SciTeX Writer

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.

Problem and Solution

#	Problem	Solution
1	LaTeX compilation is fragile -- bib, figs, tables, cross-refs, supplement each have their own failure mode	`scitex writer compile` -- one command runs bibtex → latex → bibtex → latex twice; handles supplement + revision diffs
2	Figures drift from manuscript -- author renumbers a figure; half the references go stale; `\ref{}` silently prints `??`	Reference check + float-order audit -- `writer_check_references` + `writer_check_float_order` catch dangling `\ref{}` before submission
3	Manuscript claims uncheckable -- a paper asserts "t(58) = 2.34, p = .021"; reviewer has no way to verify	Clew-backed claims -- `writer_add_claim` binds each assertion to a source session + file hash; `writer_render_claims` exposes the verification DAG

Preview

Light mode (default) and dark mode (--dark-mode)

Demo video with AI agent

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

Problem

LaTeX compilation for scientific manuscripts is painful:

Environment inconsistency — "It compiles on my machine" is not a solution when collaborating across Linux, macOS, WSL2, and HPC clusters.
Manual figure conversion — Converting between PNG, SVG, PDF, Mermaid, and TIFF formats by hand wastes time and introduces errors.
No version tracking — Generating tracked-change diffs between revisions requires manual latexdiff invocations and careful file management.
Fragmented tooling — Separate workflows for compilation, bibliography management, table formatting, and submission packaging.
AI agents cannot help — Without a programmatic interface, AI assistants have no way to compile or manage manuscripts.

Solution

SciTeX Writer solves each of these problems:

Container-based reproducible compilation — Consistent builds across all platforms via Docker, Singularity, or native installation with automatic engine selection (Tectonic, latexmk, or 3-pass).
Automatic asset conversion — Figures and tables are converted in parallel from source formats (PNG, SVG, comma-separated values (CSV), Mermaid) to LaTeX-ready output.
Built-in version tracking with diff generation — Every compilation archives the previous version and generates a latexdiff document automatically.
Unified interface — One tool for compilation, bibliography deduplication, figure/table management, and arXiv export packaging.
39 Model Context Protocol (MCP) tools for AI agents — AI assistants can compile, edit, and manage manuscripts programmatically.

Four Interfaces

Interface	For	Description
Python API	Human researchers	`import scitex_writer as sw`
Command-Line Interface (CLI) Commands	Terminal users	`scitex-writer compile`, `scitex-writer bib`
MCP Tools	AI agents	39 tools for Claude/GPT integration
Skills	AI agent discovery	Workflow guides for capabilities and patterns

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)

Export — arXiv Submission

sw.export.manuscript("./my-paper")                     # arXiv-ready tarball
sw.export.manuscript("./my-paper", output_dir="/tmp")  # Custom output dir

Tables/Figures/Bib — Create, Read, Update, Delete (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 — Introduction, Methods, Results, and Discussion (IMRAD) Writing Tips

sw.guidelines.get("abstract")
sw.guidelines.build("abstract", draft="Your draft...")
sw.guidelines.list_sections()  # ['abstract', 'introduction', 'methods', 'discussion', 'proofread']

Prompts — AI2 Asta

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

GUI — Browser-based Editor

sw.gui("./my-paper")                              # Launch editor
sw.gui("./my-paper", port=8080, dark_mode=True)  # Custom options

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

# Export - arXiv submission
scitex-writer export manuscript               # Package for arXiv upload

# 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 to 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

# GUI - Browser-based editor
scitex-writer gui                              # Launch editor (current dir)
scitex-writer gui ./my-paper                   # Open specific project
scitex-writer gui --port 8080 --no-browser     # Custom port, no auto-open

MCP Tools — 39 tools for AI Agents

Turn AI agents into autonomous manuscript compilers.

Category	Tools	Description
project	4	Clone, info, PDF paths, document types
compile	4	Manuscript, supplementary, revision, content
tables	5	CSV to 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
export	1	arXiv-ready tarball packaging
claim	6	Traceable scientific assertions
migration	2	Overleaf import/export
update	1	Template update from upstream

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

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

Full MCP tool reference

Skills — for AI Agent Discovery

Skills provide workflow-oriented guides that AI agents query to discover capabilities and usage patterns.

scitex-writer skills list              # List available skill pages
scitex-writer skills get SKILL         # Show main skill page
scitex-dev skills export --package scitex-writer  # Export to Claude Code

Skill	Content
`quick-start`	Basic manuscript workflow
`compilation`	Compile manuscript, supplementary, revision
`bibliography`	BibTeX management, enrichment
`figures-and-tables`	Figure/table insertion and conversion
`claims`	Claim tracking and rendering
`cli-reference`	CLI commands
`mcp-tools`	MCP tools for AI agents
`writing-attitude`	Evidence requirements, scientific standards
`writing-figures-stats`	Figure rules, statistical reporting
`writing-proofreading`	Proofreading corrections, language rules
`writing-abstract`	Abstract template with 7-section structure
`writing-introduction`	Introduction template with 8-section structure
`writing-methods`	Methods template with reproducibility guidelines
`writing-discussion`	Discussion template with 5-section structure
`audit-paper`	Comprehensive pre-submission manuscript audit

Additional Interfaces

Shell Scripts / Make — Direct compilation without Python.

make manuscript              # Compile manuscript
make supplementary           # Compile supplementary
make revision                # Compile revision
make all                     # Compile all documents
make manuscript-export       # Package for arXiv submission
make clean                   # Remove build artifacts
./compile.sh manuscript --draft       # Fast single-pass
./compile.sh manuscript --no-figs     # Skip figures
./compile.sh manuscript --dark-mode   # Dark mode (Monaco theme)
./compile.sh manuscript --watch       # Hot-reload
SCITEX_WRITER_DARK_MODE=true make manuscript

GUI Editor — Standalone browser-based editor with file tree, PDF preview, and compilation controls.

pip install scitex-writer[editor]
scitex-writer gui                    # Current directory
scitex-writer gui ./my-paper         # Specific project
scitex-writer gui --port 8080        # Custom port

Output Structure

./scitex-writer/
├── 00_shared/                  # Shared resources across all documents
│   ├── title.tex / authors.tex / keywords.tex / journal_name.tex
│   ├── bib_files/              # Multiple .bib files (auto-merged and deduplicated)
│   ├── latex_styles/           # Common LaTeX configurations
│   └── templates/              # LaTeX document templates
├── 01_manuscript/              # Main manuscript
│   ├── contents/               # abstract, introduction, methods, results, discussion
│   │   ├── 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 (same structure)
├── 03_revision/                # Revision response letter
│   └── contents/               # editor/, reviewer1/, reviewer2/
├── config/                     # config_manuscript.yaml
└── scripts/                    # containers, installation, shell, python

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)
GUI Editor	Browser-based editor with PDF preview (`scitex-writer gui`)
Dark Mode	Monaco/VS Code dark theme for comfortable reading (`--dark-mode`)
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

Part of SciTeX

SciTeX Writer is part of SciTeX. When used inside the orchestrator package scitex, synergy between modules enables end-to-end scientific workflows — from data analysis through publication-ready manuscripts.

The SciTeX ecosystem follows the Four Freedoms for researchers, inspired by the Free Software Definition:

Use — Run the software for any research purpose
Study — Examine how it works and adapt it to your needs
Share — Distribute copies to fellow researchers
Improve — Enhance the software and share improvements with the community

AGPL-3.0

Name		Name	Last commit message	Last commit date
Latest commit History 776 Commits
.github/workflows		.github/workflows
.scitex/writer/builds		.scitex/writer/builds
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
CLA.md		CLA.md
CONTRIBUTING.md		CONTRIBUTING.md
LICENSE		LICENSE
Makefile		Makefile
README.md		README.md
compile.sh		compile.sh
pyproject.toml		pyproject.toml

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Quick Start

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Solution

Four Interfaces

Features

Usage

Documentation

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