NetworkX from HIF

scripts/hif.py

@@ -15,8 +15,10 @@ def validate_hif(path):
     info["valid-field-names"] = 0
     fields = {"network-type", "metadata", "nodes", "edges", "incidences"}
     if not set(data).issubset(fields):
+        fields = ", ".join(fields)
+        data = ", ".join(set(data))
         warn(
-            f"Acceptable field names are: {", ".join(fields)}\nand the field names are {", ".join(set(data))}"
+            f"Acceptable field names are: {fields}\nand the field names are {data}"
         )
         info["valid-field-names"] = 1
 
@@ -33,8 +35,9 @@ def validate_hif(path):
     network_types = {"asc", "undirected", "directed"}
     if "network-type" in data:
         if data["network-type"] not in network_types:
+            network_types = ", ".join(network_types)
             warn(
-                f"Unsupported network type. Valid types are: {", ".join(network_types)}"
+                f"Unsupported network type. Valid types are: {network_types}"
             )
             info["valid-network-type"] = 1
 

scripts/nx.py

@@ -0,0 +1,11 @@
+import networkx as nx
+
+def from_hif(data) -> nx.Graph:
+    g = nx.Graph()
+    for n in data.get("nodes", []):
+        g.add_node(n["node"], bipartite=0, weight=n.get("weight", 0))
+    for e in data.get("edges", []):
+        g.add_node(e["edge"], bipartite=1, weight=e.get("weight", 0))
+    for i in data["incidences"]:
+        g.add_edge(i["node"], i["edge"], weight=i.get("weight", 0))
+    return g

tests/conftest.py

@@ -16,6 +16,17 @@ def validator():
 def empty():
     return json.load(open(f"{json_dir}/empty.json", "r"))
 
+@pytest.fixture
+def single_node():
+    return json.load(open(f"{json_dir}/single_node.json", "r"))
+
+@pytest.fixture
+def single_edge():
+    return json.load(open(f"{json_dir}/single_edge.json", "r"))
+
+@pytest.fixture
+def single_incidence():
+    return json.load(open(f"{json_dir}/single_incidence.json", "r"))
 
 @pytest.fixture
 def bad_top_level_field():

tests/test_files/single_edge.json

@@ -0,0 +1 @@
+{"incidences": [], "edges": [ { "edge": 3 } ]}

tests/test_files/single_incidence.json

@@ -0,0 +1 @@
+{"incidences": [ { "edge": "abcd", "node": 42 } ]}

tests/test_files/single_node.json

@@ -0,0 +1 @@
+{"incidences": [], "nodes": [ { "node": 42 } ]}

tests/test_nx.py

@@ -0,0 +1,26 @@
+import networkx as nx
+from scripts.nx import from_hif
+
+
+def test_empty_hypergraph(empty_hypergraph):
+    result = from_hif(empty_hypergraph)
+    expected = nx.Graph()
+    assert nx.utils.graphs_equal(result, expected)
+
+def test_single_node(single_node):
+    result = from_hif(single_node)
+    expected = nx.Graph()
+    expected.add_node(42, bipartite=0, weight=0)
+    assert nx.utils.graphs_equal(result, expected)
+
+def test_single_edge(single_edge):
+    result = from_hif(single_edge)
+    expected = nx.Graph()
+    expected.add_node(3, bipartite=1, weight=0)
+    assert nx.utils.graphs_equal(result, expected)
+
+def test_single_incidence(single_incidence):
+    result = from_hif(single_incidence)
+    expected = nx.Graph()
+    expected.add_edge("abcd", 42, weight=0)
+    assert nx.utils.graphs_equal(result, expected)