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Your First Manuscript

Create your first scientific PDF with Rxiv-Maker.

Prerequisites

Step 1: Install and Verify Rxiv-Maker

Quick Installation

pipx install rxiv-maker

Alternative Installation

Need other installation methods? See the complete installation guide for different platforms and options.

Verify Installation

rxiv --version && rxiv check-installation

Expected output: 

rxiv-maker vX.Y.Z
Checking Python environment... OK
Checking LaTeX installation... OK
Checking system dependencies... OK
All systems ready!

Missing LaTeX?

If check-installation reports missing LaTeX, see the LaTeX installation section before proceeding.

Step 2: Create Your First Manuscript

Initialize Project

rxiv init my-first-paper
cd my-first-paper

Working Directory

Make sure you are inside the my-first-paper directory before running any rxiv commands.

This creates the following file structure: 

my-first-paper/
├── 00_CONFIG.yml              # Project configuration
├── 01_MAIN.md                 # Your main manuscript
├── 02_SUPPLEMENTARY_INFO.md   # Optional supplementary content
├── 03_REFERENCES.bib          # Bibliography
├── FIGURES/                   # Scripts for generating figures
│   └── Figure__example.mmd    # Example Mermaid diagram
└── .gitignore

Understanding the Structure

File Purpose
00_CONFIG.yml Title, authors, affiliations, and formatting settings
01_MAIN.md Your manuscript content in enhanced Markdown
02_SUPPLEMENTARY_INFO.md Optional supplementary material
03_REFERENCES.bib Academic citations in BibTeX format
FIGURES/ Python/R scripts or static images for figures

Configuring Your Manuscript

Open 00_CONFIG.yml and update the essential fields:

title: "Your Actual Manuscript Title"

authors:
  - name: "Your Name"
    email: "[email protected]"
    orcid: "0000-0000-0000-0000"
    affiliation: "Your Institution"

keywords:
  - your-keyword-1
  - your-keyword-2

citation_style: "numbered"   # or "author-date"

For all available configuration options, see the Configuration Reference.

Step 3: Write Content

Open 01_MAIN.md in your editor. The generated template contains example sections (Abstract, Introduction, Methods, Results, Discussion, Conclusion) with placeholder text. Replace it with your content.

Key syntax to know:

## Abstract

Your abstract text here.

## Introduction

Citations use bracket syntax: [@smith2023; @jones2024]

Figures reference scripts in the FIGURES/ directory:

![Caption text](FIGURES/figure_script.py)
{#fig:label}

Cross-reference with: See Figure @fig:label

Step 4: Generate Your PDF

rxiv pdf

The build process:

  1. Validates your manuscript structure
  2. Processes enhanced Markdown syntax
  3. Generates figures from scripts
  4. Handles citations and cross-references
  5. Compiles to professional PDF

Your PDF appears in output/.

Success Check

You should now have:

  • A complete manuscript project structure
  • A generated PDF in the output/ folder
  • A working Rxiv-Maker workflow

What's Next?

# Edit and rebuild
edit 00_CONFIG.yml          # Update title and authors
edit 01_MAIN.md             # Add your content
rxiv pdf                    # Regenerate PDF

# Add citations
edit 03_REFERENCES.bib      # Add BibTeX entries

rxiv validate              # Check for issues
rxiv pdf --verbose         # See detailed output
rxiv check-installation    # Verify dependencies

See the Troubleshooting Guide for common issues.