Rxiv-Maker

Rxiv-Maker transforms scientific writing by converting Markdown manuscripts into publication-ready PDFs with automated figure generation, professional LaTeX typesetting, and zero LaTeX expertise required.

Key Features: Scientific cross-references, automated Python/R figures, citation management, Docker support, and modern CLI with rich output.

🚀 Getting Started

🎯 Quick Install

pip install rxiv-maker
rxiv check-installation --fix  # Auto-install dependencies
rxiv init my-paper
cd my-paper
rxiv pdf

📦 Dependencies by Platform

🍎 macOS - Homebrew (Recommended)

Install dependencies with Homebrew:

# Install Homebrew if needed
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

# Install system dependencies
brew install python@3.11 node@20 texlive
brew tap henriqueslab/rxiv-maker
brew install rxiv-maker  # Complete installation with all dependencies

# Verify installation
rxiv check-installation

🐧 Linux - Choose Your Method

Option A: APT Repository (Ubuntu/Debian - Recommended)

sudo apt update
sudo apt install ca-certificates
curl -fsSL https://raw.githubusercontent.com/HenriquesLab/apt-rxiv-maker/apt-repo/pubkey.gpg | sudo gpg --dearmor -o /usr/share/keyrings/rxiv-maker.gpg
echo 'deb [arch=amd64 signed-by=/usr/share/keyrings/rxiv-maker.gpg] https://raw.githubusercontent.com/HenriquesLab/apt-rxiv-maker/apt-repo stable main' | sudo tee /etc/apt/sources.list.d/rxiv-maker.list
sudo apt update
sudo apt install rxiv-maker

Option B: Homebrew on Linux (All Distributions)

# Install Homebrew on Linux
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

# Install rxiv-maker with all dependencies
brew tap henriqueslab/rxiv-maker  
brew install rxiv-maker

# Verify installation
rxiv check-installation

🪟 Windows - WSL2 (Recommended)

Why WSL2? WSL2 provides a full Linux environment on Windows, ensuring 100% compatibility with rxiv-maker's LaTeX and Python dependencies without the complexity of native Windows installations.

Step 1: Install WSL2 with Ubuntu

# Run Windows PowerShell as Administrator
wsl --install -d Ubuntu-22.04
# Restart computer when prompted

Step 2: Setup rxiv-maker in WSL2 Ubuntu

# Update system packages
sudo apt update && sudo apt upgrade -y

# Option A: APT Repository (Recommended - includes all dependencies)
sudo apt install ca-certificates curl gpg
curl -fsSL https://raw.githubusercontent.com/HenriquesLab/apt-rxiv-maker/apt-repo/pubkey.gpg | sudo gpg --dearmor -o /usr/share/keyrings/rxiv-maker.gpg
echo 'deb [arch=amd64 signed-by=/usr/share/keyrings/rxiv-maker.gpg] https://raw.githubusercontent.com/HenriquesLab/apt-rxiv-maker/apt-repo stable main' | sudo tee /etc/apt/sources.list.d/rxiv-maker.list
sudo apt update
sudo apt install rxiv-maker

# Option B: Python pip (manual dependency management)
sudo apt install -y python3.11 python3-pip texlive-latex-recommended texlive-fonts-recommended
pip install rxiv-maker

# Verify installation
rxiv check-installation

Step 3: Access files between Windows and WSL2

# Access Windows files from WSL2
cd /mnt/c/Users/YourUsername/Documents

# Access WSL2 files from Windows Explorer
# Navigate to: \\wsl$\Ubuntu-22.04\home\yourusername

✅ Verification

# Check installation status
rxiv check-installation

# Create test project
rxiv init test-paper
cd test-paper

# Generate your first PDF
rxiv pdf

🌐 Alternative Methods

🐳 Docker (No local dependencies)

git clone https://github.com/henriqueslab/rxiv-maker.git
cd rxiv-maker
rxiv pdf --engine docker

🌐 Google Colab (Browser-based)

Essential Commands

rxiv pdf                            # Generate PDF
rxiv validate                       # Check manuscript
rxiv clean                          # Clean output files
rxiv arxiv                          # Prepare arXiv submission

Documentation

📚 Progressive Learning Path - 5min → 15min → Daily workflows

📖 CLI Reference - Complete command documentation

🔧 Troubleshooting - Common issues and solutions

Contributing

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

See CONTRIBUTING.md for details.

Citation

If you use Rxiv-Maker in 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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© 2025 Jacquemet and Henriques Labs | Rxiv-Maker
"Because science is hard enough without fighting with LaTeX."