codex-py

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Author	SHA1	Message	Date
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	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	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

Author

SHA1

Message

Date

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

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

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

3 Commits