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aee00515f4af5cec021e7bc700e515825a214752
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Author SHA1 Message Date
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
Tarik Moussa
456dea102b chore(claude): add project harness config (permissions for uv/ruff/mypy/podman) 
codex-py hatte kein .claude/ — F-xx-Worker liefen mit nackten globalen Settings
und wurden bei jedem uv/ruff/mypy/pytest/git-Befehl geprompted. settings.json
spiegelt den knowledge-base-Stil (acceptEdits + harter deny-Block), zugeschnitten
auf den Python/uv-Stack + podman (DB) + ollama. settings.local.json gitignored.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
 2026-06-08 09:03:41 +02:00
Tarik Moussa
d48db47a7d feat: merge F-08 scaffold + integration tests (config, db, models, pipeline smoke) 2026-06-05 07:43:09 +02:00
Tarik Moussa
65918cc80a feat(tests): scaffold + integration smoke tests (config, db, models, pipeline) 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-05 07:40:25 +02:00
Tarik Moussa
01199c5e46 feat: merge F-07 CLI (Typer commands: ingest, search, discover, provenance, ask-stub) 2026-06-05 07:35:24 +02:00
Tarik Moussa
4c177a0d29 fix(cli): use datetime() for CodeLink.added_at in tests (mypy strict) 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-05 07:34:51 +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
c65fe19c24 feat: merge F-06 discover + provenance (graph queries, @cite scan, bib export) 2026-06-05 07:15:58 +02:00
Tarik Moussa
7675f63188 feat(discover,provenance): graph discovery queries + @cite scan + code_links + bib export 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-05 07:13:01 +02:00
Tarik Moussa
1e10736185 feat: merge F-05 ingest pipeline (idempotent upsert, sources+parsing+embed) 2026-06-05 07:08:29 +02:00
Tarik Moussa
5344975bb1 feat(ingest): end-to-end idempotent ingest pipeline 
Implements codex/ingest.py with:
- OpenAlex primary / Semantic Scholar fallback metadata fetch
- Abstract dense embedding (zero-vector for missing abstracts)
- Idempotent paper upsert (ON CONFLICT DO UPDATE)
- Source file parsing (.tex via latex_to_text, .pdf via nougat + grobid)
- Chunk deletion + bulk re-insert with dense embeddings
- Citation merge from OpenAlex/S2 API and GROBID PDF refs (dedup via set)
- 7 tests covering basic, tex, pdf, not-found, idempotent, arxiv-fallback,
  and no-abstract scenarios (all mocked, offline)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-05 07:04:12 +02:00
Tarik Moussa
fbf8949579 feat: merge F-04 embed layer (BGE-M3 dense+sparse via FlagEmbedding) 2026-06-05 06:56:17 +02:00
Tarik Moussa
c33fd9d697 feat: merge F-03 parsing layer (LaTeX, Nougat, GROBID) 
Review-Gate: APPROVE (Opus, cold, 2 passes)
23 tests, ruff+mypy clean.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-05 06:48:49 +02:00
Tarik Moussa
d5726ed94d feat: merge F-02 sources layer (OpenAlex, SemanticScholar, arXiv) 
Review-Gate: APPROVE (Opus, cold, 2 passes)
19 tests, ruff+mypy clean.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-05 06:48:49 +02:00
Tarik Moussa
52737abe3d fix(sources): correct OpenAlex ID prefixing, citations endpoint, S2 rate-limit 
Review-Gate findings:
- openalex: bare DOIs/arXiv IDs need doi:/arxiv: prefix (bare IDs 404);
  add _resolve_id(); fix fetch_citations to use referenced_works field
  instead of non-existent /works/{id}/references endpoint.
- semanticscholar: wait_fixed(1) was inter-retry only; add per-request
  monotonic rate-limiter (_rate_limit()) before each httpx call.
  Add _is_retryable() filter so 404s don't burn 5 retry slots.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-04 23:49:35 +02:00
Tarik Moussa
1698f7dcad feat(embed): BGE-M3 dense+sparse via FlagEmbedding (ADR-0002) 
Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
 2026-06-04 23:48:06 +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
8eca4ebe12 fix(deps): add flagembedding>=1.2 for BGE-M3 hybrid encode (ADR-0002) 
SentenceTransformer.encode() lacks return_dense/return_sparse kwargs;
BGEM3FlagModel provides the correct hybrid API.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-04 23:42:04 +02:00
Tarik Moussa
291a66dd38 fix(parsing): add root conftest.py so pytest resolves codex package 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-04 23:34:34 +02:00
Tarik Moussa
b7f19b6e2c feat(sources): OpenAlex, SemanticScholar, arXiv API clients 
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 2026-06-04 23:31:15 +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
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
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