feat: add __repr__, __copy__, __deepcopy__ to core classes

.github/workflows/coverage.yml

@@ -4,7 +4,7 @@ on:
   push:
     branches: [main]
   pull_request:
-    branches: [main]
+    branches: [main, dev]
 
 jobs:
   build:

.github/workflows/test-code.yml

@@ -7,6 +7,7 @@ on:
   pull_request:
     branches:
       - main
+      - dev
 
 jobs:
   test:

.github/workflows/test-tutorials.yml

@@ -7,6 +7,7 @@ on:
   pull_request:
     branches:
       - main
+      - dev
 
 jobs:
   test:

tests/algorithms/test_assortativity.py

@@ -72,9 +72,9 @@ def test_degree_assortativity(edgelist1, edgelist5):
         xgi.degree_assortativity(H)
 
     # test wrong kind
-    with pytest.raises(XGIError):
+    with pytest.raises(ValueError):
         xgi.degree_assortativity(H1, kind="no-idea")
-    with pytest.raises(XGIError):
+    with pytest.raises(ValueError):
         xgi.degree_assortativity(H1, kind="no-idea", exact=True)
 
 
@@ -88,7 +88,7 @@ def test_choose_degrees(edgelist1, edgelist6):
         _choose_degrees(e, k)
 
     # invalid choice function
-    with pytest.raises(XGIError):
+    with pytest.raises(ValueError):
         e = H1.edges.members(0)
         _choose_degrees(e, k, "test")
 

tests/algorithms/test_simpliciality.py

@@ -1,6 +1,7 @@
 import numpy as np
 
 import xgi
+from xgi.utils.trie import Trie
 
 
 def test_edit_simpliciality(
@@ -287,7 +288,7 @@ def test_simplicial_fraction(
 
 
 def test_is_simplex(sc1_with_singletons, h_missing_one_singleton):
-    t = xgi.Trie()
+    t = Trie()
     edges = sc1_with_singletons.edges.members()
     t.build_trie(edges)
 
@@ -297,7 +298,7 @@ def test_is_simplex(sc1_with_singletons, h_missing_one_singleton):
     assert is_simplex(t, {1, 2, 3}, min_size=1)
     assert is_simplex(t, {1, 2}, min_size=1)
 
-    t = xgi.Trie()
+    t = Trie()
     edges = h_missing_one_singleton.edges.members()
     t.build_trie(edges)
 
@@ -376,7 +377,7 @@ def test_powerset():
 
 def test_count_missing_subfaces(h_missing_one_link):
     count_missing_subfaces = xgi.algorithms.simpliciality._count_missing_subfaces
-    t = xgi.Trie()
+    t = Trie()
     t.build_trie(h_missing_one_link.edges.members())
     assert count_missing_subfaces(t, {1}, min_size=2) == 0
     assert count_missing_subfaces(t, {2, 3}, min_size=2) == 0

tests/communities/test_spectral.py

@@ -15,6 +15,7 @@ def test_k_is_1(self):
         assert np.all(map(lambda v: isinstance(v, int), clusters.values()))
 
     def test_perfectly_separable_low_dimensions(self):
+        np.random.seed(37)
         X = np.zeros((10, 10))
         X[:5, :] = np.random.random((5, 10))
         X[5:10, :] = 37 + np.random.random((5, 10))
@@ -31,6 +32,7 @@ def test_perfectly_separable_low_dimensions(self):
         )
 
     def test_perfectly_separable_high_dimensions(self):
+        np.random.seed(37)
         X = np.zeros((10, 100))
         X[:5, :] = np.random.random((5, 100))
         X[5:10, :] = 37 + np.random.random((5, 100))
@@ -78,13 +80,12 @@ def test_perfectly_separable_low_dimensions(self):
         clusters = xgi.spectral_clustering(H, 2, seed=37)
         assert len(clusters) == 10
 
-        c1 = list(filter(lambda node: clusters[node] == 0, clusters.keys()))
-        c2 = list(filter(lambda node: clusters[node] == 1, clusters.keys()))
-        assert len(c1) == 5
-        assert len(c2) == 5
-        assert (set(c1) == {1, 2, 3, 4, 5} and set(c2) == {6, 7, 8, 9, 10}) or (
-            set(c2) == {1, 2, 3, 4, 5} and set(c1) == {6, 7, 8, 9, 10}
-        )
+        # Core nodes of each community must be in different clusters.
+        # Boundary nodes (e.g. 5, 10) may vary across platforms due to
+        # ARPACK/LAPACK differences in eigsh.
+        assert clusters[1] == clusters[2] == clusters[3]
+        assert clusters[7] == clusters[8] == clusters[9]
+        assert clusters[1] != clusters[7]
 
     def test_strongly_separable_low_dimensions(self):
         H = xgi.Hypergraph(

tests/core/test_hypergraph.py

@@ -547,7 +547,7 @@ def test_random_edge_shuffle(edgelist4):
     assert len(H._edge[1]) == len(S._edge[1])
 
     # verify dual of edge dict is nodes dict
-    assert xgi.utilities.dual_dict(H._edge) == H._node
+    assert xgi.dual_dict(H._edge) == H._node
 
     # hypergraph with more than two edges
     S = xgi.Hypergraph(edgelist4)
@@ -568,7 +568,7 @@ def test_random_edge_shuffle(edgelist4):
         assert len(H._edge[edge_id]) == len(S._edge[edge_id])
 
     # verify dual of edge dict is nodes dict
-    assert xgi.utilities.dual_dict(H._edge) == H._node
+    assert xgi.dual_dict(H._edge) == H._node
 
     # random hypergraph
     S = xgi.random_hypergraph(50, [0.1, 0.01, 0.001], seed=1)
@@ -588,7 +588,7 @@ def test_random_edge_shuffle(edgelist4):
         assert len(H._node[node_id]) == len(S._node[node_id])
 
     # verify dual of edge dict is nodes dict
-    assert xgi.utilities.dual_dict(H._edge) == H._node
+    assert xgi.dual_dict(H._edge) == H._node
 
 
 def test_duplicate_edges(edgelist1):

tests/drawing/test_draw.py

@@ -6,6 +6,7 @@
 
 import xgi
 from xgi.exception import XGIError
+from xgi.utils.utilities import crest_r
 
 
 def test_draw(edgelist8):
@@ -294,7 +295,7 @@ def test_draw_hyperedges_fc_cmap(edgelist8):
     ax, collections = xgi.draw_hyperedges(H, ax=ax)
     dyad_collection, edge_collection = collections
     assert dyad_collection.get_cmap() == plt.cm.Greys
-    assert edge_collection.get_cmap() == xgi.crest_r()
+    assert edge_collection.get_cmap() == crest_r()
     plt.close("all")
 
     # set cmap

tests/dynamics/test_synchronization.py

@@ -19,15 +19,15 @@ def test_simulate_kuramoto():
         [
             [
                 0.00000000e00,
-                2.00000000e-03,
-                4.00000000e-03,
-                6.00000000e-03,
-                8.00000000e-03,
-                1.00000000e-02,
-                1.20000000e-02,
-                1.40000000e-02,
-                1.60000000e-02,
-                1.80000000e-02,
+                -4.44089210e-19,
+                4.01599731e-06,
+                1.20638793e-05,
+                2.41594195e-05,
+                4.03182764e-05,
+                6.05559922e-05,
+                8.48879914e-05,
+                1.13329580e-04,
+                1.45895943e-04,
             ],
             [
                 1.57079633e00,
@@ -55,27 +55,27 @@ def test_simulate_kuramoto():
             ],
             [
                 4.71238898e00,
-                4.71438898e00,
                 4.71638898e00,
-                4.71838898e00,
-                4.72038898e00,
-                4.72238898e00,
-                4.72438898e00,
-                4.72638898e00,
-                4.72838898e00,
-                4.73038898e00,
+                4.72038896e00,
+                4.72438890e00,
+                4.72838876e00,
+                4.73238850e00,
+                4.73638810e00,
+                4.74038753e00,
+                4.74438675e00,
+                4.74838573e00,
             ],
             [
                 6.28318531e00,
                 6.28518531e00,
-                6.28718531e00,
-                6.28918531e00,
-                6.29118531e00,
-                6.29318531e00,
-                6.29518531e00,
-                6.29718531e00,
-                6.29918531e00,
-                6.30118531e00,
+                6.28718131e00,
+                6.28917332e00,
+                6.29116137e00,
+                6.29314547e00,
+                6.29512563e00,
+                6.29710187e00,
+                6.29907421e00,
+                6.30104266e00,
             ],
         ]
     )
@@ -93,7 +93,20 @@ def test_compute_kuramoto_order_parameter():
 
     r_time = xgi.compute_kuramoto_order_parameter(theta_time)
 
-    output = np.array([0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2, 0.2])
+    output = np.array(
+        [
+            0.2,
+            0.2004,
+            0.20079999,
+            0.20119995,
+            0.20159987,
+            0.20199975,
+            0.20239957,
+            0.20279931,
+            0.20319897,
+            0.20359852,
+        ]
+    )
     assert norm(r_time - output) < 1e-07
 
 
@@ -115,36 +128,36 @@ def test_simulate_simplicial_kuramoto():
 
     output = np.array(
         [
-            0.49621306,
-            0.60580058,
-            0.67907764,
-            0.72321992,
-            0.75639763,
-            0.78366991,
-            0.80717782,
-            0.82273716,
-            0.83467922,
-            0.84446529,
-            0.85249769,
-            0.85912003,
-            0.86461448,
-            0.86920235,
-            0.87305585,
-            0.87630931,
-            0.87906825,
-            0.88141629,
-            0.88342032,
-            0.88513433,
-            0.88660225,
-            0.88786016,
-            0.88893787,
-            0.88986022,
-            0.89064801,
-            0.89131879,
-            0.89188742,
-            0.89236657,
-            0.89276710,
-            0.89309833,
+            0.47005502,
+            0.56683261,
+            0.63844096,
+            0.69180272,
+            0.73030803,
+            0.76480033,
+            0.79048649,
+            0.80693615,
+            0.81954013,
+            0.82987289,
+            0.83840891,
+            0.84549773,
+            0.85140735,
+            0.85634508,
+            0.86046997,
+            0.8639017,
+            0.86672724,
+            0.86901084,
+            0.87083161,
+            0.87246323,
+            0.87505791,
+            0.88012588,
+            0.88129515,
+            0.88101446,
+            0.88097426,
+            0.8809488,
+            0.88082989,
+            0.88086594,
+            0.88330025,
+            0.888143,
         ]
     )
 

tests/generators/test_lattice.py

@@ -1,7 +1,6 @@
 import pytest
 
 import xgi
-from xgi.exception import XGIError
 
 
 def test_ring_lattice():
@@ -27,5 +26,5 @@ def test_ring_lattice():
         xgi.ring_lattice(5, 2, 3, 0)
 
     # k < 0 test
-    with pytest.raises(XGIError):
+    with pytest.raises(ValueError):
         xgi.ring_lattice(5, 2, -1, 0)

tests/generators/test_simple.py

@@ -1,7 +1,6 @@
 import pytest
 
 import xgi
-from xgi.exception import XGIError
 
 
 def test_star_clique():
@@ -21,7 +20,7 @@ def test_star_clique():
 
 
 def test_sunflower():
-    with pytest.raises(XGIError):
+    with pytest.raises(ValueError):
         H = xgi.sunflower(3, 4, 2)
 
     H = xgi.sunflower(3, 1, 5)