inscribe

name	inscribe
description	Convert an academic PDF (local path or paper-repository URL) to Markdown with the inscriber CLI, then verify the transcription against the source PDF with parallel subagents and apply the important fixes. Use when the user asks to inscribe, convert, or transcribe a paper or PDF.
argument-hint	<pdf-path-or-url> [options, e.g. "pages 1-10", "no verification"]

Inscribe a paper (convert + verify)

$ARGUMENTS holds the input (PDF path or URL) plus options, stated either as inscriber flags or in plain words. The pipeline: run inscriber, then — unless the user said to skip it — verify the output against the source PDF with subagents and apply the fixes that matter.

1. Read the docs first

Read README.md at the repo root before anything else. It defines the CLI surface, the supported URL repositories, and every option flag — map the user's plain-language options onto flags from there, never from memory. Real runs need the machine-local ./config.toml (llama.cpp + model paths); if the run fails on configuration or the minimum llama.cpp build, surface the error verbatim and stop.

2. Run inscriber

• Python: .venv/Scripts/python.exe (Windows) or .venv/bin/python (POSIX), from the repo root.
• Default output dir out/ unless the user gave one: … -m inscriber run <INPUT> -o out/ [flags]
• OCR + VLM on real hardware takes minutes: run it in the background and monitor. Watch stderr for warnings — especially truncated page warnings (note the page numbers; they get extra scrutiny in step 4).
• On success it prints the written files to stdout: the full <base>_full.md, splits (<base>_main/_appendix/_backmatter.md unless --no-split), <base>.bib, figures/. Take <base> from that printed list, not from the input filename — by default the BibTeX citation key (e.g. chang2025amortized) names the outputs when an entry was produced.

3. Make the source PDF available for verification

The verifiers need the actual PDF next to the outputs:

• Local path input — use the user's file directly, in place. It is theirs: never move, rename, or delete it.
• URL input — download the PDF to out/<base>.source.pdf (transform to the direct-PDF link per the repository rules in README, e.g. arxiv.org/abs/X → arxiv.org/pdf/X). Only this downloaded copy is temporary: delete it in step 6 unless the user asked to keep it.

Get the page count (e.g. PyMuPDF one-liner via the venv python). If the run used --pages, only those pages exist in the output — verify only those.

4. Verification (default ON — skip only if the user said so)

Partition the processed pages into chunks of at most 10 pages. For each chunk spawn a Sonnet subagent (model: sonnet); launch chunks in parallel, in multiple rounds if the paper is long. Each subagent prompt must contain, explicitly:

1. The absolute PDF path and its page range (Read the PDF with pages: "X-Y"). Born-digital PDFs carry an exact text layer: instruct the subagent to cross-check table cells, SEM digits, and subscripts against PyMuPDF page.get_text() output (one-liner via the repo venv) instead of reading tiny numbers off the rendered page — rendered-page reads have produced confidently-wrong verdicts in both directions (claimed-blank cells that hold values; "confirmed" digits that were wrong).
2. The absolute paths of the Markdown outputs to check (the split files when they exist, else <base>_full.md) and a note that there are no page markers — locate the chunk's content by matching headings/text.
3. Any pages flagged truncated in its range (these likely end in a repetition loop with content missing after it).
4. The typical failure modes, in priority order — paste this list into the subagent prompt:
   • Tables (highest risk — verify the header row AND every numeric cell). Column-attribution damage is the most dangerous class because the values are usually correct while the labels lie: mislabeled or invented column headers (TNP-A (Set 1)/(Set 2) over four different methods), a phantom extra column shifting every label one place, an entire column silently dropped, colspan group headers collapsed so sub-labels (AR/Ind) vanish — compare the header tokens and the column COUNT against the PDF, not just the cells. Also: header subscript mangling (q_mild/q_strong/q_mixture → q&out); cell drift in sparse rows (rows of mostly — with 1–2 values placed in the wrong column); single-cell value slips (±0.24 for ±0.19); silently dropped rows. A raw HTML <table> blob (instead of a pipe table) means the restructuring fell back — its values may be fused together (159.99346.68300.4); report the correct segmentation.
   • Subscripts and short words in text/equations. θ_t → θ_i, p_train → p_min, Fail → Full — the misread is always plausible, so compare symbol-by-symbol against the PDF wherever a claim depends on the identifier.
   • Equations. Dense display equations (underbraces, multi-line arrays) are loop-prone: check completeness and LaTeX fidelity.
   • Truncated pages. Verify where the content stops, what is missing after the loop point, and report the missing span.
   • Figure descriptions (> **Image description.** blockquotes): the description must match the actual figure — axis labels, panel structure, trends, and any numbers it quotes. Also check the caption transcription.
   • Boundary damage. Dropped lines at page boundaries (header/footer stripping can overreach), bad de-hyphenation joins, and missing or duplicated content at the main/appendix/backmatter split boundaries.
   • References. Garbled author names, years, venues.
5. The report format: read-only — do not edit any file. Return only important fixes (wrong values, wrong symbols, missing/garbled content — not style), each as: target file · nearest heading · exact current text (quoted, long enough to be a unique match) · corrected text · severity (critical/minor) · confidence. Say explicitly if a section could not be verified (e.g. unreadable PDF page).

5. Review and apply fixes

• Review every reported fix yourself; for anything surprising or low-confidence, check the PDF page directly before accepting. Reject "fixes" that re-style rather than correct.
• Verifier reports err in BOTH directions: quoted "current text" that does not exist in the file (grep for it before editing — fabricated quotes happen), claimed-blank PDF cells that actually hold values, and cells "confirmed correct" that are wrong. Re-check every accepted table/math fix against the PDF's extracted text layer (PyMuPDF get_text()), not the rendered image — it is exact for born-digital PDFs and catches both failure modes cheaply.
• Apply accepted fixes to the split files (*_main.md, *_appendix.md, *_backmatter.md) — never to <base>_full.md directly. Then regenerate the full document from the corrected splits: … -m inscriber join out/<base>
• With --no-split, edit <base>_full.md directly (no join needed).
• If a truncated page is missing real content the subagent transcribed from the PDF, splice the transcription in.

6. Report and clean up

If (and only if) step 3 downloaded out/<base>.source.pdf, delete that copy (unless the user asked to keep it). A user-provided PDF is never touched. Then report: the output files, fixes applied (grouped by kind, with counts), suggestions rejected and why, and remaining risks (e.g. truncated pages, tables kept as raw HTML).