Rxiv-Maker

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

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?

🎯 For Researchers

• Write in Markdown: Focus on content, not formatting
• Automated Figures: Python/R scripts become publication figures
• Smart Citations: BibTeX integration with cross-references
• Instant PDFs: From Markdown to professional academic PDF

🚀 For Teams

• Git-Friendly: Version control for manuscripts and figures
• Reproducible: All figures generated from code
• Collaborative: Standard tools, no vendor lock-in
• Multi-Platform: Works everywhere with local installation

📈 For Publishing

• arXiv Ready: Generate submission packages automatically
• Track Changes: Visual diff between manuscript versions
• Quality Assurance: Built-in validation and error checking

🚀 Installation

Quick Installation (All Platforms):

# Using pipx (recommended)
pipx install rxiv-maker

# Verify installation
rxiv check-installation

Need help? 📖 Installation Guide

🔥 Quick Start

Get your first PDF quickly:

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

# 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

📊 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 (APA, Nature, etc.)
• CrossRef DOI resolution

🔧 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

Input Markdown:

# Introduction

{{py:exec
import pandas as pd
import numpy as np

df = pd.read_csv("FIGURES/DATA/experimental_results.csv")

# Calculate correlation between specific columns (safer than iloc)
# Assuming the CSV has columns like 'treatment_effect' and 'baseline_score'
correlation = df['treatment_effect'].corr(df['baseline_score'])
sample_size = len(df)
}}

Our analysis of {{py:get sample_size}} samples in Figure @fig:results shows 
significant improvement over previous methods [@smith2023; @jones2024].

![Research Results](EXAMPLE_MANUSCRIPT/FIGURES/SFigure__arxiv_growth.py)
{#fig:results}

The correlation coefficient was r = {{py:get correlation:.2f}} (p < 0.001).

## References

Output: Professional PDF with numbered figures, live data integration, citations, and LaTeX-quality typesetting.

📖 Documentation

• Installation - Setup and dependencies
• Getting Started - Your first manuscript
• User Guide - Complete features and workflows
• Python Execution - Jupyter-like code blocks
• CLI Reference - All commands
• Troubleshooting - Common issues

🎯 Use Cases

📄 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

🏃‍♀️ Alternative Workflows

Need specialized environments?

• 🌐 Google Colab: Browser-based editing and PDF generation
• ⚡ GitHub Actions: Automated cloud builds for teams
• 🐳 Docker: Use docker-rxiv-maker for containerized execution

🚀 Essential Commands

rxiv init my-paper          # Create new manuscript
rxiv pdf                    # Generate PDF  
rxiv validate              # Check manuscript quality
rxiv arxiv                 # Prepare arXiv submission
rxiv track-changes v1 v2   # Visual version comparison

📖 CLI Reference

🤝 Community

• 💬 GitHub Discussions - Ask questions, share tips
• 🐛 Issues - Report bugs, request features
• 📚 Example Manuscript - Complete manuscript example
• 🧪 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 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.

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🔬 From Jacquemet and Henriques Labs

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

🚀 Start Writing | 📚 User Guide | ⚙️ CLI Reference