thesis-audit-reviewer

name	thesis-audit-reviewer
description	Audit astronomy theses and papers for ADS-valid citations, coordinate/time/photometric-system consistency, survey selection effects, and over-claimed discoveries. Use for checklist-based, evidence-grounded comments on PDF/DOCX manuscripts.

Thesis Audit Reviewer

StarWhisper astronomy overlay

Read astronomy.md first. That file sets the astronomy defaults for this copy.

Literature: NASA ADS, then arXiv astro-ph.*. Do not invent papers. A synthetic Explore run, a classifier score, or a demo candidate is not a discovery. This skill does not send telescope commands.

Purpose

Produce standardized, evidence-grounded thesis audit reports through a repeatable audit workflow. This skill is an audit operating system, not a one-shot prompt for writing comments.

Use this skill for Chinese or bilingual thesis review tasks involving PDF/DOCX papers, self-check lists, problem summaries, external facts, formulas, tables, references, or supervisor-style comments.

Default review basis: use references/default_review_sources.md, derived from the user's 学位论文自检清单.docx and 学位论文问题汇总.docx, unless the user provides a newer checklist or explicitly asks for a different standard.

Default delivery mode: PDF input produces a PDF audit report; DOC/DOCX input produces a commented DOCX. Preserve Markdown, issue database, review matrix, factcheck, and coverage artifacts for traceability.

Non-Negotiable Standard

Every finding needs:

• precise location: PDF physical page, printed page/chapter if available, object type if available
• original excerpt: short, necessary quote only
• audit comment: what is wrong, in reviewer language
• evidence basis: checklist, paper context, external source, PDF image, or academic norm
• modification requirement: concrete author action
• priority: 必须修改 / 建议修改 / 格式修正
• certainty: 确认问题 / 疑似问题 / 需作者补充材料 / 无法判断

Never deliver only a summary when the user asks for a formal audit. Write in 批注和审核语言, for example: "该处……" "应补充……" "建议作者……" "不宜……".

If a conclusion lacks location, excerpt, and basis, keep it in the work notes as a lead; do not put it in the formal report.

Operating Model

Adopt the mature-skill pattern from prior document-audit work:

• Treat the report as a product generated from work artifacts, not as the audit itself.
• Build the audit denominator first: pages, sections, figures, tables, formulas, references, data facts, strong claims, and policy suggestions.
• Use deterministic tools for parsing, splitting, scaffolding, rendering, and report validation.
• Use AI judgment for academic reasoning, evidence chain evaluation, overclaim detection, and reviewer-language drafting.
• Record pass/blocked/unknown states, not only discovered issues.
• Add a fact-audit layer before normative review: identify methods, verifiable claims, method premises, internally repeated numbers, and author-computed core results.
• Finish only after the completion gate passes or after residual risks are explicitly listed.

Workflow

1. Confirm Scope

   • Identify source paper(s), checklist files, reference problem files, and requested output format.
   • If no alternative checklist/problem summary is supplied, use references/default_review_sources.md as the audit basis.
   • Determine input/output mode using references/input_output_policy.md: PDF -> PDF report; DOC/DOCX -> commented DOCX.
   • Prioritize one paper deeply. For multiple papers, create independent per-paper workspaces and do not weaken single-paper gates.
   • If the user asks to use external fact verification, browse and cite sources.
   • If the user asks for a Skill/process discussion, do not run the full audit.
   • If the user wants DOCX comments or redlines, use the Documents skill and keep this skill as the audit logic.

2. Create Project Work Area

   • Use a subfolder under the current project, e.g. subprojects/thesis_audit_<date>/.
   • Keep intermediate artifacts: source manifest, parsed pages, issue database, final reports.
   • Do not store API tokens or private credentials in files.
   • Prefer scripts/init_audit_workspace.py to create the standard directory and empty ledgers.

3. Parse Paper

   • Default scenario is ordinary thesis material that may be parsed by third-party tools; for PDF, prefer MinerU online VLM parsing when available.
   • If the user marks the paper confidential, unpublished, restricted, or not uploadable, do not use online parsing; switch to local parsing or ask for permission.
   • Use scripts/mineru_vlm_extract.py to upload the full PDF and download results when MinerU is available and upload is allowed.
   • If MinerU is unavailable, unconfigured, timed out, or upload is not allowed, run scripts/pdf_local_fallback_extract.py first. It tries local pymupdf4llm Markdown extraction, then local PyMuPDF/fitz page text extraction.
   • Use scripts/split_mineru_vlm_pages.py to create page-level object files after MinerU parsing.
   • Always verify high-risk findings against the original PDF image or rendered page; parsed text is evidence support, not final truth.
   • For DOCX, use the Documents skill or direct OOXML inspection when comments/redlines are requested.
   • For DOC/DOCX, run scripts/docx_integrity_scan.py and read references/docx_integrity_gate.md; do not rely on or long command-output previews as full-text coverage.

• Use references/standard_report_template.md.
• Use references/comment_language.md for tone and wording.
• Generate Markdown first. If requested or useful, use scripts/render_md_report_pdf.py to create a PDF copy.

11. Run Completion Gate

• Read references/completion_gate.md.
• Run scripts/validate_audit_report.py on the Markdown report before claiming completion.
• If validation fails, fix the report or explicitly state which gate is blocked and why.

12. Document the Work

• If inside a project, update existing progress/findings/docs with factual notes: what was parsed, what was verified, output paths, pitfalls.
• Do not create unrelated README or personal notes inside the Skill.

When to Load References

• Load references/audit_operating_protocol.md before planning or executing a full audit.
• Load references/default_review_sources.md before building the review matrix unless the user supplied a replacement checklist.
• Load references/input_output_policy.md before choosing the final deliverable.
• Load references/docx_integrity_gate.md for DOC/DOCX inputs or when formulas/images may be lost.
• Load references/method_and_fact_audit.md before building method profiles, claim ledgers, fact checks, or reproducibility checks.
• Load references/work_products.md when creating workspace files, ledgers, matrices, or issue databases.
• Load references/completion_gate.md before final delivery.
• Load references/standard_report_template.md before writing the final report.
• Load references/comment_language.md when drafting comments.
• Load references/issue_taxonomy.md when planning coverage or classifying findings.
• Load references/evidence_rules.md when deciding whether a statement is sufficiently supported.

Script Quick Use

python scripts/doctor.py
python scripts/init_audit_workspace.py --out subprojects/thesis_audit_YYYY_MM_DD --paper-id paper01 --title "论文题名" --source-file paper.pdf
# DOCX input example:
# python scripts/init_audit_workspace.py --out subprojects/thesis_audit_YYYY_MM_DD --paper-id paper01 --title "论文题名" --source-file paper.docx
python scripts/docx_integrity_scan.py --docx paper.docx --markdown-output work/paper01/docx_integrity.md --json-output work/paper01/docx_integrity.json
python scripts/scan_verifiable_claims.py --input work/paper01/extracted_text.md --output work/paper01/05_verifiable_claims.csv
python scripts/mineru_vlm_extract.py --file paper.pdf --out work/mineru_vlm --model-version vlm
python scripts/split_mineru_vlm_pages.py --content-list work/mineru_vlm/<extract_dir>/content_list_v2.json --out work/vlm_pages
python scripts/pdf_local_fallback_extract.py --file paper.pdf --out work/pdf_fallback
python scripts/render_md_report_pdf.py --input outputs/paper01/审查报告.md --output outputs/paper01/审查报告.pdf
python scripts/validate_audit_report.py --report outputs/paper01/审查报告.md --strict

The MinerU script reads the token from MINERU_API_TOKEN, hidden TTY input, or stdin. If the user has no token, point them to https://mineru.net/apiManage/token to register and create one. Never write the token into a command, report, or repository file. The local PDF fallback script does not need a token; treat its output as lower confidence than MinerU for scanned PDFs, formulas, complex tables, multi-column layout, headers/footers, and split reference lists.

Completion Definition

For a formal thesis audit, completion requires:

• source and parsing status recorded
• default or user-supplied review basis recorded
• input/output mode recorded: PDF report or commented DOCX
• DOCX integrity gate completed when input is DOC/DOCX, especially formula/image visibility
• object denominator created or residual gaps listed
• method profile and verifiable claim ledger created or explicitly blocked
• checklist coverage recorded, including pass and blocked rows
• all formal findings traceable to issue database entries
• external facts, internal numeric consistency, method premises, and feasible recalculations checked or marked with the correct residual status
• high-risk formulas, tables, references, and numbering checked against PDF image when needed
• final report follows the standard template and passes validation
• project progress/findings documentation updated when working inside a project

For batch work, completion means every single paper satisfies the single-paper gate first, then the batch summary is generated.