CLI Reference¶

Complete command-line interface reference for Rxiv-Maker.

Quick Help

Use rxiv <command> --help for detailed help on any command.

🎯 Quick Command Overview¶

Command	Purpose	Common Use
`rxiv init`	Create new manuscript	Starting new paper
`rxiv pdf`	Generate PDF	Main workflow
`rxiv validate`	Check manuscript	Before submission
`rxiv arxiv`	Prepare arXiv package	arXiv uploads
`rxiv clean`	Clean build files	Fresh rebuild
`rxiv track-changes`	Compare versions	Revision tracking
`rxiv get-rxiv-preprint`	Clone example	Learning
`rxiv check-installation`	Verify setup	Troubleshooting

📖 Command Reference¶

rxiv init¶

Create a new manuscript project with template structure.

Basic UsageOptionsOutput

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

# Initialize in existing directory
rxiv init . --force

# Skip interactive prompts
rxiv init my-paper --no-interactive

my-paper/
├── 00_CONFIG.yml         # Manuscript metadata
├── 01_MAIN.md           # Main content
├── 02_SUPPLEMENTARY_INFO.md # Optional
├── 03_REFERENCES.bib    # Bibliography
├── FIGURES/             # Figure scripts
└── .gitignore           # Git ignore

Parameters: - <name> - Project name (creates directory) - --force - Initialize in non-empty directory - --no-interactive - Use defaults without prompts

rxiv pdf¶

Generate publication-ready PDF from your manuscript.

Standard BuildFast IterationFull RebuildDebugging

# Basic PDF generation
rxiv pdf

# With custom output directory
rxiv pdf --output-dir submission/

# Skip validation for faster builds
rxiv pdf --skip-validation

# Skip figure regeneration
rxiv pdf --skip-figures

# Both for maximum speed
rxiv pdf --skip-validation --skip-figures

# Force regenerate all figures
rxiv pdf --force-figures

# Clean and rebuild
rxiv clean && rxiv pdf --force-figures

# Verbose output
rxiv pdf --verbose

# Debug mode
rxiv pdf --debug

# Quiet mode
rxiv pdf --quiet

Options: - [manuscript_path] - Path to manuscript directory (default: current) - --output-dir <path> - Custom output directory (default: output/) - --force-figures - Regenerate all figures ignoring cache - --skip-validation - Skip manuscript validation (faster builds) - --skip-figures - Use existing figure files - --track-changes <tag> - Track changes against git tag - --verbose - Detailed build output - --quiet - Minimal output - --debug - Enable debug logging - --draft - Add draft watermark

Output Files: - manuscript.pdf - Publication-ready PDF - manuscript.tex - Generated LaTeX source - Figures/ - Generated figure files - logs/ - Build logs and diagnostics

rxiv validate¶

Check manuscript for errors and issues.

Basic ValidationSpecific Checks

# Quick validation
rxiv validate

# Detailed report
rxiv validate --detailed

# Skip DOI validation
rxiv validate --no-doi

# Check specific manuscript
rxiv validate path/to/manuscript/

Validation Checks:

✅ Structure - Required files and directory organization
✅ Syntax - Markdown formatting and enhanced syntax
✅ Citations - BibTeX entries and references
✅ Figures - File existence and script validity
✅ Cross-references - Figure, table, and equation references
✅ Mathematics - LaTeX math syntax
✅ Configuration - YAML metadata completeness
✅ Dependencies - Required packages and tools

Options: - [manuscript_path] - Path to manuscript (default: current) - --detailed - Show detailed validation report - --no-doi - Skip DOI validation for speed - --fix-common - Auto-fix common issues

Exit Codes: - 0 - No issues found - 1 - Warnings (proceed with caution) - 2 - Errors (must fix)

rxiv arxiv¶

Prepare arXiv-ready submission package.

Basic UsageCustom Options

# Generate arXiv package
rxiv arxiv

# Output: for_arxiv.zip

# Custom zip filename
rxiv arxiv --zip-filename my-submission.zip

# Don't create zip (just directory)
rxiv arxiv --no-zip

# Custom output directory
rxiv arxiv --output-dir submission/

Package Contents:

for_arxiv.zip
├── manuscript.tex       # LaTeX source
├── manuscript.bbl       # Compiled bibliography
├── Figures/            # All figures (PNG/PDF)
│   ├── figure_01.png
│   ├── figure_02.pdf
│   └── ...
└── [additional .sty/.cls if custom]

Options: - [manuscript_path] - Path to manuscript (default: current) - --output-dir <path> - Output directory - --arxiv-dir <path> - Custom arXiv staging directory - --zip-filename <name> - Custom zip filename - --no-zip - Skip zip creation

Submission Steps: 1. Run rxiv arxiv to generate package 2. Upload for_arxiv.zip to arXiv 3. Follow arXiv's processing instructions 4. Verify PDF compilation on arXiv

rxiv clean¶

Remove generated files and build artifacts.

Standard CleanAdvanced Options

# Clean output directory
rxiv clean

# Clean specific manuscript
rxiv clean path/to/manuscript/

# Clean all including cache
rxiv clean --all

# Clean only figures
rxiv clean --figures-only

# Clean only cache
rxiv clean --cache-only

# Clean and verify
rxiv clean && rxiv validate

Removes: - Generated PDFs - LaTeX auxiliary files (.aux, .log, .bbl, etc.) - Figure cache - Build logs - Temporary files

Options: - [manuscript_path] - Path to manuscript (default: current) - --all - Remove all generated files including cache - --figures-only - Only clean figure files - --cache-only - Only clean cache - --dry-run - Show what would be deleted without deleting

rxiv track-changes¶

Compare manuscript versions and generate diff.

Basic UsageOutput Options

# Compare current with previous version
rxiv track-changes v1.0 HEAD

# Compare two git tags
rxiv track-changes v1.0 v2.0

# Custom output filename
rxiv track-changes v1.0 v2.0 --output changes.pdf

# With custom color scheme
rxiv track-changes v1.0 v2.0 --color-changes

Features: - Visual diff with additions/deletions highlighted - Works with git tags, commits, or branches - Generates standalone PDF showing changes - Preserves formatting and figures - Useful for reviewer responses

Options: - <old_ref> - Old git reference (tag/commit/branch) - <new_ref> - New git reference (tag/commit/branch) - --output <filename> - Custom output filename - --color-changes - Use colored diff - --no-highlight - Plain text diff

rxiv get-rxiv-preprint¶

Clone the official example manuscript.

# Clone official example
rxiv get-rxiv-preprint

# Creates: manuscript-rxiv-maker/
cd manuscript-rxiv-maker/MANUSCRIPT
rxiv pdf

What You Get: - Complete example manuscript - Production-ready figures - Dynamic content examples - All features demonstrated - Published on arXiv

Repository: manuscript-rxiv-maker

rxiv check-installation¶

Verify Rxiv-Maker installation and dependencies.

Basic CheckDetailed Report

# Quick system check
rxiv check-installation

# Comprehensive diagnostics
rxiv check-installation --detailed

# Save report to file
rxiv check-installation --detailed > diagnostic_report.txt

Checks: - ✅ Rxiv-Maker version - ✅ Python installation and version - ✅ LaTeX distribution - ✅ Required LaTeX packages - ✅ Python packages (matplotlib, pandas, etc.) - ✅ System commands (git, etc.) - ✅ File permissions

Options: - --detailed - Show comprehensive diagnostic information - --fix-issues - Attempt to auto-fix common issues

🔧 Global Options¶

Available for all commands:

rxiv <command> --help      # Show command help
rxiv --version            # Show version
rxiv --config <path>      # Use custom config file
rxiv --no-color          # Disable colored output
rxiv --log-level <level> # Set logging level (DEBUG, INFO, WARNING, ERROR)

📋 Configuration File Reference¶

The 00_CONFIG.yml file controls manuscript metadata and settings:

Basic Metadata¶

# Document information
title: "Your Manuscript Title"
short_title: "Short Title"  # For headers (optional)
subtitle: "Optional Subtitle"  # (optional)

# Authors
authors:
  - name: "First Author"
    affiliation: "1"
    email: "[email protected]"
    corresponding: true
    orcid: "0000-0000-0000-0000"  # optional
  - name: "Second Author"
    affiliation: "1,2"
    orcid: "0000-0000-0000-0001"  # optional

# Affiliations
affiliations:
  - id: "1"
    name: "University Name"
    department: "Department Name"  # optional
    city: "City"  # optional
    country: "Country"  # optional
  - id: "2"
    name: "Second Institution"

Content Settings¶

# Abstract and keywords
abstract: "Your abstract text here. Can be multiple sentences."
keywords:
  - "keyword1"
  - "keyword2"
  - "keyword3"

# Bibliography
bibliography: "03_REFERENCES.bib"
citation_style: "numbered"  # or "author-date"

Formatting Options¶

# Document formatting
line_numbers: false         # Show line numbers
draft_watermark: false      # Add "DRAFT" watermark
two_column: false          # Use two-column layout
font_size: "11pt"          # Font size: 10pt, 11pt, 12pt
paper_size: "a4"           # a4 or letter

# Figure settings
figure_dpi: 300            # Figure resolution
figure_format: "png"       # png or pdf

# Page layout
margin_top: "2.5cm"
margin_bottom: "2.5cm"
margin_left: "2.5cm"
margin_right: "2.5cm"

Advanced Settings¶

# LaTeX customization
latex_engine: "pdflatex"   # pdflatex or xelatex
latex_class: "article"     # Document class
latex_extra_preamble: |    # Custom LaTeX commands
  \usepackage{mypackage}
  \newcommand{\mycmd}{text}

# Build settings
cache_figures: true        # Enable figure caching
parallel_figures: 4        # Parallel figure generation
clean_aux_files: true      # Auto-clean auxiliary files

# Submission settings
arxiv_category: "cs.LG"    # arXiv category
preprint_server: "arxiv"   # arxiv, biorxiv, etc.

🔄 Common Workflows¶

Daily Writing¶

# Start of session
rxiv validate
rxiv pdf

# Make changes to 01_MAIN.md

# Quick rebuild
rxiv pdf --skip-validation

# End of session
rxiv validate --detailed
git add . && git commit -m "Update results section"

Figure Development¶

# Test figure script
python FIGURES/my_figure.py

# Generate PDF with new figure
rxiv pdf --force-figures

# If figure looks good, cache it
rxiv pdf  # Automatic caching

Pre-Submission¶

# Full validation
rxiv validate --detailed

# Clean rebuild
rxiv clean
rxiv pdf --force-figures

# Generate arXiv package
rxiv arxiv

# Track changes if revision
rxiv track-changes v1.0 HEAD

Troubleshooting¶

# Check installation
rxiv check-installation --detailed

# Clean and rebuild
rxiv clean --all
rxiv pdf --verbose

# Debug specific issue
rxiv pdf --debug > debug.log 2>&1

💡 Tips and Best Practices¶

Performance Optimization¶

# Fast iteration during writing
rxiv pdf --skip-validation --skip-figures

# Use parallel figure generation
export RXIV_PARALLEL_JOBS=4
rxiv pdf --force-figures

# Clean cache periodically
rxiv clean --cache-only

Git Integration¶

# Pre-commit validation
echo "rxiv validate" > .git/hooks/pre-commit
chmod +x .git/hooks/pre-commit

# Tag releases
git tag -a v1.0 -m "Initial submission"
git push --tags

# Track changes for revision
rxiv track-changes v1.0 v1.1

Collaboration¶

# Validate before pushing
rxiv validate --detailed

# Generate PDF for collaborators
rxiv pdf --output-dir release/

# Share specific version
git tag -a review-v1 -m "For review"

🆘 Getting Help¶

Command-Specific Help¶

# Get help for specific command
rxiv pdf --help
rxiv validate --help
rxiv init --help

Documentation¶

Installation Guide - Setup and prerequisites
First Manuscript - Getting started
User Guide - Complete feature documentation
Troubleshooting - Common issues

Community Support¶

GitHub Discussions - Q&A and community help
GitHub Issues - Bug reports and feature requests
Example Repository - Working example

📚 Additional Resources¶

Getting Started

New to Rxiv-Maker?

Installation First Manuscript
User Guide

Complete feature documentation

User Guide
Advanced

Advanced features

Python Execution LaTeX Injection
Community

Get help and support

Troubleshooting GitHub Discussions

Need more help? Check the Troubleshooting Guide or ask in GitHub Discussions.