Thesis Skills v0.5.2

Deterministic thesis and journal writing workflow
Python checkers • Safe fixers • YAML rule packs • One-click runners

中文文档 • English

Quick Start • Beginner Guide (ZH) • Features • Changelog • Architecture • Contributing

Why Thesis Skills?

The pain points we solve:

Pain Point	Traditional Workflow	Thesis Skills
Citation migration Word→LaTeX	Manual mapping, error-prone	Auto-extract & sync
Citation numbering stability	Shifts when deleting refs	Citation Lock mechanism
University format compliance	Read docs, manual check	YAML rule packs + auto-check
Language quality	Proofread manually	Deterministic lint + deep review
Bibliography import	Copy-paste from EndNote	XML/RIS/BibTeX auto-import

Version History

v0.5.2 — Deep Patch Preview 🆕

Review-oriented findings → Selective patches

Before (v0.5.1)	After (v0.5.2)	Impact
Deep findings = read-only reports	Span-based patch previews	Actionable fixes
No auto-fix for deep issues	Validated `old_text` matching	Safe application
Single fix mode	`--apply-mode safe\|suggest\|mixed`	Flexible control

Key additions:

24-fix-language-deep: Converts findings to span-based patches
Patch validation: checks old_text, rejects overlaps
Respects review_required flag (skips by default)

v0.5.1 — Deep Language Review

Sentence-aware, cross-file language screening

Metric	v0.5.0	v0.5.1	Change
Check depth	Character-level	Sentence + cross-file	+3 layers
Output fields	Basic	10+ fields (span, evidence, confidence)	Rich metadata
Review workflow	Flat list	Prioritized queue + clusters	Efficient triage

New checker: 14-check-language-deep

Connector misuse detection
Collocation analysis
Terminology consistency
Acronym first-use validation
LaTeX-aware masking (cite/ref, math, figures)

v0.5.0 — Basic Language Foundation

Deterministic language lint layer

v0.5.0 Coverage:
├── CJK/Latin spacing
├── Punctuation normalization
├── Bracket/quote balance
├── Book-title mark consistency
├── Unit spacing
├── Ellipsis & dash style
├── Zh/En punctuation boundaries
├── Number ranges
├── Enum punctuation
└── Connector blacklist

v0.4 — EndNote Import-First Support

Feature	v0.3	v0.4	Gain
Bibliography sources	Zotero only	Zotero + EndNote	+100%
Import formats	Manual BibTeX	XML/RIS/BibTeX	Auto-detect
Duplicate handling	None	DOI exact + fuzzy warn	Clean imports
Canonicalization	Zotero-specific	Source-agnostic	Universal model

v0.3 — Efficiency Revolution

4-5x workflow speedup

Workflow	v0.2 Time	v0.3 Time	Speedup
Daily citation updates (10 refs)	~85 min	~2 min	42×
Word→LaTeX migration (first time)	~210 min	~40 min	5.25×
New university format adaptation	~100 min	~56 min	1.8×
Citation sync	Manual mapping	Auto-extract	80% faster
Project discovery	Manual config	Auto-detect	90% faster

Core Features

Five-Layer Architecture

┌─────────────────────────────────────────┐
│  Layer 5: Rule-Pack Onboarding          │  ← YAML configs, starter packs
├─────────────────────────────────────────┤
│  Layer 4: Report-Driven Fixing          │  ← 20-fix-*, 24-fix-language-deep
├─────────────────────────────────────────┤
│  Layer 3: Deterministic Checking        │  ← 10-check-*, 14-check-language-deep
├─────────────────────────────────────────┤
│  Layer 2: Word-to-LaTeX Migration       │  ← 01-word-to-latex
├─────────────────────────────────────────┤
│  Layer 1: Bibliography Intake           │  ← 00-bib-endnote, 00-bib-zotero
└─────────────────────────────────────────┘

Feature Modules

Module	Status	Description
EndNote Import	✅ v0.4	XML/RIS/BibTeX → `refNNN` with deduplication
Zotero Sync	✅ v0.3	Word docx → LaTeX citation mapping
Reference Check	✅ Stable	Missing keys, orphans, duplicates
Language Lint	✅ v0.5.0	10+ deterministic rules
Deep Language Review	✅ v0.5.1	Sentence-aware screening
Deep Patch Fix	✅ v0.5.2	Selective span-based fixes
Format Check	✅ Stable	Figures, tables, centering
Content Check	✅ Stable	Required sections, abstract keywords

Quick Start

# Clone
git clone https://github.com/quzhiii/thesis-skills.git
cd thesis-skills

# Quick check example
python run_check_once.py \
  --project-root examples/minimal-latex-project \
  --ruleset university-generic \
  --skip-compile

New to LaTeX?

If you are completely new to LaTeX, start here first:

Beginner getting-started guide (Chinese)

EndNote Workflow

# 1. Export from EndNote → XML/RIS/BibTeX
# 2. Preflight check
python 00-bib-endnote/check_endnote_export.py \
  --project-root thesis --input refs.xml

# 3. Import
python 00-bib-endnote/import_library.py \
  --project-root thesis --input refs.xml --apply

Zotero Workflow

# Sync from Word to LaTeX
python 00-bib-zotero/sync_from_word.py \
  --project-root thesis --word-file thesis.docx --apply

# Run checks
python run_check_once.py \
  --project-root thesis --ruleset tsinghua-thesis --skip-compile

# Fix issues (dry-run first)
python run_fix_cycle.py \
  --project-root thesis --ruleset tsinghua-thesis --apply false

Rule Pack System

Starter packs included:

90-rules/packs/
├── university-generic/     # Generic university thesis
├── journal-generic/        # Generic journal article
└── tsinghua-thesis/        # Tsinghua University example

Create your own:

python 90-rules/create_pack.py \
  --pack-id my-university \
  --display-name "My University Thesis" \
  --starter university-generic \
  --kind university-thesis

Technical Architecture

thesis-skills/
├── core/                   # Shared implementations
│   ├── canonicalize.py     # Reference normalization
│   ├── citation_*.py       # Mapping & models
│   └── reports.py          # JSON report generation
├── 00-bib-*/               # Bibliography workflows
├── 01-word-to-latex/       # Migration workflow
├── 10-check-*/             # Deterministic checkers
├── 20-fix-*/               # Safe fixers
├── 90-rules/               # Rule pack system
└── 99-runner/              # Entry points

Template Recommendations

University	Repository
Tsinghua	tuna/thuthesis
SJTU	sjtug/SJTUThesis
USTC	ustctug/ustcthesis
Peking	CasperVector/pkuthss
Stanford	dcroote/stanford-thesis-example
Cambridge	cambridge/thesis

Acknowledgments

Special thanks to tuna/thuthesis for their open-source LaTeX thesis template, which has greatly benefited Tsinghua University students and inspired this project.

License

MIT License