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>
This commit is contained in:
Tarik Moussa
2026-06-14 01:16:24 +02:00
parent d2f9141a5c
commit 1df9be6563
13 changed files with 1930 additions and 26 deletions

View File

@@ -39,12 +39,36 @@ class TestIngest:
assert "5 chunks" in result.stdout
assert "3 citations" in result.stdout
def test_ingest_with_rich_flag(self) -> None:
"""Test `ingest --rich` passes rich=True and reports formulas/figures."""
with patch("codex.ingest.ingest_paper") as mock_ingest:
mock_ingest.return_value = IngestResult(
paper_id="2301.07041",
chunks_upserted=5,
citations_upserted=3,
formulas_upserted=12,
figures_upserted=4,
)
result = runner.invoke(app, ["ingest", "2301.07041", "--source", "paper.pdf", "--rich"])
assert result.exit_code == 0
assert "12 formulas" in result.stdout
assert "4 figures" in result.stdout
# Verify rich=True was passed
_, kwargs = mock_ingest.call_args
assert kwargs.get("rich") is True or mock_ingest.call_args[1].get("rich") is True
class TestSearch:
"""Tests for `codex search` command."""
"""Tests for `codex search` subcommands (paper + formula)."""
def test_search_command(self) -> None:
"""Test search command with mocked embedder and DB."""
"""Alias: delegates to test_search_paper_command for backwards compat."""
self.test_search_paper_command()
def test_search_paper_command(self) -> None:
"""Test `search paper` command with mocked embedder and DB."""
with (
patch("codex.embed.get_embedder") as mock_embedder,
patch("codex.db.get_conn") as mock_get_conn,
@@ -74,7 +98,7 @@ class TestSearch:
]
mock_get_conn.return_value = mock_conn
result = runner.invoke(app, ["search", "machine learning", "--limit", "2"])
result = runner.invoke(app, ["search", "paper", "machine learning", "--limit", "2"])
assert result.exit_code == 0
assert "2301.07041" in result.stdout
@@ -82,6 +106,43 @@ class TestSearch:
assert "Test Paper" in result.stdout
assert "0.123" in result.stdout
def test_search_formula_command(self) -> None:
"""Test `search formula` command with mocked DB."""
with patch("codex.db.get_conn") as mock_get_conn:
mock_conn = MagicMock()
mock_conn.__enter__.return_value = mock_conn
mock_conn.__exit__.return_value = None
mock_conn.execute.return_value.fetchall.return_value = [
{
"paper_id": "2301.07041",
"page": 3,
"raw_latex": r"\sum_{i=1}^{n} x_i",
"context": "summation formula",
"rank": 0.856,
},
]
mock_get_conn.return_value = mock_conn
result = runner.invoke(app, ["search", "formula", "summation", "--limit", "5"])
assert result.exit_code == 0
assert "2301.07041" in result.stdout
assert "p.3" in result.stdout
def test_search_formula_no_results(self) -> None:
"""`search formula` with no DB matches prints a 'no results' message."""
with patch("codex.db.get_conn") as mock_get_conn:
mock_conn = MagicMock()
mock_conn.__enter__.return_value = mock_conn
mock_conn.__exit__.return_value = None
mock_conn.execute.return_value.fetchall.return_value = []
mock_get_conn.return_value = mock_conn
result = runner.invoke(app, ["search", "formula", "nonexistent"])
assert result.exit_code == 0
assert "No matching" in result.stdout
class TestDiscoverLeads:
"""Tests for `codex discover leads` command."""