scitex-writer 0.1.0

LaTeX manuscript compilation system for scientific documents with MCP server

SciTeX Writer

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

Part of the fully open-source SciTeX project: https://scitex.ai

Quick Start

git clone https://github.com/ywatanabe1989/scitex-writer.git
./scitex-writer/scripts/compile.sh manuscript

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

1. Place media files in 01_manuscript/contents/figures/caption_and_media/:

   01_example_figure.png
   01_example_figure.tex  # Caption file
   

2. 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}
   

3. Supported formats: PNG, JPEG, PDF, SVG, TIFF, Mermaid (.mmd)

4. Figures auto-compile and include in FINAL.tex

Tables

1. Place CSV + caption in 01_manuscript/contents/tables/caption_and_media/:

   01_example_table.csv
   01_example_table.tex  # Caption file
   

2. CSV auto-converts to LaTeX table format

3. 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)

Installation

Python Package (MCP Server)

# Install from PyPI
pip install scitex-writer

# Verify installation (CLI or Python module)
scitex-writer --version
python -m scitex_writer version

# Check MCP setup
scitex-writer mcp doctor
python -m scitex_writer mcp doctor

# Start MCP server
scitex-writer mcp start
python -m scitex_writer mcp start

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

Option 1: CLI command

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

Option 2: Python module

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

Ubuntu/Debian

sudo apt-get install texlive-latex-extra latexdiff parallel imagemagick ghostscript

macOS

brew install texlive latexdiff parallel imagemagick ghostscript

HPC / Containers

# Module system
module load texlive latexdiff parallel

# Docker
docker run -v $(pwd):/work scitex-writer

# Singularity/Apptainer
singularity run scitex-writer.sif

Documentation

Details

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

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