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5 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
d1ffea1c1c fix(parsing): case-insensitive arXiv idno match; fix tmp_path types; add extract_structure test 
Review-Gate finding: GROBID emits type="arXiv" (camel-case), not "arxiv".
XPath literal match silently returned empty strings for all real responses.
Fix: iterate idno elements and compare .lower() == "arxiv".
Test fixture updated to reflect real GROBID output (type="arXiv").

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-04 23:47:18 +02:00
Tarik Moussa
c6a428d335 feat(parsing): LaTeX, Nougat, GROBID parsers with chunking 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-04 23:30:58 +02:00
Tarik Moussa
e7ac7766a5 feat: initial project scaffold 
pyproject.toml (Python 3.12, uv), codex/ package (config, db, models),
infra/ (docker-compose + schema), .env.example, .gitignore, README.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-04 11:19:10 +02:00