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7 Commits

Author SHA1 Message Date
Tarik Moussa
408e4886bb fix(wiki): basic conflict detection in CompileReport 
Add _detect_conflicts() using adversative keyword heuristic (but,
however, in contrast, …) between chunks of different bibkeys; results
populate CompileReport.conflicts and appear in wiki/log.md.
Also add CompileReport.quarantined field (used by Fix 2).

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-14 05:11:06 +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
2acb2ee213 feat(cli): wire all commands via Typer (ingest, search, discover, provenance, ask-stub) 
- Implement all CLI commands as specified in F-07: ingest, search, and discover subcommands (leads, citing, cited-by, cocited), and provenance subcommands (scan, add-link, links, bib).
- Add ask command stub that exits with code 1 (not yet implemented).
- Implement comprehensive tests with mocked dependencies (no real DB/API calls).

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>
 2026-06-05 07:22:03 +02:00
Tarik Moussa
b52a6a7412 fix: add @app.callback so codex --help exits 0 
Bare Typer() with no commands raised RuntimeError at runtime.
Callback makes the entry point callable without exposing F-07 logic.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-04 11:26:35 +02:00
Tarik Moussa
1dd7a4bea3 fix: add cli.py stub so entry point resolves before F-07 
Review-Gate finding: pyproject.toml [project.scripts] referenced
codex.cli:app which was absent; uv run codex raised ModuleNotFoundError.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-04 11:25:17 +02:00