lixplore-cli 1.0.1

Academic Literature Search & Export CLI Tool

Lixplore

Academic Literature Search & Export CLI Tool

Search across multiple academic databases (PubMed, arXiv, Crossref, DOAJ, EuropePMC) with Boolean operators, smart selection, and export to 8 formats including EndNote, Excel, and BibTeX.

📚 Complete Documentation | 🐛 Report Issues

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✨ Features

Core Features

• 🔍 Multi-Source Search - Search 5 academic databases simultaneously (PubMed, arXiv, Crossref, DOAJ, EuropePMC)
• 🔤 Boolean Operators - Advanced queries with AND, OR, NOT, parentheses
• 📊 Smart Sorting - Sort by relevance, newest, oldest, journal, or author
• 🔢 Smart Selection - Export odd/even, ranges, first/last N articles
• 💾 8 Export Formats - CSV, Excel, JSON, BibTeX, RIS, EndNote, XML
• 📖 Review Mode - View articles in separate terminal windows
• 🎯 Deduplication - Advanced duplicate removal with multiple strategies
• 📁 Organized Exports - Auto-organized folders by format type

Advanced Features

• 📥 PDF Downloads - Automatic PDF downloads from PMC, arXiv, Unpaywall, and SciHub (optional)
• 🔗 PDF Link Display - Show clickable PDF links for open access articles in terminal (NEW!)
• 📚 Reference Manager Integration - Direct Zotero API integration and Mendeley RIS export
• 📊 Statistics Dashboard - Comprehensive analytics with visualizations (publication trends, top journals, top authors)
• 🎨 Interactive TUI Mode - Browse, select, and export with an interactive terminal UI
• 📝 Citation Export - Format citations in APA, MLA, Chicago, IEEE styles
• 🔧 Custom API Integration - Plugin architecture for any REST API (Springer, BASE, etc.)
• 💡 Metadata Enrichment - Auto-enrich results from multiple APIs (Crossref, PubMed, arXiv)
• 💾 Smart Caching - 7-day cache with automatic expiration
• 📄 Pagination - Browse large result sets with automatic pagination
• 🎯 Export Profiles - Save and reuse export configurations
• 📋 Export Templates - Predefined templates (Nature, Science, IEEE)
• 🗜️ Export Compression - ZIP compression for batch exports

Documentation

• 📚 Complete Documentation Site - Comprehensive online documentation
• 📖 32+ Documentation Pages - Getting started, user guides, command reference, examples
• 🔍 All 95 Flags Documented - Detailed examples for every command-line flag
• 🎓 Step-by-Step Tutorials - From installation to advanced workflows
• 💡 Quick Examples - Built-in examples with --examples flag
• 📄 Man Page - Traditional Unix man page included

🚀 Interactive Interface

• 🎨 Enhanced TUI Mode - Beautiful text-based interface with search, browse, annotate, and export
• 📝 Annotation System - Rate, tag, comment, and organize your research library
• 📊 Statistics Dashboard - Visualize publication trends and analytics
• 💾 Smart Export - Export to 8 formats with intelligent deduplication

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🎯 Two Ways to Use Lixplore

1️⃣ Interactive TUI Mode - Visual Interface (Recommended)

Perfect for exploration, learning, and complex workflows

# Launch interactive TUI
lixplore --tui

# Or simply run without arguments
lixplore

# Navigate with arrow keys, search visually, annotate results, view stats

Features:

• Visual search interface with source selection
• Browse and select articles interactively
• Annotation management with ratings and tags
• Statistics dashboard with visualizations
• Export functionality with format selection
• Beautiful terminal UI with keyboard shortcuts

2️⃣ Command Line Mode - Direct Commands

Perfect for scripting, automation, and quick searches

# Quick search and export
lixplore -P -q "machine learning" -m 20 -X xlsx

# Advanced workflow
lixplore -A -q "COVID-19" -m 50 -D --sort newest -X csv

Note: Legacy shell (--shell) and wizard (--wizard) modes are still available but deprecated in favor of the enhanced TUI mode.

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🆕 What's New in Version 2.0

Lixplore has been massively upgraded with powerful new features:

📥 PDF Download & Link Display

Download PDFs automatically with smart fallback chain:

• PubMed Central (open access)
• arXiv (preprints)
• DOI Resolution via Unpaywall
• SciHub fallback (optional, user-configured)

lixplore -P -q "open access" -m 10 --download-pdf

Show PDF Links directly in search results (NEW!):

• Display clickable PDF links for open access articles
• Works in modern terminals (iTerm2, GNOME Terminal, Windows Terminal)
• No download required - click to open in browser

lixplore -x -q "machine learning" -m 10 --show-pdf-links

📚 Reference Manager Integration

Direct integration with your favorite reference managers:

• Zotero: API integration with collection support
• Mendeley: RIS export for easy import

Setup Zotero (one-time):

1. Get API key: https://www.zotero.org/settings/keys
2. Configure: lixplore --configure-zotero YOUR_API_KEY YOUR_USER_ID

Usage:

# Add to Zotero library
lixplore -P -q "research" -m 10 --add-to-zotero

# Add to specific collection
lixplore -P -q "AI" -m 20 --add-to-zotero --zotero-collection 4FCVPNAP

📊 Statistics Dashboard

Comprehensive analytics with beautiful ASCII visualizations:

• Publication trends by year
• Top journals and authors
• Source distribution
• Metadata completeness

lixplore -P -q "AI" -m 100 --stat

🎨 Interactive TUI Mode

Browse results with a rich interactive terminal interface:

• Navigate pages with keyboard
• Select articles visually
• Export selected items
• View detailed information

lixplore -P -q "machine learning" -m 50 -i

🔧 Custom API Integration

Add ANY API source via simple JSON configuration:

• No code modification needed
• Supports Springer, BASE, and more
• Plugin architecture for extensibility

lixplore --custom-api springer -q "quantum physics" -m 20

💡 Smart Enhancements

• Metadata Enrichment: Auto-fill missing data from multiple APIs
• Export Profiles: Save and reuse export configurations
• Citation Formatting: Export as APA, MLA, Chicago, IEEE
• Batch Export: Export to multiple formats simultaneously
• Deduplication Strategies: Multiple algorithms with customization

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🚀 Quick Start

Installation

# From PyPI (recommended)
pip install lixplore-cli

# From source
git clone https://github.com/pryndor/Lixplore_cli.git
cd Lixplore_cli
pip install -e .

Basic Usage

# Search PubMed
lixplore -P -q "cancer treatment" -m 10

# Search all sources with deduplication
lixplore -A -q "COVID-19" -m 50 -D

# Export to Excel
lixplore -P -q "diabetes" -m 20 -X xlsx -o results.xlsx

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📚 Documentation

📖 Complete Online Documentation

Visit our comprehensive documentation site for:

• Getting Started Guides - Installation and first search tutorial
• User Guides - Search, filtering, export, annotations, PDF management
• Command Reference - All 95 flags with detailed examples
• Advanced Features - Automation, AI integration, Zotero, custom APIs
• Examples - Common workflows, use cases, tool integrations

Quick Help

# Show quick examples
lixplore --examples

# Show complete help
lixplore --help

# View man page (after installing)
man lixplore

# Browse online documentation
# https://pryndor.github.io/Lixplore_cli/

Key Commands

Search Sources

-P, --pubmed       # Search PubMed
-C, --crossref     # Search Crossref
-J, --doaj         # Search DOAJ
-E, --europepmc    # Search EuropePMC
-x, --arxiv        # Search arXiv
-A, --all          # Search all sources
-s PX              # Combined (PubMed + arXiv)

Boolean Operators

# AND - both terms required
lixplore -P -q "cancer AND treatment" -m 10

# OR - either term
lixplore -P -q "cancer OR tumor" -m 10

# NOT - exclude term
lixplore -P -q "diabetes NOT type1" -m 10

# Complex queries
lixplore -P -q "(cancer OR tumor) AND treatment" -m 20

Export Formats

-X csv      # CSV format
-X xlsx     # Excel with formatting
-X json     # JSON structured data
-X bibtex   # BibTeX for LaTeX
-X ris      # RIS for reference managers
-X enw      # EndNote Tagged (recommended)
-X endnote  # EndNote XML
-X xml      # Generic XML

Smart Selection

# Export odd-numbered articles
lixplore -P -q "research" -m 50 -S odd -X csv

# Export first 10 articles
lixplore -P -q "cancer" -m 50 -S first:10 -X xlsx

# Export range
lixplore -P -q "study" -m 50 -S 10-20 -X enw

# Mixed patterns
lixplore -P -q "science" -m 50 -S 1 3 5-10 odd -X csv

Sorting

--sort newest   # Latest publications first
--sort oldest   # Earliest publications first
--sort journal  # Alphabetical by journal
--sort author   # Alphabetical by author

Review Mode

# Step 1: Search
lixplore -P -q "aspirin" -m 10

# Step 2: Review in separate terminal
lixplore -R 2

# Close review window: Press 'q' or Ctrl+C

PDF Links

# Show clickable PDF links in results
lixplore -x -q "neural networks" -m 10 --show-pdf-links

# Combine with abstracts
lixplore -P -q "cancer" -m 20 -a --show-pdf-links

# Multi-source with PDF links
lixplore -A -q "COVID-19" -m 50 -D --show-pdf-links

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🎯 Use Cases

1. Literature Review

# Search all sources, deduplicate, sort newest, export top 20
lixplore -A -q "machine learning healthcare" -m 100 -D \
  --sort newest -S first:20 -X xlsx -o ml_healthcare.xlsx

2. Boolean Search with Export

# Advanced query with multiple conditions
lixplore -P -q "(COVID-19 OR coronavirus) AND (vaccine OR treatment)" \
  -m 50 --sort newest -X enw -o covid_papers.enw

3. Quick Sample Review

# Search 50, export odd-numbered (25 articles)
lixplore -A -q "cancer immunotherapy" -m 50 -D \
  -S odd -X csv -o cancer_sample.csv

4. Historical Research

# Sort by oldest to study evolution
lixplore -P -q "diabetes" -m 100 --sort oldest \
  -X xlsx -o diabetes_history.xlsx

5. Multi-Step Workflow

# 1. Search
lixplore -P -q "neuroscience" -m 20

# 2. Review specific articles
lixplore -R 2 5 8

# 3. Export selected
lixplore -P -q "neuroscience" -m 20 -S 2 5 8 -X enw

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📊 Export Formats

All exports are automatically organized into folders:

exports/
├── csv/              # CSV files
├── excel/            # Excel files (.xlsx)
├── json/             # JSON files
├── bibtex/           # BibTeX files
├── ris/              # RIS files
├── endnote_tagged/   # EndNote Tagged (.enw)
├── endnote_xml/      # EndNote XML files
└── xml/              # Generic XML files

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🔧 Advanced Features

Smart Selection Patterns

Pattern	Syntax	Example	Result
Specific	1 3 5	-S 1 3 5	Articles #1, #3, #5
Range	1-10	-S 1-10	Articles #1 through #10
Odd	odd	-S odd	Odd-numbered articles
Even	even	-S even	Even-numbered articles
First N	first:10	-S first:10	First 10 articles
Last N	last:5	-S last:5	Last 5 articles
Mixed	1 3 5-10	-S 1 3 5-10	Combined patterns

Sort Options

• relevant - Default API order (most relevant first)
• newest - Latest publications (2025 → 2020)
• oldest - Earliest publications (1990 → 2000)
• journal - Alphabetical by journal name
• author - Alphabetical by first author

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🖥️ Platform Support

Lixplore works on all major platforms:

• ✅ Linux (all distributions)
• ✅ macOS (10.14+)
• ✅ Windows (10+)

Platform-Specific Notes

Linux

Review feature works with: xfce4-terminal, gnome-terminal, konsole, xterm, alacritty, kitty

macOS

Review feature uses Terminal.app

Windows

Review feature uses cmd.exe

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📦 Installation Methods

Method 1: PyPI (Recommended)

pip install lixplore-cli

Method 2: From Source

git clone https://github.com/pryndor/Lixplore_cli.git
cd Lixplore_cli
pip install -e .

Method 3: Using pipx (Isolated)

pipx install lixplore

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🔍 Requirements

• Python 3.7 or higher
• Internet connection for API access
• Terminal emulator (for review feature)

Dependencies

• biopython - PubMed/NCBI API access
• requests - HTTP requests
• litstudy - Literature study support
• openpyxl - Excel export support

All dependencies are automatically installed.

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📖 Man Page

After installation, install the man page:

sudo cp docs/lixplore.1 /usr/local/share/man/man1/
sudo mandb -q
man lixplore

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☕ Support the Project

If you find Lixplore useful for your research, consider supporting its development!

Why support?

• ✨ Keeps the project actively maintained and updated
• 🚀 Helps add new features and integrations
• 📚 Supports free, open-source academic tools
• 🌍 Makes research more accessible to everyone

"If you value independent research tools and open access to literature, consider buying me a coffee ☕—it helps keep development and research going!"

Your support enables:

• Regular updates and bug fixes
• New API integrations (IEEE Xplore, Scopus, Web of Science)
• Advanced features (LLM integration, citation networks, collaboration tools)
• Better documentation and tutorials
• Faster response to issues and feature requests

Other ways to support:

• ⭐ Star the repository on GitHub
• 🐛 Report bugs and issues
• 💡 Suggest new features
• 📖 Improve documentation
• 🔀 Contribute code via pull requests
• 📢 Share Lixplore with your research community

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🤝 Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

1. Fork the repository
2. Create your feature branch (git checkout -b feature/AmazingFeature)
3. Commit your changes (git commit -m 'Add some AmazingFeature')
4. Push to the branch (git push origin feature/AmazingFeature)
5. Open a Pull Request

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📝 License

This project is licensed under the MIT License - see the LICENSE file for details.

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🙏 Acknowledgments

• PubMed/NCBI for providing free API access
• arXiv for open preprint access
• Crossref for DOI metadata
• DOAJ for open access journal data
• EuropePMC for European literature access

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📧 Support & Community

• 📚 Documentation: https://pryndor.github.io/Lixplore_cli/
• 🐛 Issues: GitHub Issues
• ❓ FAQ: Documentation FAQ

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🔗 Quick Links

• 📦 PyPI Package: https://pypi.org/project/lixplore-cli/
• 💻 GitHub Repository: https://github.com/pryndor/Lixplore_cli
• 📚 Documentation: https://pryndor.github.io/Lixplore_cli/
• 🐛 Issue Tracker: https://github.com/pryndor/Lixplore_cli/issues
• 🚀 Changelog: https://pryndor.github.io/Lixplore_cli/about/changelog/
• 🤝 Contributing Guide: https://pryndor.github.io/Lixplore_cli/about/contributing/

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Made with ❤️ for the research community