Docs (xgi-org#90)

* docs: general cleanup
* fix: function name change
* new tests

Co-authored-by: leotrs <[email protected]>
Co-authored-by: nwlandry <[email protected]>
Co-authored-by: Giovanni Petri <[email protected]>

docs/source/conf.py

@@ -65,7 +65,7 @@
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
 html_static_path = ["_static"]
-html_css_files = ['custom.css']
+html_css_files = ["custom.css"]
 
 # If your documentation needs a minimal Sphinx version, state it here.
 needs_sphinx = "1.3"

requirements/default.txt

@@ -2,4 +2,5 @@ numpy>=1.19,<1.22
 scipy>=1.5,<1.8.0
 pandas>=1.0,<=1.3.5
 networkx>=2.0
-requests>=2.0
+requests>=2.0
+matplotlib>=3.3

requirements/documentation.txt

@@ -2,4 +2,5 @@ sphinx~=4.0
 sphinx_copybutton
 sphinx-rtd-theme>=0.4.2
 numpydoc>=1.1
-pillow>=8.2
+pillow>=8.2
+matplotlib>=3.3

tests/classes/test_hypergraph.py

@@ -239,28 +239,31 @@ def test_add_edge():
 
 def test_add_edge_with_id():
     H = xgi.Hypergraph()
-    H.add_edge([1, 2, 3], id='myedge')
+    H.add_edge([1, 2, 3], id="myedge")
     assert (1 in H) and (2 in H) and (3 in H)
-    assert 'myedge' in H.edges
+    assert "myedge" in H.edges
     assert [1, 2, 3] in H.edges.members()
-    assert [1, 2, 3] == H.edges.members('myedge')
-    assert H.edges.members(dtype=dict) == {'myedge': [1, 2, 3]}
+    assert [1, 2, 3] == H.edges.members("myedge")
+    assert H.edges.members(dtype=dict) == {"myedge": [1, 2, 3]}
 
 
 def test_add_edge_with_attr():
     H = xgi.Hypergraph()
-    H.add_edge([1, 2, 3], color='red', place='peru')
+    H.add_edge([1, 2, 3], color="red", place="peru")
     assert (1 in H) and (2 in H) and (3 in H)
     assert 0 in H.edges
     assert [1, 2, 3] in H.edges.members()
     assert [1, 2, 3] == H.edges.members(0)
     assert H.edges.members(dtype=dict) == {0: [1, 2, 3]}
-    assert H.edges[0] == {'color': 'red', 'place': 'peru'}
+    assert H.edges[0] == {"color": "red", "place": "peru"}
 
 
 def test_add_node_to_edge():
     H = xgi.Hypergraph()
-    H.add_edge(['apple', 'banana'], 'fruits')
-    H.add_node_to_edge('fruits', 'pear')
-    H.add_node_to_edge('veggies', 'lettuce')
-    assert H.edges.members(dtype=dict) == {'fruits': ['apple', 'banana', 'pear'], 'veggies': ['lettuce']}
+    H.add_edge(["apple", "banana"], "fruits")
+    H.add_node_to_edge("fruits", "pear")
+    H.add_node_to_edge("veggies", "lettuce")
+    assert H.edges.members(dtype=dict) == {
+        "fruits": ["apple", "banana", "pear"],
+        "veggies": ["lettuce"],
+    }

tests/classes/test_simplicialcomplex.py

@@ -1,9 +1,22 @@
 import pytest
-
 import xgi
 from xgi.exception import XGIError
 
 
+def test_constructor(edgelist5, dict5, incidence5, dataframe5):
+    S_list = xgi.SimplicialComplex(edgelist5)
+    S_df = xgi.SimplicialComplex(dataframe5)
+
+    with pytest.raises(XGIError):
+        S_dict = xgi.SimplicialComplex(dict5)
+    with pytest.raises(XGIError):
+        S_mat = xgi.SimplicialComplex(incidence5)
+
+    assert list(S_list.nodes) == list(S_df.nodes)
+    assert list(S_list.edges) == list(S_df.edges)
+    assert list(S_list.edges.members(0)) == list(S_df.edges.members(0))
+
+
 def test_add_simplex():
     S = xgi.SimplicialComplex()
     S.add_simplex([1, 2, 3])
@@ -28,6 +41,22 @@ def test_add_edge():
         S.add_edge([1, 2, 3])
 
 
+def test_add_simplices_from(edgelist5):
+    S1 = xgi.SimplicialComplex()
+    S1.add_simplices_from(edgelist5, max_order=None)
+
+    S2 = xgi.SimplicialComplex()
+    S2.add_simplices_from(edgelist5, max_order=2)
+
+    assert S1.nodes == S2.nodes
+
+    assert S1.max_edge_order() == 3
+    assert S2.max_edge_order() == 2
+
+    assert set(S1.edges(order=1).members()) == set(S2.edges(order=1).members())
+    assert set(S1.edges(order=2).members()) == set(S2.edges(order=2).members())
+
+
 def test_remove_simplex_id(edgelist6):
     S = xgi.SimplicialComplex()
     S.add_simplices_from(edgelist6)

tests/generators/test_classic.py

@@ -1,5 +1,5 @@
+import networkx as nx
 import pytest
-
 import xgi
 
 
@@ -23,3 +23,20 @@ def test_star_clique():
     assert H.num_nodes == 13
     assert H.num_edges == 97
     assert H.max_edge_order() == 3
+
+
+def test_flag_complex():
+    edges = [[0, 1], [1, 2], [2, 0], [0, 3]]
+    G = nx.Graph(edges)
+
+    S = xgi.flag_complex(G)
+
+    simplices = [
+        frozenset({0, 1, 2}),
+        frozenset({0, 1}),
+        frozenset({0, 2}),
+        frozenset({1, 2}),
+        frozenset({0, 3}),
+    ]
+
+    assert S.edges.members() == simplices