Optimize test-only sweep for touched nodes (#47)

[leynos]

Summary

This branch localises test-only post-mutation reciprocity healing to graph-owned
changed adjacency lists. It preserves invariant repair while avoiding work on
unrelated graph edges.

Closes #47.

Review walkthrough

• Graph mutation tracking owns the touched queue and restores it with the graph when deletion rolls back.
• Reachability repair tracking records mutation pairs only in test builds, preserving Kani compilation.
• Direct CPU healing tests cover insertion, deletion, reachability repair, locality, and queue draining.
• Maintainer guidance and the dated ADR addendum define the test-only ownership and rollback boundary.

Validation

• make check-fmt: passed.
• make lint: passed (Rustdoc, Clippy, and Whitaker).
• make test: passed (1,089 passed; 1 skipped).
• make markdownlint: passed.
• make nixie: passed.
• make kani: passed (all four practical harnesses).
• coderabbit review --agent: zero findings.
• Five-run hyperfine mutation-property comparison: mean reduced from 3.209 s to 0.875 s (approximately 73%).

References

• Issue #47
• Lody session

Summary by Sourcery

Optimize test-only HNSW mutation healing by repairing reciprocity only on graph-owned adjacency lists touched by recent mutations.

Enhancements:

• Localize test-only HNSW reciprocity healing to adjacency lists changed by mutations instead of scanning unrelated graph edges.
• Track touched adjacency lists across insertion, deletion, reconnection, and reachability repair, including restoring tracking state when mutations roll back.

Documentation:

• Document the ownership, lifecycle, and rollback requirements for the test-only touched-node healing queue.
• Record the localized reciprocity sweep and its test-only boundary in the post-processing ADR.

Tests:

• Add coverage for localized insertion healing, deletion and reachability tracking, queue draining, rollback preservation, and untouched asymmetric edges.

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Summary

Replace the test-only full-graph reciprocity sweep with graph-owned tracking of changed (node, level) adjacency lists.

Changes

• Track touched adjacency lists during insertion, deletion, reconnection, and reachability repair.
• Drain the touched-list queue during heal_for_test.
• Repair and validate reciprocity only for touched lists.
• Preserve unrelated one-way edges.
• Add regression tests for local repair and deletion tracking.
• Update docs/adr-001-commit-post-processing.md with ownership and consumption boundaries.
• Address issue #47.

Validation

• Pass formatting, linting, tests, documentation checks, and stress tests.
• Reduce the mutation property mean from 3.209 seconds to 0.875 seconds across five benchmark runs.

Walkthrough

Track graph mutations as node-layer pairs. Drain these pairs after insertion and reachability healing. Repair and validate reciprocity only for affected adjacency lists. Update tests and the ADR to document the scoped process.

Changes

Touched-node healing

Layer / File(s)	Summary
Track graph mutations chutoro-core/src/hnsw/graph/core.rs, chutoro-core/src/hnsw/graph/test_helpers/*	Store touched node-layer pairs in test builds. Record successful edge additions, removals, and references removed during deletion. Validate the deletion queue.
Apply scoped reciprocity healing chutoro-core/src/hnsw/cpu/test_helpers.rs, chutoro-core/src/hnsw/insert/*, docs/adr-001-commit-post-processing.md	Collect touched pairs after insertion and healing. Repair and validate only their edges. Update the test helper API, regression coverage, and ADR.

Suggested labels: Issue

Poem

Touched nodes mark the way,
Changed edges join the fray.
Full sweeps fade from sight,
Local checks restore the right.
Graphs heal fast by day.

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Caution

Pre-merge checks failed

Please resolve all errors before merging. Addressing warnings is optional.

• Ignore

❌ Failed checks (1 error, 2 warnings)

Check name	Status	Explanation	Resolution
Testing (Overall)	❌ Error	Add tests for CpuHnsw::heal_for_test: the locality test calls TestHelpers directly, while the only hook coverage is a property test that does not assert untouched asymmetric edges.	Exercise heal_for_test with touched and unrelated asymmetric edges. Assert queue draining and tracking for insertion, removal, and reachability repair.
Developer Documentation	⚠️ Warning	The PR adds graph-owned test-only touched-node APIs, but developers-guide.md is unchanged and lacks this guidance; accepted ADR-001 is edited in place without a dated addendum.	Add maintainer guidance for the touched-node queue and healing boundary to docs/developers-guide.md. Record the ADR update as a dated addendum.
Concurrency And State	⚠️ Warning	Failed deletion restores nodes and entry but leaves touched pairs recorded during the aborted mutation, so the graph and its healing state diverge.	Snapshot and restore touched state with nodes and entry, or stage touched pairs until reachability succeeds; add a failed-delete queue assertion.

✅ Passed checks (17 passed)

Check name	Status	Explanation
Linked Issues check	✅ Passed	The changes satisfy issue #47 by tracking mutations, limiting reciprocity healing, measuring performance, and preserving correctness coverage.
Out of Scope Changes check	✅ Passed	All code and documentation changes support the touched-node sweep optimisation described by issue #47.
Docstring Coverage	✅ Passed	Docstring check was indeterminate for this PR — some files could not be analyzed in time. Not blocking.
User-Facing Documentation	✅ Passed	Pass this check: the diff changes only test-only HNSW healing and tracking; production API behaviour is unchanged, and docs/users-guide.md is not required.
Module-Level Documentation	✅ Passed	Accept the check: every changed Rust module has a //! docstring describing its purpose, test utility, or relationship to the HNSW graph and insertion components.
Testing (Unit And Behavioural)	✅ Passed	Pass: retain the new queue and locality tests; existing deletion error/rollback tests and the mutation property exercise insert/delete/reconfigure through CpuHnsw and check all invariants after eac...
Testing (Property / Proof)	✅ Passed	Use the existing proptest for random add/delete/reconfigure sequences and invariant checks after each heal; focused tests cover queue locality, and no proof assumption was introduced.
Testing (Compile-Time / Ui)	✅ Passed	Accept this check: the diff confines new fields and helpers to cfg(test), changes no exported API or UI/text output, and adds focused runtime assertions; trybuild and snapshots are not applicable.
Unit Architecture	✅ Passed	The diff is test-only. record/take use explicit mutable APIs, healing uses write_graph, and read helpers use &self; no hidden dependency or query-side write was introduced.
Domain Architecture	✅ Passed	The changed HNSW code uses domain concepts such as graph nodes, layers, edges, and reachability, with no HTTP, SQL, filesystem, environment, vendor, or transport concerns.
Observability	✅ Passed	Keep this check passing: changed tracking and healing code is behind cfg(test) or test-only modules, and production paths add no operational behaviour requiring logs, metrics, or tracing.
Security And Privacy	✅ Passed	Keep the change: all new tracking is behind cfg(test), uses numeric node/layer pairs, and adds no secrets, credentials, external-input sinks, or sensitive-data logging.
Performance And Resource Use	✅ Passed	Pass the check: keep touched pairs graph-owned and drained; cfg(test) bounds the set by capacity and max level, while the reported benchmark reduced mean time by about 73%.
Architectural Complexity And Maintainability	✅ Passed	Keep this design: the test-only BTreeSet is graph-owned and explicitly drained, directly replacing the full sweep; the diff adds no dependencies, cycles, or speculative extension layer.
Rust Compiler Lint Integrity	✅ Passed	Accept the change: the diff adds no broad lint suppressions or clone calls; every new touched-state API has callers, and the retained full-sweep helper remains used by two tests.
Title check	✅ Passed	The title accurately describes the localized test-only sweep and references issue #47.
Description check	✅ Passed	The description clearly explains the touched-node optimization, validation, performance result, and issue #47.

✨ Finishing Touches

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• Commit unit tests in branch issue-47-optimise-test-only-sweep-to-process-only-touched-nodes

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Reviewer's Guide

This PR replaces the test-only full-graph reciprocity sweep with a graph-owned set of touched adjacency lists, and updates test helpers and ADR docs so post-mutation healing and validation only process edges for nodes that were actually changed.

Sequence diagram for test-only touched-list healing

sequenceDiagram
    participant Mutation as Graph mutation
    participant Graph
    participant Executor as InsertionExecutor
    participant Heal as CpuHnsw test hook
    participant Repair as Reciprocity repair

    Mutation->>Graph: record_touched_nodes(pairs)
    Mutation->>Executor: commit mutation
    Executor->>Graph: record_touched_nodes(touched)
    Heal->>Graph: drain_touched_nodes()
    Graph-->>Heal: touched (node, level) pairs
    Heal->>Repair: enforce_bidirectional_for_touched(touched, max_connections)
    Repair-->>Heal: localized reciprocity repair

Loading

Flow diagram for localized post-mutation validation

flowchart LR
    A[Mutation changes adjacency lists] --> B[Graph records touched node-level pairs]
    B --> C[heal_for_test drains touched set]
    C --> D[Repair and validate touched outgoing edges]
    D --> E[Untouched edges are not swept]

Loading

File-Level Changes

Change	Details	Files
Introduce test-only tracking of touched (node, level) adjacency lists on the Graph and consume them in the CPU HNSW test healing hook.	Add a cfg(test) BTreeSet<(usize, usize)> field to Graph to record touched node/level pairs and initialize it in Graph::new. Implement Graph::record_touched_nodes and Graph::take_touched_nodes in test helpers to accumulate and drain touched pairs between healing passes. Update CpuHnsw::heal_for_test to run reachability healing first, then drain touched nodes from the graph and enforce bidirectionality only for those touched adjacency lists.	chutoro-core/src/hnsw/graph/core.rs chutoro-core/src/hnsw/graph/test_helpers/mod.rs chutoro-core/src/hnsw/cpu/test_helpers.rs
Ensure insert, delete, edge add/remove, and reachability reconnection all enqueue the adjacency lists they mutate into the touched set.	Modify Graph::delete_node to record adjacency lists whose references were stripped before reconnecting layers. Refactor strip_references_to into strip_references_to and strip_node_references to return the (node, level) pairs whose neighbour lists changed. Update try_add_edge and remove_edge to track when an edge is added or removed and record the corresponding (origin, level) in the touched set. Adjust an existing delete-node test to clear any prior touched entries and assert that delete queues exactly the adjacency lists it changes.	chutoro-core/src/hnsw/graph/test_helpers/mod.rs chutoro-core/src/hnsw/graph/test_helpers/tests.rs
Localize reciprocity repair and validation to touched edges in insertion/test helpers and add tests to prove untouched edges remain unchanged.	Have InsertionExecutor record touched adjacency lists at insert time (including all levels for the new node) under cfg(test). Replace enforce_bidirectional_all with enforce_bidirectional_for_touched on the executor, wired to the new TestHelpers method. Implement TestHelpers::enforce_bidirectional_for_touched, collect_touched_edges, and validate_touched_edges_reciprocal so healing/validation only iterates edges from touched nodes/levels. Refactor validate_all_edges_reciprocal to use collect_edges for clarity and reuse. Add a regression test that builds a small graph, marks a subset as touched, runs localized enforcement, and asserts unrelated edges are left untouched.	chutoro-core/src/hnsw/insert/executor.rs chutoro-core/src/hnsw/insert/executor/tests/mod.rs chutoro-core/src/hnsw/insert/test_helpers.rs
Document the new test-only touched-set ownership and processing boundary in the ADR on commit post-processing.	Extend ADR 001 to note that the previous healing hook scanned every edge after bootstrap and each mutation. Record the decision to maintain a test-only, graph-owned set of changed (node, level) pairs, append only from mutation helpers, and drain/validate them in CpuHnsw::heal_for_test, with callers barred from injecting or reusing drained batches.	docs/adr-001-commit-post-processing.md

Assessment against linked issues

Issue	Objective	Addressed	Explanation
#47	Track adjacency lists touched by insertion, deletion, reconnection, and test-only repair operations.	✅
#47	Replace the test-only full-graph reciprocity sweep with localized repair and validation limited to touched node-level pairs.	✅
#47	Preserve reciprocity correctness while reducing mutation-test overhead, with documentation and validation of the optimization.	✅

Possibly linked issues

• Optimise test-only sweep to process only touched nodes #47: The PR directly implements the issue’s requested touched-node tracking and localized test-only reciprocity sweep.

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Inline comments:
In `@chutoro-core/src/hnsw/graph/test_helpers/mod.rs`:
- Around line 53-54: Snapshot the touched-node state before deletion in the
relevant test helper, and restore it alongside nodes and entry when
ensure_reachability fails. Ensure a failed delete_node leaves touched unchanged
so the subsequent heal_for_test cannot process stale deletion pairs or modify
adjacency lists.

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📥 Commits

Reviewing files that changed from the base of the PR and between 29a6920 and 7ee2cf2.

📒 Files selected for processing (8)

• chutoro-core/src/hnsw/cpu/test_helpers.rs
• chutoro-core/src/hnsw/graph/core.rs
• chutoro-core/src/hnsw/graph/test_helpers/mod.rs
• chutoro-core/src/hnsw/graph/test_helpers/tests.rs
• chutoro-core/src/hnsw/insert/executor.rs
• chutoro-core/src/hnsw/insert/executor/tests/mod.rs
• chutoro-core/src/hnsw/insert/test_helpers.rs
• docs/adr-001-commit-post-processing.md

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Absence of Expected Change Pattern

• chutoro/chutoro-core/src/hnsw/graph/core.rs is usually changed with: chutoro/chutoro-core/src/hnsw/node.rs

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