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chore/scrub-private-ip
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Author SHA1 Message Date
Tarik Moussa
9e5184385a merge: reconcile data-quality roadmap with audit-remediation main (#12-15) 
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>
 2026-06-22 15:11:26 +02:00
Tarik Moussa
5672358bbe feat(graph): warn on low citing-paper coverage in graph report (R-D) 
Add graph.citing_coverage() (papers with >=1 out-edge / total) and a graph_min_citing_coverage setting (default 0.8). codex graph report now surfaces 'Citing coverage: N/M papers with out-edges (P%)' in text and JSON, and warns when the share is below threshold -- low citing coverage starves PageRank/coupling even when the paper count looks healthy (the DQ-1 sub-item). Separate from the existing total-count graph_min_corpus_size warning.

Tests: citing_coverage unit tests + CLI tests (line shown, warning fires/suppressed, JSON field). Full suite green; ruff + mypy clean. Live: graph report shows 29/29 (100%), no warning.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
 2026-06-18 07:59:25 +02:00
Tarik Moussa
92928bab99 feat(cli): graph-report titles + JSON warning; wire recommend/cocited (U-1,U-3,U-4,C-9) 
- 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>
 2026-06-15 21:43:19 +02:00
Tarik Moussa
664600fdc7 fix(graph): resolve cited_id to papers.id via openalex_id JOIN 
build_citation_graph now does:
  SELECT c.citing_id, COALESCE(p.id, c.cited_id) AS cited_id
  FROM citations c
  LEFT JOIN papers p ON p.openalex_id = c.cited_id

Before: cited_id (OpenAlex IDs) never matched papers.id (DOIs) →
  13 cross-citations between ingested papers were invisible in graph.
After: in-KB papers use their canonical DOI key; dangling references
  keep their raw OpenAlex ID unchanged.

Test: test_cross_citation_uses_doi_when_in_kb (42 passed).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-15 07:15:21 +02:00
Tarik Moussa
1f1e0e82b3 fix(F-15): address Opus review findings (CRITICAL + WARN) 
CRITICAL:
- cli.py: invert cite-boost formula: divide distance by (1 + alpha*pr)
  instead of multiply — high-PageRank papers now correctly rank higher
- cli.py: wire graph_min_corpus_size config into graph report; warning
  emitted to stderr so JSON stdout stays parseable

WARN:
- graph.py: document that damping is ignored in small-graph uniform branch
- cli.py: sort dangling citations before slicing for stable output
- cli.py: replace raise typer.Exit(0) with return in empty-graph path
- tests: fix *extra_args helper signatures; add cite-boost ordering test
  and small-corpus warning test

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-15 03:40:30 +02:00
Tarik Moussa
fd51b70000 feat(F-15): citation graph — PageRank, coupling, co-citation, CLI 
- codex/graph.py: build_citation_graph (DiGraph from DB), citation_pagerank
  (graceful uniform fallback < 5 nodes), find_related (bibliographic coupling),
  find_co_cited, dangling_citations
- codex/config.py: graph_cite_boost_alpha=0.3, graph_min_corpus_size=15
- codex/cli.py: graph report [--top-n] [--json], graph related <paper-id>
  [--min-shared]; search paper --cite-boost (PageRank score weighting)
- tests/graph/: 39 tests (graph functions + CLI) — 326 total green

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-15 03:31:36 +02:00