https://github.com/henriqueslab/rxiv-maker
Rxiv-Maker is a GitHub-native framework that converts markdown into a publication-ready PDF. It automates scientific preprint generation with a focus on reproducibility and version control
https://github.com/henriqueslab/rxiv-maker
article-template preprint preprints publishing
Last synced: 5 days ago
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Rxiv-Maker is a GitHub-native framework that converts markdown into a publication-ready PDF. It automates scientific preprint generation with a focus on reproducibility and version control
- Host: GitHub
- URL: https://github.com/henriqueslab/rxiv-maker
- Owner: HenriquesLab
- License: mit
- Created: 2025-06-11T10:44:12.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2026-06-09T10:03:35.000Z (5 days ago)
- Last Synced: 2026-06-09T11:23:06.285Z (5 days ago)
- Topics: article-template, preprint, preprints, publishing
- Language: Python
- Homepage: https://rxiv-maker.henriqueslab.org
- Size: 23.3 MB
- Stars: 33
- Watchers: 0
- Forks: 5
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Codeowners: .github/CODEOWNERS
Awesome Lists containing this project
README
[](https://doi.org/10.48550/arXiv.2508.00836)
[](https://github.com/henriqueslab/rxiv-maker/blob/main/LICENSE)
[](https://github.com/HenriquesLab/rxiv-maker/stargazers)
# Rxiv-Maker
Rxiv-Maker converts enhanced Markdown into professional PDFs with automated figure generation, citation management, and LaTeX typesetting. Write in Markdown, get publication-ready output for arXiv, bioRxiv, and other preprint servers.
## Installation
**macOS** (includes LaTeX automatically):
```bash
brew install henriqueslab/formulas/rxiv-maker
```
**Linux / Windows (WSL)**:
```bash
pipx install rxiv-maker # or: uv tool install rxiv-maker
```
Verify setup:
```bash
rxiv check-installation
```
LaTeX is required. See the [installation guide](https://rxiv-maker.henriqueslab.org/getting-started/installation/) for platform-specific LaTeX instructions.
## Quick Start
```bash
rxiv init my-paper
cd my-paper
rxiv pdf
```
To explore a complete working example:
```bash
rxiv get-rxiv-preprint
cd manuscript-rxiv-maker/MANUSCRIPT
rxiv pdf
```
## Features
- **Enhanced Markdown** - Scientific cross-references (`@fig:plot`, `@eq:formula`), auto-numbered figures/tables/equations, LaTeX math
- **Automated figures** - Python and R scripts executed during PDF generation, with intelligent caching
- **Executable code blocks** - Jupyter-like `{{py:exec}}` and `{{py:get variable}}` for live data in manuscripts
- **Citation management** - BibTeX with `[@citation]` syntax, multiple styles, inline DOI resolution
- **Dual output** - PDF and DOCX from the same source
- **arXiv/bioRxiv submission** - Generate submission packages automatically
- **Track changes** - Visual diff between manuscript versions
- **VS Code extension** - Syntax highlighting, citation autocompletion, one-click builds
## Documentation
**[rxiv-maker.henriqueslab.org](https://rxiv-maker.henriqueslab.org)** - Installation, guides, CLI reference, troubleshooting.
For contributors: **[CONTRIBUTING.md](CONTRIBUTING.md)**
## Ecosystem
| Repository | Purpose |
|------------|---------|
| [rxiv-maker](https://github.com/HenriquesLab/rxiv-maker) | Core CLI tool |
| [docker-rxiv-maker](https://github.com/HenriquesLab/docker-rxiv-maker) | Pre-configured container with LaTeX |
| [manuscript-rxiv-maker](https://github.com/HenriquesLab/manuscript-rxiv-maker) | Complete example (arXiv:2508.00836) |
| [vscode-rxiv-maker](https://marketplace.visualstudio.com/items?itemName=HenriquesLab.rxiv-maker) | VS Code extension |
## Publications
| Publication | Venue |
|-------------|-------|
| [Rxiv-Maker: an automated template engine for streamlined scientific publications](https://arxiv.org/abs/2508.00836) | arXiv (2025) |
| [Customizable FDM-based zebrafish embryo mold for live imaging](https://doi.org/10.1101/2025.11.24.689779) | bioRxiv (2025) |
| [mAIcrobe: an open-source framework for high-throughput bacterial image analysis](https://doi.org/10.1101/2025.10.21.683709) | bioRxiv (2025) |
| [Filopodome proteomics identifies CCT8 as a MYO10 interactor critical for filopodia functions](https://doi.org/10.64898/2025.12.03.691809) | bioRxiv (2025) |
| [EZInput: A Cross-Environment Python Library for Easy UI Generation in Scientific Computing](https://arxiv.org/abs/2601.08859) | arXiv (2026) |
| [Packaging Jupyter notebooks as installable desktop apps using LabConstrictor](https://arxiv.org/abs/2603.10704) | arXiv (2026) |
Using Rxiv-Maker for your research? [Let us know](https://github.com/HenriquesLab/rxiv-maker/issues/new?template=publication_submission.yml).
## Community
- [GitHub Discussions](https://github.com/henriqueslab/rxiv-maker/discussions) - Questions and tips
- [Issues](https://github.com/henriqueslab/rxiv-maker/issues) - Bug reports and feature requests
- [Google Colab](https://colab.research.google.com/github/HenriquesLab/rxiv-maker/blob/main/notebooks/rxiv_maker_colab.ipynb) - Try without installing
## Citation
```bibtex
@misc{saraiva_2025_rxivmaker,
title={Rxiv-Maker: an automated template engine for streamlined scientific publications},
author={Bruno M. Saraiva and Ant\'{o}nio 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](LICENSE) for details.