Swap the SQLite backing store for petalbrain Postgres + pgvector, modeled
on vault-mcp. All second-brain relational tables now live in the
`second_brain` schema (owned by the lovebug role); embeddings are written
to the shared public.embeddings table.
Locked design decisions (per Travis):
- DB: existing petalbrain Postgres, second_brain schema, lovebug role.
- Connection: containerized homelab-postgres:5432, plain psycopg_pool
(min=1/max=10), no PgBouncer.
- ORM stays SQLAlchemy; int autoincrement PKs + naive UTC DateTime.
- Embeddings: reuse shared public.embeddings keyed by
(source_schema='second_brain', source_table='extractions', source_id,
model='nomic-embed-text'). Summaries only for this round.
- Pipeline: chunk_text → Ollama nomic-embed-text → delete-before-insert
upsert, with graceful degradation (no DB / no Ollama → log + skip).
- Alembic stands up second-brain's own schema; public.embeddings stays
out-of-band.
- File-based wiki compiler is unchanged.
No SQLite data import — starting clean.
This commit is the scaffolding only; `alembic upgrade head` and a smoke
test of the embedding path are the next checkpoint.
Run extraction under the Max OAuth subscription via `claude -p` instead
of the per-token Anthropic API. The new src/second_brain/llm/claude_cli.py
spawns the CLI in a hermetic tempdir so the host project's CLAUDE.md,
hooks, MCP config, and settings don't leak into the prompt. Uses
--json-schema with LLMExtraction.model_json_schema() so the CLI guarantees
valid structured output — replaces the brittle markdown-fence stripping
in the old engine. The Anthropic SDK is preserved as an optional "api"
backend selectable via config.
While in here, fix a handful of blockers that the smoke test surfaced:
- scheduler filtered ANALYZED instead of TRANSCRIBED, so it never
actually advanced any sources
- process command read sources in a closed session, raising
DetachedInstanceError before any work happened
- config.prompts_dir walked one parent too many, resolving outside
the project and forcing the fallback prompt for every domain
- compiler called git rev-parse against a vault that was never
git-init'd; now auto-inits with an empty seed commit and skips empty
commits cleanly
- datetime.utcnow() deprecated in 3.12+ — single utcnow() helper in
models.py keeps naive UTC semantics so no DB migration is needed
- sess.query(...).get() deprecated in SA 2.x → sess.get(...)
- dead `import anthropic` removed from compiler
Smoke test (article → process → accept → compile) succeeds end-to-end
with ANTHROPIC_API_KEY unset. a-review run saved under reviews/.
Co-Authored-By: Claude Opus 4 <noreply@anthropic.com>
