fix(build): coerce null/malformed edge weight to the 1.0 default (#1960)

An explicit "weight": null in the extraction JSON survived .get("weight", 1.0)
(the key is present, so the default never applied) and reached Louvain/Leiden as
None, crashing modularity with a TypeError (graspologic's Leiden even panics on
NaN). build_from_json now coerces weight and confidence_score to float at the
ingest choke point, falling back to 1.0 for null / non-numeric / NaN / inf /
negative values while preserving valid ones. Repairs (not drops) the key so
graph.json round-trips clean and a cluster-only/--update reload never re-ingests
the null.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>

graphify/build.py

@@ -22,6 +22,7 @@
 #
 from __future__ import annotations
 import json
+import math
 import os
 import re
 import sys
@@ -706,6 +707,24 @@ def build_from_json(extraction: dict, *, directed: bool = False, root: str | Pat
         if src not in node_set or tgt not in node_set:
             continue  # skip edges to external/stdlib nodes - expected, not an error
         attrs = {k: v for k, v in edge.items() if k not in ("source", "target")}
+        # Sanitize numeric edge fields (#1960): an explicit ``"weight": null`` in
+        # the extraction JSON survives ``.get("weight", 1.0)`` (the key is present,
+        # so the default never applies) and reaches Louvain/Leiden as None,
+        # crashing modularity arithmetic with a TypeError (graspologic's Leiden
+        # even panics on NaN). Coerce to float and fall back to the schema default
+        # of 1.0 for anything the clustering backends reject — None, non-numeric
+        # strings, NaN/inf, negatives — while numeric strings coerce cleanly.
+        # Repair (not drop) the key so graph.json round-trips a clean value and a
+        # cluster-only/--update reload never re-ingests the null.
+        for _num_key in ("weight", "confidence_score"):
+            if _num_key in attrs:
+                try:
+                    _num_val = float(attrs[_num_key])
+                except (TypeError, ValueError):
+                    _num_val = 1.0
+                if not math.isfinite(_num_val) or _num_val < 0:
+                    _num_val = 1.0
+                attrs[_num_key] = _num_val
         # Backfill source_file from the endpoint nodes (every node carries one).
         # Semantic/LLM edges occasionally omit it, which downstream validation
         # flags and leaves query results with no file reference (#1279).

tests/test_build.py

@@ -58,6 +58,48 @@ def test_build_from_json_edge_count():
     G = build_from_json(load_extraction())
     assert G.number_of_edges() == 4
 
+def test_null_weight_edge_builds_and_clusters(tmp_path):
+    """#1960: an explicit ``"weight": null`` (JSON null -> None) used to survive
+    ``.get("weight", 1.0)`` and crash Louvain/Leiden modularity with a TypeError.
+    It must now coerce to the 1.0 default, build, and cluster without raising."""
+    from graphify.cluster import cluster
+    extraction = {
+        "nodes": [
+            {"id": "a", "label": "A", "file_type": "code", "source_file": "a.py"},
+            {"id": "b", "label": "B", "file_type": "code", "source_file": "b.py"},
+            {"id": "c", "label": "C", "file_type": "code", "source_file": "c.py"},
+        ],
+        "edges": [
+            {"source": "a", "target": "b", "relation": "references", "weight": None,
+             "confidence_score": None},
+            {"source": "b", "target": "c", "relation": "references", "weight": 2.5},
+        ],
+    }
+    G = build_from_json(extraction)
+    assert G["a"]["b"]["weight"] == 1.0            # null coerced to default
+    assert G["a"]["b"]["confidence_score"] == 1.0  # null confidence_score too
+    assert G["b"]["c"]["weight"] == 2.5            # a valid weight is preserved
+    cluster(G)  # must not raise (Louvain/Leiden modularity)
+
+
+def test_malformed_weights_normalize():
+    """Non-numeric / NaN / inf / negative weights fall back to 1.0 (the backends
+    reject them); a missing weight key is left absent (backends default it)."""
+    extraction = {
+        "nodes": [{"id": f"n{i}", "label": str(i), "file_type": "code",
+                   "source_file": f"{i}.py"} for i in range(4)],
+        "edges": [
+            {"source": "n0", "target": "n1", "relation": "references", "weight": "3.5"},
+            {"source": "n1", "target": "n2", "relation": "references", "weight": float("nan")},
+            {"source": "n2", "target": "n3", "relation": "references", "weight": -4},
+        ],
+    }
+    G = build_from_json(extraction)
+    assert G["n0"]["n1"]["weight"] == 3.5     # numeric string coerces
+    assert G["n1"]["n2"]["weight"] == 1.0     # NaN -> default
+    assert G["n2"]["n3"]["weight"] == 1.0     # negative -> default
+
+
 def test_nodes_have_label():
     G = build_from_json(load_extraction())
     assert G.nodes["n_transformer"]["label"] == "Transformer"