Manubot provides Python utilities for automated scholarly manuscript generation, targeting researchers and academics. It streamlines the process of manuscript preparation, citation management, and AI-assisted revision, aiming to enhance reproducibility and open science practices.

How It Works

Manubot utilizes a command-line interface with subcommands for process, cite, webpage, and ai-revision. The process command handles manuscript content preparation for Pandoc, including bibliographic processing and templating. The cite command retrieves and formats bibliographic metadata from persistent identifiers like DOIs. The ai-revision command leverages OpenAI models for automated text improvements.

Quick Start & Requirements

• Install via pip: pip install --upgrade manubot
• Requires Pandoc to be installed separately.
• The pandoc-manubot-cite filter requires panflute (version compatibility with Pandoc is crucial, e.g., pip install panflute==1.12.5 for Pandoc 2.9).
• Official documentation: https://manubot.github.io/manubot/

Highlighted Details

• Supports citation by persistent identifiers (DOI, PubMed ID, PMC, arXiv) via the pandoc-manubot-cite filter.
• Automates manuscript deployment to a webpage directory structure.
• Integrates AI models (e.g., GPT-3) for manuscript revision.
• Allows for manual reference metadata loading in JSON or YAML formats.

Maintenance & Community

• Development supported by grants from the Alfred P. Sloan Foundation and the Gordon & Betty Moore Foundation.
• Pre-commit hooks are used for development environment checks.
• Release process is managed via GitHub Actions for PyPI deployment.

Licensing & Compatibility

• Licensed under a free/libre and open-source license (LICENSE.md).
• Explicitly welcomes adoption by academic and commercial entities.

Limitations & Caveats

• Citation and reference processing in manubot process is now handled by the pandoc-manubot-cite filter, requiring explicit skipping of citations via --skip-citations.
• AI revision features incur costs associated with OpenAI API usage.