{"id":31060619,"url":"https://github.com/henriqueslab/rxiv-maker","last_synced_at":"2026-06-09T12:00:27.639Z","repository":{"id":300937712,"uuid":"1000151388","full_name":"HenriquesLab/rxiv-maker","owner":"HenriquesLab","description":"Rxiv-Maker is a GitHub-native framework that converts markdown into a publication-ready PDF. 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Write in Markdown, get publication-ready output for arXiv, bioRxiv, and other preprint servers.\n\n## Installation\n\n**macOS** (includes LaTeX automatically):\n```bash\nbrew install henriqueslab/formulas/rxiv-maker\n```\n\n**Linux / Windows (WSL)**:\n```bash\npipx install rxiv-maker    # or: uv tool install rxiv-maker\n```\n\nVerify setup:\n```bash\nrxiv check-installation\n```\n\nLaTeX is required. See the [installation guide](https://rxiv-maker.henriqueslab.org/getting-started/installation/) for platform-specific LaTeX instructions.\n\n## Quick Start\n\n```bash\nrxiv init my-paper\ncd my-paper\nrxiv pdf\n```\n\nTo explore a complete working example:\n```bash\nrxiv get-rxiv-preprint\ncd manuscript-rxiv-maker/MANUSCRIPT\nrxiv pdf\n```\n\n## Features\n\n- **Enhanced Markdown** - Scientific cross-references (`@fig:plot`, `@eq:formula`), auto-numbered figures/tables/equations, LaTeX math\n- **Automated figures** - Python and R scripts executed during PDF generation, with intelligent caching\n- **Executable code blocks** - Jupyter-like `{{py:exec}}` and `{{py:get variable}}` for live data in manuscripts\n- **Citation management** - BibTeX with `[@citation]` syntax, multiple styles, inline DOI resolution\n- **Dual output** - PDF and DOCX from the same source\n- **arXiv/bioRxiv submission** - Generate submission packages automatically\n- **Track changes** - Visual diff between manuscript versions\n- **VS Code extension** - Syntax highlighting, citation autocompletion, one-click builds\n\n## Documentation\n\n**[rxiv-maker.henriqueslab.org](https://rxiv-maker.henriqueslab.org)** - Installation, guides, CLI reference, troubleshooting.\n\nFor contributors: **[CONTRIBUTING.md](CONTRIBUTING.md)**\n\n## Ecosystem\n\n| Repository | Purpose |\n|------------|---------|\n| [rxiv-maker](https://github.com/HenriquesLab/rxiv-maker) | Core CLI tool |\n| [docker-rxiv-maker](https://github.com/HenriquesLab/docker-rxiv-maker) | Pre-configured container with LaTeX |\n| [manuscript-rxiv-maker](https://github.com/HenriquesLab/manuscript-rxiv-maker) | Complete example (arXiv:2508.00836) |\n| [vscode-rxiv-maker](https://marketplace.visualstudio.com/items?itemName=HenriquesLab.rxiv-maker) | VS Code extension |\n\n## Publications\n\n| Publication | Venue |\n|-------------|-------|\n| [Rxiv-Maker: an automated template engine for streamlined scientific publications](https://arxiv.org/abs/2508.00836) | arXiv (2025) |\n| [Customizable FDM-based zebrafish embryo mold for live imaging](https://doi.org/10.1101/2025.11.24.689779) | bioRxiv (2025) |\n| [mAIcrobe: an open-source framework for high-throughput bacterial image analysis](https://doi.org/10.1101/2025.10.21.683709) | bioRxiv (2025) |\n| [Filopodome proteomics identifies CCT8 as a MYO10 interactor critical for filopodia functions](https://doi.org/10.64898/2025.12.03.691809) | bioRxiv (2025) |\n| [EZInput: A Cross-Environment Python Library for Easy UI Generation in Scientific Computing](https://arxiv.org/abs/2601.08859) | arXiv (2026) |\n| [Packaging Jupyter notebooks as installable desktop apps using LabConstrictor](https://arxiv.org/abs/2603.10704) | arXiv (2026) |\n\nUsing Rxiv-Maker for your research? [Let us know](https://github.com/HenriquesLab/rxiv-maker/issues/new?template=publication_submission.yml).\n\n## Community\n\n- [GitHub Discussions](https://github.com/henriqueslab/rxiv-maker/discussions) - Questions and tips\n- [Issues](https://github.com/henriqueslab/rxiv-maker/issues) - Bug reports and feature requests\n- [Google Colab](https://colab.research.google.com/github/HenriquesLab/rxiv-maker/blob/main/notebooks/rxiv_maker_colab.ipynb) - Try without installing\n\n## Citation\n\n```bibtex\n@misc{saraiva_2025_rxivmaker,\n  title={Rxiv-Maker: an automated template engine for streamlined scientific publications},\n  author={Bruno M. Saraiva and Ant\\'{o}nio D. Brito and Guillaume Jaquemet and Ricardo Henriques},\n  year={2025},\n  eprint={2508.00836},\n  archivePrefix={arXiv},\n  url={https://arxiv.org/abs/2508.00836}\n}\n```\n\n## License\n\nMIT License - see [LICENSE](LICENSE) for details.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhenriqueslab%2Frxiv-maker","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhenriqueslab%2Frxiv-maker","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhenriqueslab%2Frxiv-maker/lists"}