fix: accept 'links' key from NetworkX <=3.1 alongside 'edges'

graphify/build.py

@@ -32,6 +32,9 @@ def build_from_json(extraction: dict, *, directed: bool = False) -> nx.Graph:
     directed=True produces a DiGraph that preserves edge direction (source→target).
     directed=False (default) produces an undirected Graph for backward compatibility.
     """
+    # Normalise: NetworkX node_link_data() serialises edges as "links"; remap to "edges".
+    if "edges" not in extraction and "links" in extraction:
+        extraction = dict(extraction, edges=extraction["links"])
     errors = validate_extraction(extraction)
     # Dangling edges (stdlib/external imports) are expected - only warn about real schema errors.
     real_errors = [e for e in errors if "does not match any node id" not in e]

graphify/validate.py

@@ -36,14 +36,15 @@ def validate_extraction(data: dict) -> list[str]:
                     f"'{node['file_type']}' - must be one of {sorted(VALID_FILE_TYPES)}"
                 )
 
-    # Edges
-    if "edges" not in data:
+    # Edges - accept both "edges" (graphify schema) and "links" (NetworkX node_link_data default)
+    edge_list = data.get("edges") if "edges" in data else data.get("links")
+    if edge_list is None:
         errors.append("Missing required key 'edges'")
-    elif not isinstance(data["edges"], list):
+    elif not isinstance(edge_list, list):
         errors.append("'edges' must be a list")
     else:
         node_ids = {n["id"] for n in data.get("nodes", []) if isinstance(n, dict) and "id" in n}
-        for i, edge in enumerate(data["edges"]):
+        for i, edge in enumerate(edge_list):
             if not isinstance(edge, dict):
                 errors.append(f"Edge {i} must be an object")
                 continue

tests/test_build.py

@@ -39,3 +39,31 @@ def test_build_merges_multiple_extractions():
     G = build([ext1, ext2])
     assert G.number_of_nodes() == 2
     assert G.number_of_edges() == 1
+
+
+def test_build_from_json_with_links_key():
+    """NetworkX <= 3.1 used "links" as the edge key in node_link_data().
+    build_from_json() must accept "links" as a fallback for "edges" so that
+    data produced by older NetworkX versions (or any serialiser that uses
+    "links") is handled correctly."""
+    data = {
+        "directed": False, "multigraph": False, "graph": {},
+        "nodes": [{"id": "n1"}, {"id": "n2"}],
+        "links": [{"source": "n1", "target": "n2"}],  # old NetworkX key
+    }
+    built = build_from_json(data)
+    assert built.number_of_nodes() == 2
+    assert built.number_of_edges() == 1     # was 0 before the fix
+
+
+def test_build_from_json_with_edges_key():
+    """NetworkX >= 3.2 uses "edges" as the default key — must still work."""
+    import networkx as nx
+    G = nx.Graph()
+    G.add_node("n1", label="A")
+    G.add_node("n2", label="B")
+    G.add_edge("n1", "n2")
+    nx_data = nx.node_link_data(G)
+    built = build_from_json(nx_data)
+    assert built.number_of_nodes() == 2
+    assert built.number_of_edges() == 1

tests/test_validate.py

@@ -85,3 +85,32 @@ def test_assert_valid_raises_on_errors():
 
 def test_assert_valid_passes_silently():
     assert_valid(VALID)  # should not raise
+
+
+def test_links_key_accepted_as_edges():
+    """validate_extraction() must accept 'links' as a fallback for 'edges'
+    to support data produced by NetworkX node_link_data()."""
+    data = {
+        "nodes": [
+            {"id": "n1", "label": "Foo", "file_type": "code", "source_file": "foo.py"},
+            {"id": "n2", "label": "Bar", "file_type": "code", "source_file": "bar.py"},
+        ],
+        "links": [
+            {"source": "n1", "target": "n2", "relation": "calls",
+             "confidence": "EXTRACTED", "source_file": "foo.py", "weight": 1.0},
+        ],
+    }
+    errors = validate_extraction(data)
+    assert errors == [], f"Unexpected errors: {errors}"
+
+def test_edges_key_takes_priority_over_links():
+    """If both 'edges' and 'links' are present, 'edges' must be used."""
+    data = {
+        "nodes": [
+            {"id": "n1", "label": "Foo", "file_type": "code", "source_file": "foo.py"},
+        ],
+        "edges": [],          # empty — should be used
+        "links": "not-a-list",  # invalid — should be ignored
+    }
+    errors = validate_extraction(data)
+    assert errors == [], f"Unexpected errors: {errors}"