Scientific Writer Documentation

Welcome to the Scientific Writer documentation! Scientific Writer is a deep research and writing tool that combines the power of AI-driven deep research with well-formatted written outputs of various forms—from scientific papers and grant proposals to clinical reports and conference presentations.

This guide will help you navigate the available resources.

📚 Documentation Overview

💡 New! Check out the Complete Documentation Index for a comprehensive navigation guide with learning paths and quick reference.

For New Users

Start here to get up and running quickly:

1. Main README - Quick start, installation, and basic usage
2. Complete Features Guide - Comprehensive overview of all capabilities
3. Skills Overview - Available skills and what they can do
4. Plugin Installation - Claude Code plugin setup (recommended)

For Developers

Integrate Scientific Writer into your Python projects:

1. API Reference - Full programmatic API documentation
2. Development Guide - Contributing and development setup
3. Releasing Guide - Versioning and publishing workflow

For Troubleshooting

Having issues? Check these resources:

1. Troubleshooting Guide - Common issues and solutions
2. Changelog - Version history and breaking changes

🎯 Usage Modes

Scientific Writer can be used in three ways:

1. 🌟 Claude Code Plugin (Recommended) - Use directly in your IDE

   • One-command setup: /scientific-writer:init
   • All 19+ skills available immediately
   • No CLI required
   • See: Plugin Installation Guide

2. 💻 Command Line Interface (CLI) - Interactive scientific writing

   • Run: scientific-writer or uv run scientific-writer
   • Full-featured interactive mode
   • See: CLI Quick Start

3. 🔧 Python API - Programmatic integration

   • Import: from scientific_writer import generate_paper
   • Async API with progress streaming
   • See: API Reference

🎯 Quick Navigation by Task

I Want to Generate a...

Document Type	Start Here
Scientific Paper	README Quick Start → Features: Scientific Papers
Grant Proposal	Features: Grant Proposals → Skills: Research Grants
Research Poster	Features: Research Posters → Skills: LaTeX Posters
Literature Review	Features: Literature Reviews → Skills: Literature Review
Scientific Diagram	Features: Scientific Schematics → Skills: Scientific Schematics

I Want to...

Task	Documentation
Use the Python API	API Reference → README: API Usage
Understand research lookup	Features: Real-Time Research Lookup → API: Research Lookup
Auto-detect existing papers	Features: Intelligent Paper Detection
Process data files	Features: Data & File Integration → README: File Handling
Convert documents	Features: Document Conversion → Skills: MarkItDown
Get peer review	Features: Peer Review with ScholarEval → Skills: Scholar Evaluation
Fix an issue	Troubleshooting Guide
Contribute code	Development Guide

📖 Complete Documentation Index

User Documentation

1. README.md - Main package documentation

   • Quick Start
   • Installation
   • Features Overview
   • Basic Usage (CLI and API)
   • Quick Reference
   • Examples

2. FEATURES.md - Complete features guide

   • Document Generation (papers, posters, grants, reviews, schematics)
   • AI-Powered Capabilities (research lookup, peer review, editing)
   • Intelligent Paper Detection
   • Data & File Integration
   • Document Conversion
   • Developer Features

3. API.md - Programmatic API reference

   • API Functions
   • Data Models
   • Usage Patterns
   • Advanced Features
   • Environment Variables
   • Error Handling
   • Best Practices

4. SKILLS.md - Available skills and capabilities

   • Writing Skills (scientific writing, literature review, peer review, scholar evaluation, grants, posters, schematics)
   • Document Manipulation Skills (MarkItDown, DOCX, PDF, PPTX, XLSX)
   • Usage Examples

5. TROUBLESHOOTING.md - Common issues and solutions

   • Installation issues
   • LaTeX compilation errors
   • API key problems
   • Runtime errors
   • Performance issues

Developer Documentation

6. DEVELOPMENT.md - Development and contributing

   • Setting up development environment
   • Code structure
   • Testing
   • Contributing guidelines

7. RELEASING.md - Version management and publishing

   • Versioning strategy
   • Release process
   • Publishing to PyPI
   • Git tagging

8. CHANGELOG.md - Version history

   • Release notes
   • Breaking changes
   • New features
   • Bug fixes

Advanced

9. CLAUDE.md - System instructions for the agent
   • Agent behavior guidelines
   • Skill integration
   • Tool usage patterns

🔍 Search Tips

When looking for specific information:

By Topic

• API usage: Search in API.md
• CLI commands: Search in README.md and FEATURES.md
• Skills/capabilities: Search in SKILLS.md
• Errors/issues: Search in TROUBLESHOOTING.md
• Recent changes: Check CHANGELOG.md

By Keywords

• generate_paper() → API.md
• scientific-writer → README.md
• NSF/NIH/DOE/DARPA → SKILLS.md
• CONSORT/circuit/pathway → SKILLS.md
• MarkItDown → SKILLS.md
• ScholarEval → SKILLS.md
• data files → FEATURES.md
• research lookup → FEATURES.md

💡 Getting Help

If you can't find what you're looking for:

1. Check the Troubleshooting Guide
2. Search the Changelog for recent updates
3. Review the Skills Overview to see all capabilities
4. Open an issue on GitHub with your question

🚀 Quick Links

• Installation
• CLI Quick Start
• API Quick Start
• Common Commands
• Example Code
• PyPI Package

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Last Updated: January 22, 2025 (v2.7.0)