test: add Thalamic → corpus-ipc → Brainstem CPU smoke harness by rmems · Pull Request #56 · Limen-Neural/brainstem-daemon

rmems · 2026-09-15T05:22:02Z

User description

Closes #43 (LIM-1135).

Adds a CPU-only integration smoke that proves a representative telemetry frame can cross the published corpus-ipc 0.1 contract into a loaded Brainstem runtime without Thalamic owning an SNN.

Merged onto current main after #53 (liveness / readiness / degraded health). Distill sidecar restore, neuromod 0.6, crates.io corpus-ipc 0.1, bounded ingress queues, the deterministic restart/fault-injection harness, and the health reporter from #53 are kept from main. This PR adds typed JSON IpcMessage ingress, run_for_ticks / RuntimeStats, and the Thalamic fixture.

What landed

tests/thalamic_brainstem_smoke.rs plus tests/fixtures/thalamic_producer.rs (no neuromod / SpikingNetwork).
Typed ingress validation (src/ingress/corpus.rs, --features corpus-ipc) over IpcMessage::Stimuli(StimulusBatch): width, freshness, future timestamps, valid_mask, session_id, schema token corpus-ipc.stimulus.v1.
ZMQ SUB decodes JSON IpcMessage frames; modulator-only frames are drained in the same tick; rejected frames still advance the network and increment rejected_batches.
BrainstemDaemon::run_for_ticks for bounded, signal-free ticks (always shuts down the source, even if sink flush fails). It calls StimulusSource::initialize the same way run does after feat(runtime): separate liveness, readiness, and degraded health #53.
Live restore still uses Distill sidecar JSON (restore_network); the smoke writes a sidecar fixture rather than a neuromod serde envelope.

Review follow-up

Addressed CodeAnt, Codex, cubic, Cursor Bugbot, DeepSource, and Codacy findings: future timestamps, zero-width new(), safety_healthy clobber, try_exists, clone_from/reuse of modulator buffers, ephemeral ZMQ bind via get_last_endpoint, RAII temp dirs under CARGO_TARGET_TMPDIR, Default for ThalamicProducer (explicit healthy fields; new() calls Default), rejected-frame tick accounting, idle-tick modulator hold, splitting schema/freshness checks out of accept_stimulus_batch, and Option::map_or_else for the smoke fixture scratch root.

How to test

cargo fmt --check
cargo clippy --locked --all-targets -- -D warnings
cargo test --locked
CC=gcc CXX=g++ cargo clippy --locked --all-targets --all-features -- -D warnings
CC=gcc CXX=g++ cargo test --locked --all-features

Linear Issue: LIM-1135

Summary by cubic

Closes #43 (LIM-1135). Adds a CPU-only smoke harness where a Thalamic fixture with no spiking network publishes a typed IpcMessage::Stimuli(StimulusBatch) frame through the corpus-ipc contract into a loaded Brainstem runtime, gated behind --features corpus-ipc so default stub builds don't need libzmq. The runtime loads model_path as a JSON checkpoint instead of silently building a blank network, and ZMQ ingress decodes and validates typed JSON frames instead of the legacy binary readout packet. The smoke runs through BrainstemDaemon::run_for_ticks.

Bug Fixes

Ingress rejects wrong widths, stale or future timestamps, bad schema tokens, and unexpected IpcMessage variants; rejected frames are counted but the tick loop still advances the network.
Idle ZMQ ticks hold the last neuromodulator snapshot so dopamine, cortisol, acetylcholine, and tempo don't reset.
Checkpoint loading fails closed on wrong schema, dimension mismatch, non-finite parameters, or blank weights; missing files fall back to a blank network, and try_exists errors fail loudly.
session_id and valid_mask survive the wire, and modulator-only frames are drained within the same tick.
run and run_for_ticks share source initialization and checkpoint boot through boot_network, so a ZMQ source is not double-connected and health events stay in lockstep.

Dependencies

Uses corpus-ipc 0.1.0 from crates.io with its IpcMessage / StimulusBatch types; the ZMQ SUB source connects via CORPUS_IPC_ZMQ_READOUT_IPC.
Bumps MSRV to 1.98.1 so corpus-ipc 0.1.0 compiles.

^{Written for commit 25f22e4. Summary will update on new commits.}

CodeAnt-AI Description

Validate typed stimulus ingress and run bounded Thalamic-to-Brainstem CPU smoke tests

What Changed

Brainstem now accepts typed corpus-ipc JSON stimulus batches with schema, channel width, timestamp freshness, future-time, and payload validation.
Stimulus metadata such as validity masks, batch IDs, timestamps, and producer sessions is preserved; invalid channels are excluded from network input.
Rejected frames no longer stop the tick loop, and runtime statistics report accepted, rejected, and processed batches.
Neuromodulator-only frames are drained without delaying sensory input, while idle ticks retain the latest neuromodulator values.
Added a CPU-only integration smoke covering Thalamic telemetry, checkpoint loading, IPC round-tripping, rejection handling, and safety behavior when Brainstem is unavailable.

Impact

✅ Fewer tick-loop interruptions from invalid IPC frames
✅ Clearer rejection of stale, incompatible, or malformed stimuli
✅ Preserved missing-channel and neuromodulator state across idle ticks

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LIM-1135 / GH#43. Load an explicit JSON checkpoint, decode published IpcMessage::Stimuli frames (valid_mask included), reject schema incompatibility, and keep the Thalamic fixture healthy when Brainstem is unavailable. Pin corpus-ipc 0.1.0 and MSRV 1.98.1. Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

linear-code · 2026-09-15T05:22:05Z

LIM-1135

coderabbitai · 2026-09-15T05:22:12Z

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📥 Commits

Reviewing files that changed from the base of the PR and between 57ff758 and be808bc.

📒 Files selected for processing (13)

CHANGELOG.md
Cargo.toml
README.md
docs/ci.md
src/backend.rs
src/checkpoint/mod.rs
src/daemon.rs
src/ingress/corpus.rs
src/ingress/mod.rs
src/ingress/tests.rs
src/lib.rs
tests/fixtures/thalamic_producer.rs
tests/thalamic_brainstem_smoke.rs

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codeant-ai · 2026-09-15T05:22:14Z

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Status	Commit	Started (UTC)	Finished (UTC)
✅ Incremental review completed	`a4f8a06`	Sep 17, 2026 · 21:14	21:14
✅ Reviewed your PR	`22ad7e2`	Sep 15, 2026 · 05:22	05:24

codeant-ai · 2026-09-15T05:22:15Z

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chatgpt-codex-connector · 2026-09-15T05:22:18Z

Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-15T05:33:29.681026Z	`22ad7e2`	Draft marked ready
🔒 Security Review	✅ Completed 2026-09-15T05:31:35.023763Z	`22ad7e2`	Draft marked ready

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amazon-q-developer

This PR successfully adds a CPU-only integration smoke test harness proving that telemetry frames can cross the published corpus-ipc contract into Brainstem runtime without Thalamic owning an SNN. The implementation is comprehensive and well-tested.

Key changes reviewed:

✅ New checkpoint loading with explicit validation (schema version, dimensions, finite parameters, non-blank weights)
✅ Typed ingress validation for corpus-ipc messages with proper width, freshness, and schema checks
✅ Runtime stats tracking for bounded tick runs in test harnesses
✅ Comprehensive test coverage including round-trip validation, error handling, and edge cases

Security & Quality:

✅ No hardcoded credentials or sensitive data
✅ Proper input validation throughout
✅ Error handling follows fail-fast principles
✅ Test coverage validates all acceptance criteria

No blocking defects found. The code is production-ready and well-architected.

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deepsource-io · 2026-09-15T05:22:54Z

DeepSource Code Review

We reviewed changes in 57ff758...25f22e4 on this pull request. Below is the summary for the review, and you can see the individual issues we found as inline review comments.

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Code Review Summary

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codacy-production · 2026-09-15T05:23:12Z

Up to standards ✅

🟢 Issues 0 issues

Results:
0 new issues

View in Codacy

🟢 Metrics 106 complexity · 12 duplication

Metric Results

Complexity 106

Duplication 12

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All reported issues were addressed across 18 files

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cursor

Cursor Bugbot has reviewed your changes using high effort and found 2 potential issues.

Bugbot Autofix prepared fixes for both issues found in the latest run.

✅ Fixed: Rejected frames skip network ticks
- Typed ingress rejects now return skip-ingress Ok(None) instead of Err, so run_tick still advances the network on zeroed stimuli.
✅ Fixed: Idle ticks drop held modulators
- EAGAIN and rejected-frame ticks now return the last neuromodulator snapshot so idle steps keep dopamine/cortisol/acetylcholine/tempo.

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^{Reviewed by Cursor Bugbot for commit 22ad7e2. Configure here.}

Protocol validation failures (Ping, stale, width, other IpcMessage variants) now skip ingress with Ok(None) instead of Err, so run_tick still advances the SNN. Idle EAGAIN ticks return the last neuromodulator snapshot so dopamine/cortisol/acetylcholine/tempo no longer reset.

cubic-dev-ai

All reported issues were addressed across 1 file (changes from recent commits).

_{Requires human review: Auto-approval blocked because this review re-detected 1 unresolved issue already reported by Cubic.

Re-trigger cubic}

Bring the Thalamic smoke onto current main: Distill sidecar restore (#52/#59), crates.io corpus-ipc 0.1 / neuromod 0.6 (#58), and bounded ingress queues (#51). Keep typed JSON IpcMessage ingress and run_for_ticks. Review fixes: reject future timestamps, count skipped-invalid frames, drain modulator-only ZMQ frames, shutdown the source after a failed flush, try_exists on live checkpoints, preserve session_id/valid_mask, and RAII temp dirs in the smoke harness. Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

…ingress Implement ThalamicProducer::default with explicit healthy fields and have new() call Default so RS-A1008 does not treat default() as a recursive Self constructor. Reuse last_modulators via clone_from in skip_ingress. Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

Split stimulus schema and freshness checks out of accept_stimulus_batch so the function stays under the 50-line limit. Write smoke fixtures under CARGO_TARGET_TMPDIR (or crate target/) instead of the shared system temp dir. Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

Bring in #53 liveness/readiness/degraded health. Keep typed ingress, run_for_ticks/RuntimeStats, valid_mask decoding, and the Codacy fixture temp-dir plus accept_stimulus_batch split. run_tick now reports both health events and smoke counters; run_for_ticks initializes the source the same way as run so ZMQ is not double-connected from the binary. Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

DeepSource RS antipattern: replace map + unwrap_or_else with map_or_else. Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

run_tick would exceed clippy::too-many-arguments after merging #53 health reporting with RuntimeStats. Bundle those observers in TickReport. Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

run and run_for_ticks both connect the stimulus source then validate the restored network. Extract boot_network so health events stay in lockstep and Codacy duplication from the merge stays down. Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

Extract drive_ticks and finish_bounded_run so the bounded smoke entry stays under 50 lines without changing shutdown-on-flush-error behavior. Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

rmems marked this pull request as ready for review September 15, 2026 05:22

codeant-ai Bot added the size:XXL This PR changes 1000+ lines, ignoring generated files label Sep 15, 2026

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rmems added this to the v0.3.0 — Spikenaut SNN runtime milestone Sep 17, 2026

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cursoragent and others added 3 commits September 17, 2026 21:19

Merge origin/main into cursor/thalamic-corpus-ipc-smoke-368b

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Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

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cursoragent and others added 5 commits September 17, 2026 21:30

fix: use Option::map_or_else for smoke fixture scratch root

8923700

DeepSource RS antipattern: replace map + unwrap_or_else with map_or_else. Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

Merge remote Codacy map_or_else smoke fixture fix

f6b0625

Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

fix: group tick health and stats to satisfy clippy argument limit

84bdd80

run_tick would exceed clippy::too-many-arguments after merging #53 health reporting with RuntimeStats. Bundle those observers in TickReport. Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

coderabbitai Bot added the documentation Improvements or additions to documentation label Sep 17, 2026

fix: split run_for_ticks helpers to stay under Codacy line limit

25f22e4

Extract drive_ticks and finish_bounded_run so the bounded smoke entry stays under 50 lines without changing shutdown-on-flush-error behavior. Co-authored-by: Raul Cardenas Montoya <montoyaraul34@gmail.com>

rmems merged commit 4158c6e into main Sep 17, 2026
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rmems deleted the cursor/thalamic-corpus-ipc-smoke-368b branch September 17, 2026 21:45

rmems mentioned this pull request Sep 18, 2026

chore(release): prepare brainstem-daemon 0.3.0 for crates.io #60

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