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
- 🔍 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
- 📥 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
- 📚 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
--examplesflag - 📄 Man Page - Traditional Unix man page included
- 🎨 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
📢 IMPORTANT: TUI mode is currently under active development. While functional, some advanced features are still being refined. All 95 command-line flags are fully compatible and production-ready in CLI mode. Future updates will focus on bringing TUI mode to feature parity with CLI mode.
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 statsFeatures (Currently Available):
- ✅ 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
⚠️ Note: Some advanced CLI features are being integrated into TUI mode
Perfect for scripting, automation, and quick searches
All 95 flags fully functional and tested!
# Quick search and export
lixplore -P -q "machine learning" -m 20 -X xlsx
# Advanced workflow with deduplication
lixplore -A -q "COVID-19" -m 50 -D --sort newest -X csv
# Citation export with enrichment
lixplore -P -q "CRISPR" -m 30 --enrich crossref -C apa
# Batch export to multiple formats
lixplore -x -q "quantum computing" -m 25 -X csv,bibtex,ris --zipAll Features Available:
- ✅ 95 command-line flags fully compatible
- ✅ Multi-source search (PubMed, arXiv, Crossref, DOAJ, EuropePMC)
- ✅ Boolean operators and advanced queries
- ✅ 8 export formats (CSV, Excel, JSON, BibTeX, RIS, EndNote, XML)
- ✅ Citation formatting (APA, MLA, Chicago, IEEE)
- ✅ Metadata enrichment and PDF downloads
- ✅ Deduplication with multiple strategies
- ✅ Export profiles and templates
- ✅ Complete annotation system
Note: Legacy shell (--shell) and wizard (--wizard) modes are still available but deprecated in favor of the enhanced TUI mode.
Lixplore has been massively upgraded with powerful new features:
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-pdfShow 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-linksDirect integration with your favorite reference managers:
- Zotero: API integration with collection support
- Mendeley: RIS export for easy import
Setup Zotero (one-time):
- Get API key: https://www.zotero.org/settings/keys
- 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 4FCVPNAPComprehensive analytics with beautiful ASCII visualizations:
- Publication trends by year
- Top journals and authors
- Source distribution
- Metadata completeness
lixplore -P -q "AI" -m 100 --statBrowse 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 -iAdd 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- 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
Before installing Lixplore, ensure you have:
1. Python Installed:
# Check Python version (requires 3.8 or higher)
python --version
# or
python3 --version2. pip Installed:
# Check pip version
pip --version
# or
pip3 --version3. (Windows Only) Microsoft C++ Build Tools:
If you're on Windows and encounter build errors during installation, you need Microsoft C++ Build Tools:
Option A: Quick Install (Recommended)
- Download and install Microsoft C++ Build Tools: https://visualstudio.microsoft.com/visual-cpp-build-tools/
- Select "Desktop development with C++" during installation
- Restart your terminal after installation
Option B: Full Visual Studio
- Install Visual Studio Community: https://visualstudio.microsoft.com/downloads/
- Select "Desktop development with C++" workload
Why? The
gensimpackage (a dependency) requires C++ compilation on Windows. This is a one-time setup.
# From PyPI (recommended)
pip install lixplore-cli
# Upgrade to latest version
pip install --upgrade lixplore-cli
# From source
git clone https://github.com/pryndor/Lixplore_cli.git
cd Lixplore_cli
pip install -e .Error Message:
Failed to build gensim
error: Microsoft Visual C++ 14.0 or greater is required
Solution:
- Install Microsoft C++ Build Tools (see Prerequisites above)
- Restart your terminal/PowerShell
- Try installing again:
pip install lixplore-cli
Alternative Solution (if build tools don't work):
# Install pre-built binary wheels first
pip install --upgrade pip setuptools wheel
pip install gensim --no-cache-dir
pip install lixplore-cliSolution:
# Try using pip3
pip3 install lixplore-cli
# Or use Python module syntax
python -m pip install lixplore-cliSolution (Linux/Mac):
# Install for current user only
pip install --user lixplore-cliSolution (Windows - Run as Administrator):
- Right-click Command Prompt → "Run as administrator"
- Then:
pip install lixplore-cli
# Check if installed correctly
lixplore --version
# Run quick test
lixplore --help# 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.xlsxVisit 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
# 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/-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)# 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-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# 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--sort newest # Latest publications first
--sort oldest # Earliest publications first
--sort journal # Alphabetical by journal
--sort author # Alphabetical by author# 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# 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# 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# 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# Search 50, export odd-numbered (25 articles)
lixplore -A -q "cancer immunotherapy" -m 50 -D \
-S odd -X csv -o cancer_sample.csv# Sort by oldest to study evolution
lixplore -P -q "diabetes" -m 100 --sort oldest \
-X xlsx -o diabetes_history.xlsx# 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 enwAll 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
| 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 |
relevant- Default API order (most relevant first)newest- Latest publications (2025 → 2020)oldest- Earliest publications (1990 → 2000)journal- Alphabetical by journal nameauthor- Alphabetical by first author
Lixplore works on all major platforms:
- ✅ Linux (all distributions)
- ✅ macOS (10.14+)
- ✅ Windows (10+)
Review feature works with: xfce4-terminal, gnome-terminal, konsole, xterm, alacritty, kitty
Review feature uses Terminal.app
Review feature uses cmd.exe
pip install lixplore-cligit clone https://github.com/pryndor/Lixplore_cli.git
cd Lixplore_cli
pip install -e .pipx install lixplore-cli- Python 3.7 or higher
- Internet connection for API access
- Terminal emulator (for review feature)
biopython- PubMed/NCBI API accessrequests- HTTP requestslitstudy- Literature study supportopenpyxl- Excel export support
All dependencies are automatically installed.
After installation, install the man page:
sudo cp docs/lixplore.1 /usr/local/share/man/man1/
sudo mandb -q
man lixploreIf 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
We're actively working to bring all CLI features into the TUI mode. Upcoming updates will include:
- 🔄 All 95 Flags in TUI - Full integration of all command-line features
- 📊 Advanced Filtering - Date ranges, author search, DOI lookup in TUI
- 🎨 Enhanced UI - Improved navigation and visual design
- 📥 PDF Integration - Direct PDF download and viewing from TUI
- 🔧 Custom API Support - GUI for adding custom data sources
- 📋 Profile Management - Visual interface for export profiles
- 🎯 Citation Formatting - Interactive citation style selection
- 📈 Advanced Statistics - More visualization options
Current Status: Core TUI features working (search, browse, annotate, export). CLI mode has 100% feature parity with all flags.
Contributions are welcome! Please feel free to submit a Pull Request.
- Fork the repository
- Create your feature branch (
git checkout -b feature/AmazingFeature) - Commit your changes (
git commit -m 'Add some AmazingFeature') - Push to the branch (
git push origin feature/AmazingFeature) - Open a Pull Request
This project is licensed under the MIT License - see the LICENSE file for details.
- 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
- 📚 Documentation: https://pryndor.github.io/Lixplore_cli/
- 🐛 Issues: GitHub Issues
- ❓ FAQ: Documentation FAQ
- 📦 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/
Made with ❤️ for the research community
