- C-14: embed.py header now states that only the dense path is wired (search
'hybrid' is dense + Postgres FTS); encode_sparse/encode are reserved for a
future sparse-retrieval layer, not yet consumed.
- U-2: --cite-boost help clarifies it re-ranks within the top results (a
tie-breaker), not a hard re-ranking — matching the small alpha effect.
Accepted (documented heuristics, no change): R-3 conflict detection is a
keyword-only signal labelled as such; R-12 classify_section is mostly 'body'
because chunks are word-windows that rarely start at a section header.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
- U-1: 'graph report' shows the paper title next to each in-KB hub (dangling
OpenAlex-id hubs are flagged), instead of bare ids.
- U-3: '--json' now includes a 'small_corpus_warning' field (null unless below
graph_min_corpus_size) instead of silently dropping the warning.
- C-9: new 'codex discover recommend <id>' wires semanticscholar.fetch_recommendations
(was implemented + tested but unreachable).
- U-4: new 'codex graph cocited <id>' wires graph.find_co_cited (likewise).
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
database_url, migration_database_url, mcp_auth_token and the mathpix app
id/key are now pydantic SecretStr, so they render as '**********' in any
repr/log/traceback instead of leaking the plaintext credential. Consumers
(db.get_conn, cli.migrate, mcp._require_http_token, mathpix.extract_formulas)
call .get_secret_value() at the point of use. Tests updated to the SecretStr
type.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
find_gaps defaulted its probe topics to paper titles, so a title — which
retrieves mostly its own single bibkey — fell below synthesis_gap_min_coverage
and flagged almost every paper as a 'gap'. Coverage-map gaps now run only for
explicitly-requested topics; the CLI gains a repeatable --topic option. The
code-vs-corpus gap path (precise) is unchanged and still default.
Tests: the two cases that relied on default-title coverage gaps now pass explicit
topics; added a regression that no coverage gaps appear without --topic.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
M-1: schema.sql could not be re-applied (leading CREATE TABLE/INDEX lacked
IF NOT EXISTS), apply_schema was never called, and the live migration just
failed on a missing chunks.section column. Fixes:
- schema.sql: all CREATE TABLE/INDEX now use IF NOT EXISTS — the whole file is
re-applyable as a no-op.
- codex migrate: new CLI command that applies schema.sql. Connects via
MIGRATION_DATABASE_URL (falls back to DATABASE_URL) and catches
InsufficientPrivilege with guidance — because the app role is DML-only and
core tables are owned by 'postgres' (the privilege dimension found during the
live migration incident).
- config: migration_database_url (optional privileged connection).
- db: apply_schema docstring corrected (idempotency now true) + privilege note.
- T-2: static test that schema.sql is fully idempotent; migrate privilege-error
test.
Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
Add _detect_conflicts() using adversative keyword heuristic (but,
however, in contrast, …) between chunks of different bibkeys; results
populate CompileReport.conflicts and appear in wiki/log.md.
Also add CompileReport.quarantined field (used by Fix 2).
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Implement all CLI commands as specified in F-07: ingest, search, and discover subcommands (leads, citing, cited-by, cocited), and provenance subcommands (scan, add-link, links, bib).
- Add ask command stub that exits with code 1 (not yet implemented).
- Implement comprehensive tests with mocked dependencies (no real DB/API calls).
Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>
Bare Typer() with no commands raised RuntimeError at runtime.
Callback makes the entry point callable without exposing F-07 logic.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Review-Gate finding: pyproject.toml [project.scripts] referenced
codex.cli:app which was absent; uv run codex raised ModuleNotFoundError.
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
