rxiv-maker 1.18.3

Write scientific preprints in Markdown. Generate publication-ready PDFs efficiently.

Rxiv-Maker

Write scientific preprints in Markdown. Generate publication-ready PDFs efficiently.

💡 Best Experience: Use the VS Code Extension for syntax highlighting and citations.

Rxiv-Maker converts enhanced Markdown into professional PDFs with automated figure generation, citation management, and LaTeX typesetting. While LaTeX installation is required, users don't need to write LaTeX code directly.

✨ Why Rxiv-Maker?

• Write in Markdown: Focus on content, not LaTeX formatting
• Automated Figures: Python/R scripts become publication figures
• Smart Citations: BibTeX integration with cross-references and DOI resolution
• Dual Output: Generate both PDF and DOCX from the same source
• Git-Friendly: Version control for manuscripts and figures
• Reproducible: All figures generated from code
• arXiv Ready: Generate submission packages automatically
• Track Changes: Visual diff between manuscript versions

🚀 Installation

🍎 macOS (Recommended - includes LaTeX automatically)

brew tap henriqueslab/formulas
brew install rxiv-maker
rxiv check-installation

Upgrade:

brew upgrade rxiv-maker

📖 Homebrew Formula - Includes Python, LaTeX (MacTeX), and all dependencies

🐧 Linux / Windows (WSL)

Using pipx (recommended):

pipx install rxiv-maker
rxiv check-installation

Using uv (faster alternative):

uv tool install rxiv-maker
rxiv check-installation

Requirements:

• Python 3.11+: For rxiv-maker CLI and figure generation
• LaTeX Distribution: Install via system package manager
  • Ubuntu/Debian: sudo apt install texlive-latex-recommended
  • Fedora/RHEL: sudo dnf install texlive-latex

Upgrade:

pipx upgrade rxiv-maker  # or: uv tool upgrade rxiv-maker

📖 Need help? See the complete installation guide for detailed platform-specific instructions.

🔥 Quick Start

Get your first PDF quickly:

# Create manuscript
rxiv init my-paper
cd my-paper

# Generate PDF
rxiv pdf

Or explore the complete example manuscript:

# Clone the official example with one command
rxiv get-rxiv-preprint
cd manuscript-rxiv-maker/MANUSCRIPT

# Generate PDF
rxiv pdf

🎯 Getting Started Guide

🏆 Key Features

🎨 Enhanced Markdown

• Scientific cross-references (@fig:plot, @eq:formula)
• Auto-numbered figures, tables, and equations
• Mathematical notation with LaTeX math
• Code blocks with syntax highlighting
• Markdown comments (<!-- note -->) for TODOs and notes

📊 Automated Figures & Data Analysis

• Execute Python/R scripts during PDF generation
• 🐍 NEW: Jupyter-like executable Python code blocks
• Real-time data analysis with {{py:exec}} and {{py:get variable}}
• Matplotlib, ggplot2, and custom visualizations
• Version-controlled figure code and analysis modules

📚 Citation Management

• BibTeX integration with [@citation] syntax
• Automatic bibliography generation
• Multiple citation styles: Choose between numbered [1, 2] or author-date (Smith, 2024) citations
• Configurable author name formatting: Format bibliography as Smith, J.A. or Smith, John A. or John A. Smith
• Inline DOI resolution: Paste DOIs directly in text 10.1038/... and auto-convert to citations
• CrossRef/DataCite DOI validation and metadata fetching

📖 Learn more: Quick Reference Cheat-Sheet

🔧 Developer Experience

• Modern CLI with rich output and progress bars
• Consistent environments with package management
• Git-friendly workflow with meaningful diffs
• Comprehensive validation and error reporting

🌟 Example Manuscript

💡 Get this complete example instantly:

rxiv get-rxiv-preprint

This clones manuscript-rxiv-maker with all features demonstrated.

Input Markdown:

## Introduction

Recent advances in microscopy have enabled new insights into
cellular dynamics [@smith2023; @jones2024].

![Experimental Results](FIGURES/results_plot.py)
{#fig:results}

Our analysis (Figure @fig:results) shows significant improvement
over previous methods. Statistical analysis revealed p < 0.001.

Output: Professional PDF with auto-numbered figures, formatted citations, and LaTeX typesetting.

💡 See the complete working example: rxiv get-rxiv-preprint - clones manuscript-rxiv-maker with advanced features including Python execution, DOI auto-resolution, and dynamic data integration.

📖 Documentation

For Users

Visit our official documentation website for comprehensive guides:

• Installation Guide - Setup for all platforms
• First Manuscript Tutorial - 5-minute walkthrough
• User Guide - Complete features and workflows
• CLI Reference - All commands and options
• Troubleshooting - Solutions to common issues

For Developers

• CONTRIBUTING.md - Contribution guidelines
• CI-LOCAL-TESTING.md - Local CI workflow testing
• Developer Docs - Technical documentation and API details

🎯 Use Cases

📄 Research Preprints, Reproducible Figures, and Collaborative Workflows

📄 Research Preprints

• arXiv preprints with automated submission packages
• bioRxiv and other preprint servers with professional formatting
• Conference papers with consistent styling

📊 Preprint Features

• Reproducible figures generated from Python/R scripts
• Live data integration that updates with analysis changes
• Professional formatting optimized for preprint servers

🎓 Preprint Workflows

• arXiv submissions with cross-references and mathematical notation
• Collaborative preprint writing with version control
• Supplementary materials with automated generation

🏃‍♀️ Ecosystem & Workflows

Three ways to use rxiv-maker:

• 🖥️ Local Installation: Install directly on your system (recommended)
• 🐳 Docker: Pre-configured container with all dependencies
• ☁️ Cloud: GitHub Actions or Google Colab for browser-based editing

🔗 Ecosystem - Related repositories and tools

Ecosystem Overview

graph LR
    A[rxiv-maker<br/>Core CLI] --> B[PyPI]
    A --> C[Homebrew]
    D[docker-rxiv-maker<br/>Container] --> E[Docker Hub]
    D -.includes.-> A
    F[vscode-rxiv-maker<br/>VS Code] -.enhances.-> A
    G[manuscript-rxiv-maker<br/>Example] -.demonstrates.-> A

    style A fill:#2563eb,stroke:#1e40af,stroke-width:3px,color:#fff
    style D fill:#ea580c,stroke:#c2410c,stroke-width:2px,color:#fff
    style F fill:#7c3aed,stroke:#6d28d9,stroke-width:2px,color:#fff
    style G fill:#059669,stroke:#047857,stroke-width:2px,color:#fff
    style B fill:#64748b,stroke:#475569,color:#fff
    style C fill:#64748b,stroke:#475569,color:#fff
    style E fill:#64748b,stroke:#475569,color:#fff

Related Repositories

Repository	Purpose	Access
rxiv-maker	Main CLI tool and Python package	brew install rxiv-maker
docker-rxiv-maker	Pre-configured container with LaTeX + dependencies	docker pull henriqueslab/rxiv-maker-base
manuscript-rxiv-maker	Complete example (published as arXiv:2508.00836)	rxiv get-rxiv-preprint
vscode-rxiv-maker	VS Code extension with syntax highlighting	VS Code Marketplace
Documentation	User guides, API reference, tutorials	Visit website

🚀 Quick Commands

Essential commands to get started:

rxiv init my-paper       # Create new manuscript
rxiv pdf                 # Generate PDF
rxiv validate           # Check manuscript quality
rxiv upgrade            # Upgrade to latest version

📋 Complete Command Reference - Repository management, export options, and advanced workflows

Core Commands

rxiv init my-paper          # Create new manuscript
rxiv get-rxiv-preprint     # Clone complete example manuscript
rxiv pdf                    # Generate PDF
rxiv docx                   # Export to DOCX for collaborative review
rxiv validate              # Check manuscript quality
rxiv arxiv                 # Prepare arXiv submission
rxiv track-changes v1 v2   # Visual version comparison

Repository Management

# Initial setup
rxiv repo-init             # Interactive setup
rxiv config                # Interactive configuration menu

# Create and manage repositories
rxiv create-repo my-paper  # Create new manuscript repository (with GitHub integration)
rxiv repos                 # List all manuscript repositories
rxiv repos-search          # Search and clone from GitHub

# Configuration
rxiv config set-repo-parent-dir ~/manuscripts
rxiv config set-repo-org YourGitHubOrg
rxiv config --non-interactive  # Show current settings

Maintenance

# Upgrade commands (auto-detects Homebrew, pip, uv, pipx)
rxiv upgrade                 # Interactive upgrade with confirmation
rxiv upgrade --yes           # Upgrade without confirmation
rxiv upgrade --check-only    # Check for updates only

# Changelog and version information
rxiv changelog               # View changelog and release notes
rxiv changelog --recent 5    # View last 5 versions

💡 CI/Automation Note: All interactive commands support non-interactive mode or configuration files for use in CI/CD pipelines and automated workflows. Use --non-interactive flag or configure via ~/.rxiv-maker/config for non-TTY environments.

📖 Complete CLI Reference - Full command documentation with examples and options.

📚 Publications Using Rxiv-Maker

Publication	Authors	Venue	DOI
Rxiv-Maker: an automated template engine for streamlined scientific publications	BM Saraiva et al.	arXiv (2025)	10.48550/arXiv.2508.00836
Customizable FDM-based zebrafish embryo mold for live imaging	MX Rivera Pineda et al.	bioRxiv (2025)	10.1101/2025.11.24.689779
mAIcrobe: an open-source framework for high-throughput bacterial image analysis	AD Brito et al.	bioRxiv (2025)	10.1101/2025.10.21.683709
Filopodome proteomics identifies CCT8 as a MYO10 interactor critical for filopodia functions	A Popović et al.	bioRxiv (2025)	10.64898/2025.12.03.691809

📸 View Publication Previews - See manuscript thumbnails and access preprints

Using Rxiv-Maker for your research? Submit your publication via GitHub Issue

🤝 Community

• 💬 GitHub Discussions - Ask questions, share tips
• 🐛 Issues - Report bugs, request features
• 📚 Example Manuscript - Clone instantly: rxiv get-rxiv-preprint
• 🧪 Google Colab - Try without installing

🏗️ Contributing

We welcome contributions! Whether it's:

• 🐛 Bug reports and fixes
• ✨ New features and improvements
• 📖 Documentation enhancements
• 🧪 Testing and validation

Quick contributor setup:

git clone https://github.com/henriqueslab/rxiv-maker.git
cd rxiv-maker
pip install -e ".[dev]"
pre-commit install

📄 Citation

If Rxiv-Maker helps your research, please cite:

@misc{saraiva_2025_rxivmaker,
  title={Rxiv-Maker: an automated template engine for streamlined scientific publications}, 
  author={Bruno M. Saraiva and António D. Brito and Guillaume Jaquemet and Ricardo Henriques},
  year={2025},
  eprint={2508.00836},
  archivePrefix={arXiv},
  url={https://arxiv.org/abs/2508.00836}
}

📜 License

MIT License - see LICENSE for details.

---

🔬 From Jacquemet and Henriques Labs

"Because science is hard enough without fighting with LaTeX."

🚀 Start Writing | 📚 User Guide | ⚙️ CLI Reference