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Author SHA1 Message Date
Garry Tan
ff10796a00 fix(wave): v0.15.1 - 4 hot issues + scope expansion (#248) 
* fix(wave): 4 hot issues + 3 scope expansions (v0.13.1)

Addresses four user-filed regressions after v0.13.0 plus three adjacent
footgun closures.

* #170 — CREATE INDEX [CONCURRENTLY] IF NOT EXISTS idx_pages_updated_at_desc
  on pages (updated_at DESC). Engine-aware migration v12 with invalid-index
  cleanup on Postgres, plain CREATE on PGLite. ~700x on 30k+ row brains.
  Contributed by @fuleinist (#215).

* #219 — Minions schema default max_stalled 1 -> 5. v13 migration ALTERs
  the default and UPDATEs existing non-terminal rows (waiting/active/
  delayed/waiting-children/paused) so live queues get rescued on upgrade.
  Adds MinionJobInput.max_stalled with [1,100] clamp. New --max-stalled
  CLI flag on `jobs submit`. Reported by @macbotmini-eng.

* #218 — package.json postinstall surfaces errors instead of silencing.
  trustedDependencies whitelists @electric-sql/pglite. doctor
  schema_version check fails loudly when migrations never ran and links
  to #218. README + INSTALL_FOR_AGENTS warn against `bun install -g`.
  Reported by @gopalpatel.

* #223 — @electric-sql/pglite pinned to exactly 0.4.3 (was ^0.4.4).
  PGLiteEngine.connect() wraps PGlite.create() errors with a message
  pointing at the issue + gbrain doctor. Does NOT suggest 'missing
  migrations' as a cause (create-time abort happens before migrations
  run). Pin is unverified against macOS 26.3; error-wrap is the safety
  net. Reported by @AndreLYL.

* Scope: `gbrain jobs submit` gains --backoff-type/--backoff-delay/
  --backoff-jitter/--timeout-ms/--idempotency-key (MinionJobInput audit).
* Scope: `gbrain jobs smoke --sigkill-rescue` regression case (opt-in,
  CI-only) that simulates a killed worker and asserts the new default
  rescues.
* Scope: `gbrain doctor --index-audit` reports zero-scan Postgres indexes
  as drop candidates (informational; no auto-drop).

Infrastructure:
* Migration interface extended with sqlFor: { postgres?, pglite? } and
  transaction: boolean. Runner picks the engine-specific branch and
  bypasses engine.transaction() when transaction:false (required for
  CONCURRENTLY). BrainEngine.kind readonly discriminator added.
* scripts/check-jsonb-pattern.sh CI guard extended to block
  `max_stalled DEFAULT 1` from regressing.

Tests:
* 15 new unit tests: v12/v13 structural + behavioral assertions,
  max_stalled default/clamp/backfill, PGLite error-wrap source guard,
  engine kind discriminator.
* 3 regression tests pinned by IRON RULE.
* Full unit suite: 1416 pass.
* Full E2E suite against Postgres 16 + pgvector: 126 pass.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* chore: bump version and changelog (v0.13.1)

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* docs: sync documentation for v0.13.1

CLAUDE.md "Key files" and "Commands" sections refreshed to match the
v0.13.1 fix wave:

- Note `BrainEngine.kind` discriminator on engine.ts
- Document v0.13.1 connect() error-wrap on pglite-engine.ts
- Refresh src/core/minions/ layout (no shell handler, no protected-names,
  no quiet-hours/stagger — that was v0.13-development scaffolding that
  did not ship)
- Add src/core/migrate.ts entry with `Migration` interface extensions
  (`sqlFor`, `transaction: false`)
- Document new `gbrain jobs submit` flags (--max-stalled, --backoff-type,
  --backoff-delay, --backoff-jitter, --timeout-ms, --idempotency-key)
- Document `gbrain jobs smoke --sigkill-rescue` regression guard
- Document `gbrain doctor --index-audit` and the schema_version=0
  surface that catches #218 postinstall failures
- Extend check-jsonb-pattern.sh note with the max_stalled DEFAULT 1
  regression guard
- Touch up test file blurbs for migrate.test.ts, pglite-engine.test.ts,
  minions.test.ts with v0.13.1 coverage

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* test(e2e): run files sequentially to eliminate shared-DB race

The E2E suite was flaky. ~3 of every 5 runs had 4-10 failures clustered
in Links, Timeline, Versions, Minions resilience, Parallel Import, and
Page CRUD tests. Symptoms included "expected 16 pages, got 8" (half),
"expected 1 link inserted, got 0", timeline entries missing after
round-trip, and similar data-shape mismatches.

Root cause: bun test runs test FILES in parallel (each in a worker
process). 13 E2E files share one DATABASE_URL, and `setupDB()` in
`test/e2e/helpers.ts` does `TRUNCATE ... CASCADE` on all tables before
each file's `importFixtures()`. File A's TRUNCATE would race with file
B's in-flight INSERT stream, producing the observed half-populated or
wrong-count states.

An earlier attempt used a Postgres advisory lock held on a dedicated
single-connection client for the lifetime of each file's run. It broke
because bun's default 5000 ms hook timeout fires on queued beforeAll()
calls: with 13 files serializing through the lock, files 2-13 would
time out waiting for file 1 to finish.

This commit switches to sequential file execution at the harness level
via scripts/run-e2e.sh, which loops through test/e2e/*.test.ts one at
a time, tracks aggregate pass/fail counts, and exits non-zero on the
first failing file. No lock, no timeout issues, no changes to any test
file. package.json test:e2e points at the new script.

Verified: 5 back-to-back runs against the same Postgres container,
each completing in ~5 min. Every run: 13 files, 138 tests, 0 fails.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

* chore: bump version to 0.15.1 (fix wave locked to MINOR line)

Master v0.14.2 was the last /investigate root-cause wave on the
v0.14.x line. This fix wave opens v0.15.x: four hot issues (#170,
#218, #219, #223) close v0.13.x regressions that v0.14.x didn't
cover, so the MINOR bump reflects the semantic shift — new schema
migrations (v14, v15), a new CLI surface (`--max-stalled`,
`--sigkill-rescue`, `--index-audit`), a new BrainEngine contract
(`kind` discriminator + extended `Migration` interface), and a new
install-time contract (PGLite 0.4.3 pin + `trustedDependencies`).

Locked to 0.15.1 in advance: other work may land before/after this
PR, but the version is fixed so reviewers can cite a stable number.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
 2026-04-21 13:19:23 -07:00
Garry Tan
b5fa3d044a fix: 8 root-cause fixes from /investigate (v0.14.2) (#259) 
* fix: 8 root-cause fixes from /investigate wave

Consolidated bundle of bug fixes from /investigate on the 8 deferred bugs.
Each fix was designed to go at the structural gap, not the symptom. Codex
verified 20 load-bearing claims on the plan; 12 triggered plan revisions.

Bug 2  — GBRAIN_POOL_SIZE env knob + init finally blocks (no auto-detect).
         Covers both the singleton pool (db.ts) and instance pool (import.ts:140).
Bug 3  — Centralize migration ledger writes in apply-migrations runner.
         Removed appendCompletedMigration from v0_11_0, v0_12_0, v0_12_2,
         v0_13_0, v0_13_1. Added 3-partial wedge cap + --force-retry reset.
         'complete wins' preserved; no partial can regress a completed migration.
Bug 5  — v0.14.0 migration registered. src/commands/migrations/v0_14_0.ts
         ships Phase A (ALTER minion_jobs.max_stalled SET DEFAULT 3) + Phase B
         (pending-host-work ping for shell-jobs adoption).
Bug 6/10 — jsonb_agg(DISTINCT ...) in legacy traverseGraph (both engines).
         Presentation-level dedup; schema still preserves provenance rows.
Bug 7  — doctor --fast reads DB URL source via getDbUrlSource() in config.ts.
         Precise message: 'Skipping DB checks (--fast mode, URL present from env)'
         replaces the misleading 'No database configured'.
Bug 8  — max_stalled default bumped 1→3 in schema-embedded.ts, pglite-schema.ts,
         schema.sql (new installs). v0_14_0 Phase A ALTER for existing installs.
         autopilot-cycle handler yields to event loop between phases so the
         worker's lock-renewal timer fires on huge brains. (Deep AbortSignal
         threading through runEmbedCore/runExtractCore/runBacklinksCore/performSync
         deferred to v0.15 queue polish.)
Bug 9  — Gate sync.last_commit on no-failures across all three sync paths
         (incremental, full via runImport, gbrain import git continuity).
         recordSyncFailures() helper + ~/.gbrain/sync-failures.jsonl with
         dedup key path+commit+error-hash. New flags: --skip-failed (ack) +
         --retry-failed (re-attempt). Doctor surfaces unacknowledged failures.
Bug 11 — brain_score breakdown fields on BrainHealth (embed_coverage_score,
         link_density_score, timeline_coverage_score, no_orphans_score,
         no_dead_links_score); sum equals brain_score by construction.
         dead_links now on the type (resolves featuresTeaserForDoctor drift).
         orphan_pages kept as 'islanded' (no inbound AND no outbound) and
         docs updated to match — explicit semantic instead of doc drift.

New tests: test/traverse-graph-dedup.test.ts, test/sync-failures.test.ts,
test/brain-score-breakdown.test.ts, test/migration-resume.test.ts,
test/migrations-v0_14_0.test.ts. Extended: migrate, doctor, apply-migrations.

All 1696 unit tests pass locally. postgres-jsonb E2E regression unchanged
(none of these touch the JSONB write surface).

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

* docs: v0.14.2 CHANGELOG + CLAUDE.md; align migration-flow E2E with runner-owned ledger

CHANGELOG: v0.14.2 entry in the standard release-summary format
(two-line headline + lead + numbers table + "what this means" +
"To take advantage of v0.14.2" self-repair block + itemized
changes grouped by reliability / observability / graph correctness /
new migration / tests / deferred-to-v0.15).

CLAUDE.md: new "Key commands added in v0.14.2" section covers
--skip-failed, --retry-failed, --force-retry, GBRAIN_POOL_SIZE env,
and the new doctor checks (sync_failures, brain_score breakdown).
Migration orchestrator docs updated to describe v0_14_0.ts + the
runner-owned ledger contract from Bug 3.

test/e2e/migration-flow.test.ts: three assertions updated to match
the Bug 3 contract — orchestrators no longer append to completed.jsonl
directly, so direct-orchestrator E2E calls leave the ledger empty.
Preferences assertions remain (that's still the orchestrator's side
of the contract). Runner's ledger write is covered by the unit suite
(test/apply-migrations.test.ts + test/migration-resume.test.ts).

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 4.6 <noreply@anthropic.com>
 2026-04-20 23:14:38 +08:00