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

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

# Checks - Pre-submission validation
scitex-writer check-references                 # Cross-refs, citations, labels, duplicate headings
scitex-writer check-limits                     # Section word limits + reference cap (config-driven)

# Update - Sync engine files from the template
scitex-writer update-project                   # Preview drifted engine files (safe; pass --yes to apply)

# 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 install                     # 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

Turn AI agents into autonomous manuscript compilers.

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

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

Full MCP tool reference

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

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.

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

./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

# 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

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

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}
   

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)