Tarik Moussa e1c0a98262 fix(ingest): make both upsert UNIQUE gaps visible (audit C-15 follow-up) ...

Per review: the two latent upsert conflicts should be observable even where not
auto-fixed.
- bibkey collision (auto-suffixed) now logs a warning so a paper landing as
  'BobenkoLutz2023a' instead of '…2023' isn't silent.
- openalex_id collision (two papers claiming the same OpenAlex work — a real data
  conflict, not auto-renamable) now raises a clear ValueError naming the
  openalex_id and the offending paper, instead of the raw psycopg UniqueViolation.

Regression test added for the openalex_id error path.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

2026-06-15 22:25:30 +02:00

..

parsing

feat(config): wrap credentials in SecretStr (audit S-4)

2026-06-15 21:32:13 +02:00

sources

fix(sources): drop no-op try/except + url-encode S2 ids (audit R-4, R-5)

2026-06-15 21:39:48 +02:00

__init__.py

feat: initial project scaffold

2026-06-04 11:19:10 +02:00

__main__.py

fix(ingest): D-04 bibkey heuristic + D-05a/b/c regression tests + __main__

2026-06-15 03:07:06 +02:00

cli.py

docs: clarify sparse-not-wired and cite-boost tie-breaker (audit C-14, U-2)

2026-06-15 21:47:40 +02:00

config.py

feat(config): wrap credentials in SecretStr (audit S-4)

2026-06-15 21:32:13 +02:00

db.py

feat(config): wrap credentials in SecretStr (audit S-4)

2026-06-15 21:32:13 +02:00

discover.py

fix(discover): resolve cited_id via shared resolver (audit C-1)

2026-06-15 11:12:55 +02:00

embed.py

docs: clarify sparse-not-wired and cite-boost tie-breaker (audit C-14, U-2)

2026-06-15 21:47:40 +02:00

graph.py

fix(discover): resolve cited_id via shared resolver (audit C-1)

2026-06-15 11:12:55 +02:00

ingest.py

fix(ingest): make both upsert UNIQUE gaps visible (audit C-15 follow-up)

2026-06-15 22:25:30 +02:00

mcp_server.py

feat(config): wrap credentials in SecretStr (audit S-4)

2026-06-15 21:32:13 +02:00

models.py

feat(F-09): rich parsing — formula + figure extraction

2026-06-14 01:16:24 +02:00

provenance.py

feat(discover,provenance): graph discovery queries + @cite scan + code_links + bib export

2026-06-05 07:13:01 +02:00

quality.py

feat(F-16): chunk quality gate + section classification

2026-06-15 01:22:44 +00:00

synthesis.py

fix(synthesis): make coverage-map gaps opt-in (audit R-8)

2026-06-15 16:32:01 +02:00

wiki.py

fix(wiki): token-boundary grounding match + sharper ref-list filter (C-6, R-2)

2026-06-15 21:46:02 +02:00