paper-parser

paper-parser

1. Purpose and scope

paper-parser is the entry node of the Mobius DAG. It reads a single PDF (arXiv preprint, journal article, or technical report) and produces the paper sub-tree of the canonical SimSpec — equations as LaTeX and sympy, figures as PNGs with captions and sub-panel structure, and numerical claims with verbatim source quotes and UCUM-normalized units.

The skill does NOT:

• reason about physics (that is physics-interpreter's job — governing equations get tagged here, classified there)
• compose simulation specifications (that is simspec-author)
• verify claims against simulation output (that is science-integrity / paper-diff)
• generate visualizations (that is viz-mapper)
• emit Python primitives or simulator code (that is primitive-generator)

Everything downstream of paper-parser assumes that the JSON returned here is correct, lossless within the limits documented below, and reproducible across re-runs given the same PDF bytes.

2. Input

Required:

• pdf_path: str — absolute path to a readable PDF file. Multi-column arXiv layout is the assumed common case.

Optional:

• page_range: tuple[int, int] | None — inclusive (start, end) page hint. Default scans the entire document. Useful when the orchestrator wants to skip references or supplementary material on a known-structured paper.
• focus_sections: list[str] | None — section title hints (e.g. ["Methods", "Results"]). Treated as a soft prior on which pages matter for claim extraction; never used to drop pages outright.

The PDF is opened read-only. Nothing is written next to the input. All artefacts go to /tmp/mobius_figures/ and /tmp/mobius_parser_cache/.

3. Output

A JSON object matching the paper sub-tree of the SimSpec schema:

{
  "doi": "10.xxxx/...",
  "arxivId": "2501.12345",
  "title": "...",
  "authors": ["..."],
  "abstract": "...",
  "equations": [
    {
      "id": "eq-1",
      "latex": "\\nabla \\cdot \\vec{E} = \\rho/\\epsilon_0",
      "sympy_repr": "Eq(Derivative(E, x) + ..., rho/epsilon_0)",
      "variables": ["E", "rho", "epsilon_0"],
      "page": 3,
      "bbox": [120.5, 410.0, 480.2, 442.7],
      "surrounding_context": "...prose ±200 chars around the equation...",
      "confidence": "high"
    }
  ],
  "figures": [
    {
      "id": "fig-1",
      "png_path": "/tmp/mobius_figures/<sha256>/fig-1.png",
      "caption": "Verbatim caption text...",
      "subpanels": [
        {"label": "a", "bbox_in_figure": [0.0, 0.0, 0.5, 1.0], "png_path": "..."}
      ],
      "inline_numerical_claims": [
        {"value": 532.0, "unit": "nm", "location_hint": "panel (a) wavelength"}
      ],
      "page": 5,
      "confidence": 0.86
    }
  ],
  "numerical_claims": [
    {
      "id": "claim-1",
      "value": 1.4e-3,
      "unit_ucum": "kg.m-3",
      "value_uncertainty": 0.05e-3,
      "section": "Results",
      "source_quote": "the measured density was 1.4 x 10^-3 kg/m^3 +/- 0.05 x 10^-3",
      "claim_type": "measurement",
      "confidence": 0.92
    }
  ]
}