[1:] - c[1]) < 1e-4
@@ -36,6 +59,19 @@ def test_hec_centrality():
 
 
 def test_node_edge_centrality():
+    # test empty hypergraph
+    H = xgi.Hypergraph()
+    assert xgi.node_edge_centrality(H) == (dict(), dict())
+    # Test no edges
+    H.add_nodes_from([0, 1, 2])
+    assert xgi.node_edge_centrality(H) == ({0: np.NaN, 1: np.NaN, 2: np.NaN}, dict())
+    # test disconnected
+    H.add_edge([0, 1])
+    assert xgi.node_edge_centrality(H) == (
+        {0: np.NaN, 1: np.NaN, 2: np.NaN},
+        {0: np.NaN},
+    )
+
     H = xgi.Hypergraph([[0, 1, 2, 3, 4]])
     c = H.nodes.node_edge_centrality.asnumpy()
     assert norm(c - c[0]) < 1e-6
@@ -48,6 +84,28 @@ def test_node_edge_centrality():
     assert abs(c[0] - c[1]) < 1e-6
 
 
+def test_line_vector_centrality():
+    H = xgi.Hypergraph()
+    c = xgi.line_vector_centrality(H)
+    assert c == dict()
+
+    with pytest.raises(XGIError):
+        H = xgi.Hypergraph()
+        H.add_nodes_from([0, 1, 2])
+        H.add_edge([0, 1])
+        xgi.line_vector_centrality(H)
+
+    H = xgi.sunflower(3, 1, 3) << xgi.sunflower(3, 1, 5)
+    c = xgi.line_vector_centrality(H)
+    assert len(c[0]) == 4  # sizes 2 through 5
+    assert np.allclose(c[0], [0, 0.40824829, 0, 0.24494897])
+    assert set(c.keys()) == set(H.nodes)
+
+    with pytest.raises(Exception):
+        H = xgi.Hypergraph([["a", "b"], ["b", "c"], ["a", "c"]])
+        xgi.line_vector_centrality(H)
+
+
 def ratio(r, m, kind="CEC"):
     """Generate the ratio between largest and second largest centralities
     for the sunflower hypergraph with one core node.
@@ -59,18 +117,13 @@ def ratio(r, m, kind="CEC"):
     m : int
         Size of edges
     kind : str, default: "CEC"
-        "CEC", "HEC", or "ZEC"
+        "CEC" or "HEC"
 
     Returns
     -------
     float
         Ratio
 
-    Raises
-    ------
-    XGIError
-        If edge size is too small for ZEC
-
     References
     ----------
     Three Hypergraph Eigenvector Centralities,
@@ -79,9 +132,5 @@ def ratio(r, m, kind="CEC"):
     """
     if kind == "CEC":
         return 2 * r * (m - 1) / (np.sqrt(m**2 + 4 * (m - 1) * (r - 1)) + m - 2)
-    elif kind == "ZEC":
-        if m > 4:
-            raise XGIError("Choose a larger m value.")
-        return r**0.5
     elif kind == "HEC":
         return r ** (1.0 / m)

tests/classes/test_function.py

@@ -5,7 +5,6 @@
 
 
 def test_num_edges_order(edgelist2):
-
     H = xgi.Hypergraph(edgelist2)
 
     assert xgi.num_edges_order(H, 0) == 0
@@ -723,7 +722,6 @@ def test_incidence_density(edgelist1):
 
 
 def test_subfaces(edgelist5):
-
     assert xgi.subfaces(edgelist5) == [
         (0,),
         (1,),

tests/drawing/test_layout.py

@@ -6,7 +6,6 @@
 
 
 def test_random_layout():
-
     H = xgi.random_hypergraph(10, [0.2], seed=1)
 
     # seed
@@ -27,7 +26,6 @@ def test_random_layout():
 
 
 def test_pairwise_spring_layout():
-
     H = xgi.random_hypergraph(10, [0.2], seed=1)
 
     # seed
@@ -47,7 +45,6 @@ def test_pairwise_spring_layout():
 
 
 def test_barycenter_spring_layout(hypergraph1):
-
     H = xgi.random_hypergraph(10, [0.2], seed=1)
 
     # seed
@@ -83,7 +80,6 @@ def test_barycenter_spring_layout(hypergraph1):
 
 
 def test_weighted_barycenter_spring_layout(hypergraph1):
-
     H = xgi.random_hypergraph(10, [0.2], seed=1)
 
     # seed

tests/dynamics/test_synchronization.py

@@ -85,7 +85,6 @@ def test_simulate_kuramoto():
 
 
 def test_compute_kuramoto_order_parameter():
-
     N = 5
     n_steps = 10
     dt = 0.002

tests/generators/test_classic.py

@@ -65,7 +65,6 @@ def test_flag_complex():
 
 
 def test_flag_complex_d2():
-
     G = nx.erdos_renyi_graph(15, 0.3, seed=3)
 
     S = xgi.flag_complex(G, max_order=2)

tests/generators/test_nonuniform.py

@@ -7,7 +7,6 @@
 
 
 def test_chung_lu_hypergraph():
-
     k1 = {1: 1, 2: 2, 3: 3, 4: 4}
     k2 = {1: 2, 2: 2, 3: 3, 4: 3}
     H = xgi.chung_lu_hypergraph(k1, k2)
@@ -27,7 +26,6 @@ def test_chung_lu_hypergraph():
 
 
 def test_dcsbm_hypergraph():
-
     n = 50
     k1 = {i: random.randint(1, n) for i in range(n)}
     k2 = {i: sorted(k1.values())[i] for i in range(n)}
@@ -48,7 +46,6 @@ def test_dcsbm_hypergraph():
 
 
 def test_random_hypergraph():
-
     # seed
     H1 = xgi.random_hypergraph(10, [0.1, 0.001], seed=1)
     H2 = xgi.random_hypergraph(10, [0.1, 0.001], seed=2)
@@ -65,7 +62,6 @@ def test_random_hypergraph():
 
 
 def test_random_simplicial_complex():
-
     # seed
     S1 = xgi.random_simplicial_complex(10, [0.1, 0.001], seed=1)
     S2 = xgi.random_simplicial_complex(10, [0.1, 0.001], seed=2)
@@ -82,7 +78,6 @@ def test_random_simplicial_complex():
 
 
 def test_random_flag_complex():
-
     # seed
     S1 = xgi.random_flag_complex(10, 0.1, seed=1)
     S2 = xgi.random_flag_complex(10, 0.1, seed=2)
@@ -99,7 +94,6 @@ def test_random_flag_complex():
 
 
 def test_random_flag_complex_d2():
-
     # seed
     S1 = xgi.random_flag_complex_d2(10, 0.1, seed=1)
     S2 = xgi.random_flag_complex_d2(10, 0.1, seed=2)

tests/generators/test_uniform.py

@@ -21,7 +21,6 @@ def test_uniform_configuration_model_hypergraph():
 
 
 def test_uniform_HSBM():
-
     # sum of sizes != n
     with pytest.raises(XGIError):
         m = 2

tests/readwrite/test_bipartite_edgelist.py

@@ -41,7 +41,6 @@
     ),
 )
 def test_read_bipartite_edgelist(file_string, extra_kwargs):
-
     _, filename = tempfile.mkstemp()
 
     with open(filename, "w") as file:

tests/readwrite/test_incidence_matrix.py

@@ -38,7 +38,6 @@
     ),
 )
 def test_read_incidence_matrix(file_string, extra_kwargs):
-
     _, filename = tempfile.mkstemp()
 
     with open(filename, "w") as file:

tests/readwrite/test_xgi_data.py

@@ -1,32 +1,56 @@
+import tempfile
 import time
+from os.path import join
 
 import pytest
 
-from xgi import load_xgi_data
+from xgi import download_xgi_data, load_xgi_data, read_json
 from xgi.exception import XGIError
 
 
 @pytest.mark.webtest
 @pytest.mark.slow
 def test_load_xgi_data():
-    H = load_xgi_data("email-enron", cache=False)
-    assert H.num_nodes == 148
-    assert H.num_edges == 10885
-    assert H["name"] == "email-Enron"
-    assert H.nodes["4"]["name"] == "[email protected]"
-    assert H.edges["0"]["timestamp"] == "2000-01-11T10:29:00"
+    # test loading the online data
+    H1 = load_xgi_data("email-enron", cache=False)
+    assert H1.num_nodes == 148
+    assert H1.num_edges == 10885
+    assert H1["name"] == "email-Enron"
+    assert H1.nodes["4"]["name"] == "[email protected]"
+    assert H1.edges["0"]["timestamp"] == "2000-01-11T10:29:00"
 
     start = time.time()
     H2 = load_xgi_data("email-enron", max_order=2, cache=True)
     elapsed_time = time.time() - start
+
     assert len(H2.edges.filterby("order", 2, mode="gt")) == 0
-    assert len(H.edges.filterby("order", 2, mode="gt")) == 1283
+    assert len(H1.edges.filterby("order", 2, mode="gt")) == 1283
 
     start = time.time()
-    H2 = load_xgi_data("email-enron", max_order=2)
+    H3 = load_xgi_data("email-enron", max_order=2)
     cached_elapsed_time = time.time() - start
 
     assert cached_elapsed_time < elapsed_time
+    assert H2.edges.members() == H3.edges.members()
 
     with pytest.raises(XGIError):
         load_xgi_data("test")
+
+    # test the empty argument
+    assert load_xgi_data() is None
+
+    with pytest.warns(Warning):
+        load_xgi_data("email-enron", read=True)
+
+    dir = tempfile.mkdtemp()
+    download_xgi_data("email-enron", dir)
+    H4 = load_xgi_data("email-enron", read=True, path=dir)
+    assert H1.edges.members() == H4.edges.members()
+
+
+def test_download_xgi_data():
+    dir = tempfile.mkdtemp()
+    download_xgi_data("email-enron", dir)
+    H = read_json(join(dir, "email-enron.json"))
+    H_online = load_xgi_data("email-enron")
+    assert H.edges.members() == H_online.edges.members()

tests/test_convert.py

@@ -52,7 +52,6 @@ def test_to_hyperedge_dict(edgelist1):
 
 
 def test_from_bipartite_pandas_dataframe(dataframe5):
-
     H1 = xgi.from_bipartite_pandas_dataframe(
         dataframe5, node_column="col2", edge_column="col1"
     )

tests/utils/test_utils.py

@@ -17,7 +17,6 @@ def test_dual_dict(dict5):
 
 
 def test_powerset():
-
     edge = [1, 2, 3, 4]
 
     PS = xgi.powerset(edge)
@@ -47,7 +46,6 @@ def test_powerset():
 
 
 def test_find_triangles():
-
     G = nx.erdos_renyi_graph(20, 0.2, seed=0)
     triangles = xgi.find_triangles(G)
 

tutorials/case_study_zhang2022.ipynb

@@ -176,7 +176,6 @@
     "\n",
     "# compute Lyapunov exponents for all alpha values\n",
     "for j, HG in enumerate(HGs):  # for all hypergraphs\n",
-    "\n",
     "    for i, alpha in enumerate(alphas):\n",
     "        lyap_1 = compute_eigenvalues(HG, order=1, weight=1 - alpha)\n",
     "        lyap_2 = compute_eigenvalues(HG, order=2, weight=alpha)\n",
@@ -191,7 +190,6 @@
     "\n",
     "# compute Lyapunov exponents for all alpha values\n",
     "for j, MSC in enumerate(MSCs):  # for all simplicial complexes\n",
-    "\n",
     "    for i, alpha in enumerate(alphas):\n",
     "        lyap_1 = compute_eigenvalues(MSC, order=1, weight=1 - alpha)\n",
     "        lyap_2 = compute_eigenvalues(MSC, order=2, weight=alpha)\n",
@@ -318,7 +316,6 @@
     "lyaps_HG_2 = np.zeros((len(p_1s), len(alphas), N))\n",
     "\n",
     "for j, p_1 in enumerate(p_1s):\n",
-    "\n",
     "    ps = [\n",
     "        p_1,\n",
     "        p_2,\n",