fix(export): tolerate id-less persisted hyperedges in attach_hyperedges (#2775)

CHANGELOG.md

@@ -14,6 +14,7 @@ Full release notes with details on each version: [GitHub Releases](https://githu
 - Fix: a lazy CommonJS `require(...)` inside a function body (the idiom for breaking circular dependencies) now emits the same `imports_from`/`imports` dependency edges as a top-level require, attributed to the enclosing function, instead of being silently dropped; a dynamic `require(variable)` is still skipped (#2700, thanks @rajanpanth).
 - Fix: a JS/TS identifier bound by an import whose target resolves outside the scanned corpus (e.g. a `lucide-react` icon) is now shadowed, so using it as a value no longer fabricates an INFERRED `indirect_call` onto an unrelated same-named callable elsewhere in the corpus; a relative/in-corpus import still resolves to its real target (#2757, thanks @phudayyy).
 - Fix: an OCaml qualified call `M.f` to an external module (one not defined in the same file, e.g. Hardcaml's `Reg_spec.create`) no longer binds to a same-named local `let f` — which produced a false `calls` edge and, when the caller was that local `f`, a `f -> f` self-loop. External qualified calls are kept as a distinct target labelled by the full path; unqualified calls and calls into a locally-defined module still resolve locally, and cross-file `Geo.area` still collapses onto another file's `area`.
+- Fix: an incremental re-extract no longer dies at the merge step with `KeyError: 'id'` when a prior `graph.json` carries id-less hyperedges (which the semantic/LLM extractor routinely emits and `build.py` persists verbatim); `attach_hyperedges` now seeds its dedup set only from persisted entries that actually have an `id`, symmetric with the guard already applied to the incoming set (#2775, thanks @otterswimware). The first run always worked, so this surfaced as flaky extraction rather than a deterministic crash.
 
 ## 0.9.43 (2026-08-14)
 

graphify/export.py

@@ -163,7 +163,13 @@ def _yaml_str(s: str) -> str:
 def attach_hyperedges(G: nx.Graph, hyperedges: list) -> None:
     """Store hyperedges in the graph's metadata dict."""
     existing = G.graph.get("hyperedges", [])
-    seen_ids = {h["id"] for h in existing}
+    # Skip id-less persisted entries when seeding the dedup set (#2775): the
+    # semantic extractor emits hyperedges with no `id` and build.py persists them
+    # verbatim, so a prior graph.json can contain id-less hyperedges. A hard
+    # `h["id"]` here raised `KeyError: 'id'` on every incremental re-extract,
+    # symmetric with the `.get("id")` guard the loop below already applies to the
+    # incoming set.
+    seen_ids = {h["id"] for h in existing if h.get("id")}
     for h in hyperedges:
         if h.get("id") and h["id"] not in seen_ids:
             existing.append(h)

tests/test_hypergraph.py

@@ -137,6 +137,20 @@ def test_attach_hyperedges_skips_entry_without_id():
     assert G.graph.get("hyperedges", []) == []
 
 
+def test_attach_hyperedges_tolerates_id_less_persisted():
+    # Regression for #2775: the semantic extractor emits hyperedges with no `id`
+    # and build.py persists them verbatim, so a prior graph.json can carry id-less
+    # hyperedges. On the next (incremental) run, attach_hyperedges read that
+    # persisted set with a hard `h["id"]` and died with `KeyError: 'id'`, writing
+    # nothing. Reading the persisted set must tolerate missing ids.
+    G = nx.DiGraph()
+    G.graph["hyperedges"] = [{"nodes": ["a", "b"], "type": "project", "attributes": {}}]
+    attach_hyperedges(G, [{"id": "flow_a", "label": "Flow A", "nodes": ["A", "B"]}])
+    # No crash; the id-less persisted entry is retained and the new id-bearing
+    # incoming hyperedge is appended.
+    assert len(G.graph["hyperedges"]) == 2
+
+
 # ---------------------------------------------------------------------------
 # 3. to_json includes hyperedges key
 # ---------------------------------------------------------------------------