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merge: reconcile data-quality roadmap with audit-remediation main (#12-15)

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Resolved 4 conflicts: cli.py (R-D citing-coverage warning + main's small-corpus JSON/hub-title changes both kept); ingest.py (C-7 paper.id=caller-id pin first, then DQ-2 abstract recovery); test_ingest.py + test_openalex.py (kept both branches' tests).

C-7/DQ-5 overlap (both canonicalise papers.id): kept both layers — openalex._canonical_id normalizes fetch_paper's id (DQ-5); ingest pins papers.id to the caller's bare id (C-7); they converge on the bare canonical id. Fixed the auto-merged test_fetch_paper_success that had contradictory bare/URL assertions. 402 tests pass; ruff + mypy clean.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
This commit is contained in:
Tarik Moussa
2026-06-22 15:11:26 +02:00
parent e817022097 d64edfc324
commit 9e5184385a
29 changed files with 900 additions and 193 deletions
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26
codex/config.py
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@@ -9,7 +9,7 @@ from __future__ import annotations
from functools import lru_cache
from pydantic import AliasChoices, Field
from pydantic import AliasChoices, Field, SecretStr
from pydantic_settings import BaseSettings, SettingsConfigDict
@@ -26,14 +26,25 @@ class Settings(BaseSettings):
# ------------------------------------------------------------------
# Database
# ------------------------------------------------------------------
database_url: str = Field(
default="postgresql://researcher:change_me@localhost:5432/papers",
database_url: SecretStr = Field(
default=SecretStr("postgresql://researcher:change_me@localhost:5432/papers"),
description=(
"libpq-compatible connection string consumed by psycopg. "
"Example: postgresql://user:pass@host:5432/dbname"
),
)
migration_database_url: SecretStr | None = Field(
default=None,
description=(
"Optional privileged connection string used by `codex migrate` to apply "
"schema DDL. The app's database_url is typically a least-privilege DML "
"role that cannot CREATE/ALTER owner-held tables (raises "
"InsufficientPrivilege); point this at an owner/superuser connection. "
"Falls back to database_url when unset."
),
)
# ------------------------------------------------------------------
# External services
# ------------------------------------------------------------------
@@ -137,7 +148,7 @@ class Settings(BaseSettings):
# ------------------------------------------------------------------
# F-09 Rich Parsing
# ------------------------------------------------------------------
mathpix_app_id: str | None = Field(
mathpix_app_id: SecretStr | None = Field(
default=None,
description=(
"MathPix App ID for cloud formula extraction. "
@@ -145,7 +156,7 @@ class Settings(BaseSettings):
),
)
mathpix_app_key: str | None = Field(
mathpix_app_key: SecretStr | None = Field(
default=None,
description=(
"MathPix App Key for cloud formula extraction. "
@@ -246,7 +257,7 @@ class Settings(BaseSettings):
description="Bind port for HTTP transport (ignored for stdio).",
)
mcp_auth_token: str | None = Field(
mcp_auth_token: SecretStr | None = Field(
default=None,
description=(
"Bearer token required when mcp_transport='http'. "
@@ -295,7 +306,8 @@ class Settings(BaseSettings):
le=1.0,
description=(
"Weight of the PageRank citation-boost in hybrid search. "
"Final score = dense_score * (1 + alpha * pagerank_score). "
"boosted_distance = distance / (1 + alpha * pagerank_score) — dividing "
"lowers the cosine distance of high-PageRank papers (lower = closer). "
"Set to 0.0 to disable the boost without removing the flag."
),
)