GitHub - zhangchenhaobest/scitex-writer: LaTeX manuscript compilation with automatic versioning, diff generation, and MCP server for AI assistants. Part of SciTeX.

scitex.ai · docs · pip install scitex-writer

LaTeX compilation system for scientific manuscripts with automatic versioning, diff generation, and cross-platform reproducibility.

Part of the SciTeX ecosystem — empowers both human researchers and AI agents.

🎬 Demo

📄 Demo prompt and progress report (org | pdf) | Manuscript output | Revision output

📦 Installation

# LaTeX dependencies (Ubuntu/Debian)
sudo apt-get install texlive-latex-extra latexdiff parallel imagemagick ghostscript

# LaTeX dependencies (macOS)
brew install texlive latexdiff parallel imagemagick ghostscript

# Python package + MCP server
pip install scitex-writer

Quick Start

git clone https://github.com/ywatanabe1989/scitex-writer.git my-paper
cd my-paper && make manuscript   # or: ./compile.sh manuscript

Four Interfaces

Interface	For	Description
📜 Shell/Make	Direct compilation	`make manuscript`, `./compile.sh`
🐍 Python API	Human researchers	`import scitex_writer as sw`
🖥️ CLI Commands	Terminal users	`scitex-writer compile`, `scitex-writer bib`
🔧 MCP Tools	AI agents	28 tools for Claude/GPT integration

📜 Shell Scripts / Make

# Make commands (recommended)
make manuscript              # Compile manuscript
make supplementary           # Compile supplementary
make revision                # Compile revision
make all                     # Compile all documents
make clean                   # Remove build artifacts

# Shell scripts (direct)
./compile.sh manuscript --draft       # Fast single-pass
./compile.sh manuscript --no-figs     # Skip figures
./compile.sh manuscript --no-tables   # Skip tables
./compile.sh manuscript --watch       # Hot-reload

🐍 Python API

Compile — Build PDFs

import scitex_writer as sw

sw.compile.manuscript("./my-paper")                    # Full compile
sw.compile.manuscript("./my-paper", draft=True)       # Fast draft mode
sw.compile.supplementary("./my-paper")
sw.compile.revision("./my-paper", track_changes=True)

Tables/Figures/Bib — CRUD Operations

# Tables
sw.tables.list("./my-paper")
sw.tables.add("./my-paper", "results", "a,b\n1,2", "Results summary")
sw.tables.remove("./my-paper", "results")

# Figures
sw.figures.list("./my-paper")
sw.figures.add("./my-paper", "fig01", "./plot.png", "My figure")
sw.figures.remove("./my-paper", "fig01")

# Bibliography
sw.bib.list_files("./my-paper")
sw.bib.add("./my-paper", "@article{Smith2024, title={...}}")
sw.bib.merge("./my-paper")  # Merge + deduplicate

Guidelines — IMRAD Writing Tips

sw.get_guideline("abstract")
sw.build_guideline("abstract", draft="Your draft...")
sw.list_guidelines()  # ['abstract', 'introduction', 'methods', 'discussion', 'proofread']

Prompts — AI2 Asta

from scitex_writer import generate_asta
result = generate_asta("./my-paper", search_type="related")

🖥️ CLI Commands

scitex-writer --help                           # Show all commands

# Compile - Build PDFs
scitex-writer compile manuscript               # Compile manuscript
scitex-writer compile manuscript --draft       # Fast single-pass
scitex-writer compile supplementary            # Compile supplementary
scitex-writer compile revision                 # Compile revision letter

# Bibliography - Reference management
scitex-writer bib list-files                   # List .bib files
scitex-writer bib list-entries                 # List all entries
scitex-writer bib get Smith2024                # Get specific entry
scitex-writer bib add '@article{...}'          # Add entry
scitex-writer bib remove Smith2024             # Remove entry
scitex-writer bib merge                        # Merge and deduplicate

# Tables - CSV↔LaTeX management
scitex-writer tables list                      # List tables
scitex-writer tables add results data.csv "Caption"
scitex-writer tables remove results

# Figures - Image management
scitex-writer figures list                     # List figures
scitex-writer figures add fig01 plot.png "Caption"
scitex-writer figures remove fig01

# Guidelines - IMRAD writing tips
scitex-writer guidelines list                  # List available sections
scitex-writer guidelines abstract              # Get abstract guidelines
scitex-writer guidelines abstract -d draft.tex # Build prompt with draft

# Prompts - AI2 Asta integration
scitex-writer prompts asta                     # Generate related papers prompt
scitex-writer prompts asta -t coauthors        # Find collaborators

# MCP server management
scitex-writer mcp list-tools                   # List all MCP tools (markdown)
scitex-writer mcp doctor                       # Check server health
scitex-writer mcp installation                 # Show Claude Desktop config
scitex-writer mcp start                        # Start MCP server

🔧 MCP Tools — 28 tools for AI Agents

Turn AI agents into autonomous manuscript compilers.

Category	Tools	Description
project	4	Clone, info, PDF paths, document types
compile	3	Manuscript, supplementary, revision
tables	5	CSV↔LaTeX, list/add/remove tables
figures	5	Convert, render PDF, list/add/remove
bib	6	List files/entries, CRUD, merge/dedupe
guidelines	3	List, get, build with draft
prompts	1	AI2 Asta prompt generation
usage	1	Project guide

Claude Desktop (~/.config/Claude/claude_desktop_config.json):

{
  "mcpServers": {
    "scitex-writer": {
      "command": "scitex-writer",
      "args": ["mcp", "start"]
    }
  }
}

→ Full MCP tool reference

Output Structure

./scitex-writer/
├── 00_shared/                  # Shared resources across all documents
│   ├── title.tex               # Manuscript title
│   ├── authors.tex             # Author names and affiliations
│   ├── keywords.tex            # Keywords for the manuscript
│   ├── journal_name.tex        # Target journal name
│   ├── bib_files/              # Multiple .bib files (auto-merged and deduplicated)
│   ├── latex_styles/           # Common LaTeX configurations
│   └── templates/              # LaTeX document templates
│
├── 01_manuscript/              # Main manuscript
│   ├── contents/               # Modular content sections
│   │   ├── abstract.tex
│   │   ├── introduction.tex
│   │   ├── methods.tex
│   │   ├── results.tex
│   │   ├── discussion.tex
│   │   ├── figures/            # Figure captions + media
│   │   └── tables/             # Table captions + CSV data
│   ├── archive/                # Version history (gitignored)
│   ├── manuscript.tex          # Compiled LaTeX
│   ├── manuscript_diff.tex     # Change-tracked version
│   └── manuscript.pdf          # Output PDF
│
├── 02_supplementary/           # Supplementary materials
│   ├── contents/               # Supplementary content sections
│   │   ├── supplementary_methods.tex
│   │   ├── supplementary_results.tex
│   │   ├── figures/            # Supplementary figures
│   │   └── tables/             # Supplementary tables
│   ├── archive/                # Version history (gitignored)
│   ├── supplementary.tex       # Compiled LaTeX
│   └── supplementary.pdf       # Output PDF
│
├── 03_revision/                # Revision response letter
│   ├── contents/               # Reviewer responses
│   │   ├── editor/             # E_01_comments.tex, E_01_response.tex
│   │   ├── reviewer1/          # R1_01_comments.tex, R1_01_response.tex
│   │   └── reviewer2/          # R2_01_comments.tex, R2_01_response.tex
│   ├── archive/                # Version history (gitignored)
│   ├── revision.tex            # Compiled LaTeX
│   └── revision.pdf            # Output PDF
│
├── config/                     # Configuration files
│   └── config_manuscript.yaml  # Citation style, engine settings
│
└── scripts                     # Compilation scripts
    ├── containers/             # Container image builds (Apptainer/Singularity)
    ├── installation/           # Environment setup and dependency installation
    ├── maintenance/            # Repository maintenance (usage, update, demos)
    ├── powershell/             # Windows PowerShell scripts
    ├── python/                 # Python utilities
    └── shell/                  # Core compilation scripts

Features

Details

Feature	Description
Separated Files	Modular sections (abstract, intro, methods, results, discussion)
Built-in Templates	Pre-configured manuscript, supplementary materials, and revision
Bibliography	Multi-file with auto-deduplication, 20+ citation styles
Assets	Parallel figure/table processing (PNG, PDF, SVG, Mermaid, CSV)
Multi-Engine	Auto-selects best engine (Tectonic 1-3s, latexmk 3-6s, 3-pass 12-18s)
Cross-Platform	Linux, macOS, WSL2, Docker, Singularity, HPC clusters

Usage

PDF Compilation

# Basic compilation
./scripts/shell/compile_manuscript.sh          # Manuscript
./scripts/shell/compile_supplementary.sh       # Supplementary
./scripts/shell/compile_revision.sh            # Revision letter

# Performance options
./scripts/shell/compile_manuscript.sh --draft      # Fast single-pass
./scripts/shell/compile_manuscript.sh --no-figs    # Skip figures
./scripts/shell/compile_manuscript.sh --no-tables  # Skip tables
./scripts/shell/compile_manuscript.sh --no-diff    # Skip diff generation

# Engine selection
./scripts/shell/compile_manuscript.sh --engine tectonic  # Fastest
./scripts/shell/compile_manuscript.sh --engine latexmk   # Standard
./scripts/shell/compile_manuscript.sh --engine 3pass     # Most compatible

# Development
./scripts/shell/compile_manuscript.sh --watch  # Hot-reload on file changes
./scripts/shell/compile_manuscript.sh --clean  # Remove cache

Figures

Place media files in 01_manuscript/contents/figures/caption_and_media/:
```
01_example_figure.png
01_example_figure.tex  # Caption file
```

Caption file format (01_example_figure.tex):

%% Figure caption
\caption{Your figure caption here. Explain panels (A, B, C) if applicable.}
\label{fig:example_figure_01}

Supported formats: PNG, JPEG, PDF, SVG, TIFF, Mermaid (.mmd)
Figures auto-compile and include in FINAL.tex

Tables

Place CSV + caption in 01_manuscript/contents/tables/caption_and_media/:
```
01_example_table.csv
01_example_table.tex  # Caption file
```
CSV auto-converts to LaTeX table format

Caption file format (01_example_table.tex):

%% Table caption
\caption{Your table caption. Define abbreviations used.}
\label{tab:example_table_01}

References

Organize references in multiple .bib files - they auto-merge with deduplication:

00_shared/bib_files/
├── methods_refs.bib      # Method-related references
├── field_background.bib  # Background literature
└── my_papers.bib         # Your own publications

Change citation style in config/config_manuscript.yaml:

unsrtnat (numbered, order of citation)
plainnat (numbered, alphabetical)
apalike (author-year, APA style)
IEEEtran (IEEE format)
naturemag (Nature style)

Documentation

Details

Guide	Description
Installation	Setup for all environments
Quick Start	Common workflows
Content Creation	Writing manuscripts
Bibliography	Reference management
Architecture	Technical details

AGPL-3.0 · ywatanabe@scitex.ai

Name		Name	Last commit message	Last commit date
Latest commit History 580 Commits
.github/workflows		.github/workflows
00_shared		00_shared
01_manuscript		01_manuscript
02_supplementary		02_supplementary
03_revision		03_revision
config		config
docs		docs
examples		examples
scripts		scripts
src/scitex_writer		src/scitex_writer
tests		tests
.gitignore		.gitignore
.readthedocs.yaml		.readthedocs.yaml
CHANGELOG.md		CHANGELOG.md
LICENSE		LICENSE
Makefile		Makefile
README.md		README.md
compile.sh		compile.sh
pyproject.toml		pyproject.toml

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