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feat(F-09): rich parsing — formula + figure extraction #1

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user2595 merged 6 commits from feat/F-09-rich-parsing into main 2026-06-14 01:52:24 +00:00
Conversation 0 Commits 6 Files Changed 20 +3596 -26

6 Commits

Author SHA1 Message Date
Tarik Moussa
cd42e9abc8 fix(F-09): address review-gate findings — resource leak + idempotency 
- mathpix.py + figures.py: wrap fitz page-loop in try/finally so
  doc.close() is guaranteed even on exception (no file-handle leak)
- ingest.py: DELETE FROM formulas/figures WHERE paper_id before re-insert
  so --rich re-ingest is idempotent (BIGSERIAL has no natural UNIQUE key;
  ON CONFLICT DO NOTHING was a no-op)

Gate: 158 passed, ruff clean, mypy clean

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-14 02:23:21 +02:00
Tarik Moussa
1df9be6563 feat(F-09): rich parsing — formula + figure extraction 
- codex/parsing/mathpix.py: pix2tex (local, CPU) primary + MathPix API
  optional; bbox heuristic h>15px, math-char-count>5; singleton model cache
- codex/parsing/figures.py: pymupdf embedded-image extraction → PNG;
  caption detection via proximity + "Figure/Fig./Abbildung" prefix
- codex/models.py: FormulaChunk + FigureChunk dataclasses (R-10/R-11)
- codex/ingest.py: --rich flag wires formula+figure extraction post-ingest
- codex/cli.py: search_app sub-typer (paper + formula subcommands),
  --rich flag on ingest; wiki_app from F-12 preserved intact
- codex/config.py: mathpix_app_id/key, pix2tex_fallback, figures_dir
- infra/schema.sql: formulas + figures tables with HNSW pgvector indexes
- pyproject.toml: pymupdf>=1.24, pix2tex>=0.1.4
- tests/parsing/test_mathpix.py + test_figures.py: 31 tests (mock pix2tex
  + MathPix HTTP, real pymupdf on synthetic PDF)

Gate: 158 passed, ruff clean, mypy clean (20 files)
Requirements: R-10 R-11 R-12 R-13 R-14 → done

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-14 01:16:24 +02:00
Tarik Moussa
d2f9141a5c fix(cli): remove F-09 spillover from F-12 branch, keep only wiki group 
cli.py and config.py were accidentally contaminated with uncommitted F-09
changes (search_app restructure, rich ingest, mathpix/figures settings).
This restores both files to main-baseline + F-12-only additions:
- cli.py: wiki_app group (compile/list/check), restore @app.command search
- config.py: wiki_dir, wiki_llm_model, wiki_llm_url, wiki_top_k only

All 127 tests green, ruff+mypy clean.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-13 20:28:22 +02:00
Tarik Moussa
4d361fd8dc feat(cli): wiki compile/list/check command group (F-12) 
Adds codex wiki compile/list/check Typer subgroup to cli.py.
Adds wiki_dir, wiki_llm_model, wiki_llm_url, wiki_top_k settings
to config.py (F-12 section only).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-13 20:22:55 +02:00
Tarik Moussa
aee00515f4 feat(wiki): concept schema loader + concepts.yaml (F-12) 
Adds wiki/concepts.yaml (5 curated seeds: discrete-conformal-map,
circle-packing, lobachevsky-function, discrete-yamabe-flow,
hyperideal-tetrahedron) and codex/wiki.py with full load_concepts()
implementation (Concept dataclass, YAML parser, graceful empty list).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-13 20:22:51 +02:00
Tarik Moussa
c6eaf999a1 chore(env): add NOUGAT_URL to .env.example (F-11 / D-02) 
Documents the Nougat HTTP server endpoint. Resolves D-02 drift finding.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-13 20:14:07 +02:00