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Lixplore-cli

Academic Literature Search & Export CLI Tool

Python Version License: MIT Documentation GitHub PyPI version Downloads Issues Buy Me A Coffee

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


✨ 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

🎯 Two Ways to Use Lixplore

1️⃣ Full-screen TUI - Research Cockpit

Perfect for exploring, reading and curating papers

pip install "lixplore-cli[tui]"   # adds Textual (Python 3.9+)
lixplore --tui
┌ ◆ Lixplore  (semaglutide OR tirzepatide) AND obesity   ● PubMed ● EuropePMC ○ arXiv  [Search] ┐
├──────────────┬──────────────────────────────────────────────┬─────────────────────────────────┤
│ Search    ^F │     Title                    Author  Year Src│ GLP-1 Receptor Agonists in      │
│ Library   ^L │ 4★  GLP-1 Receptor Agonists  Yuan Y  2026 PM │ Heart Failure: A Systematic …   │
│ Alerts    ^N │ ●   An RNA thermogenic ther… Thorne  2026 PM │ Yuan Y, Chen C, Li X +2         │
│ Stats     ^T │     Patient characteristics… Tewksb… 2026 EP │ Drugs · 2026 · PubMed           │
│              │                                              │ ── Your notes ──────────        │
│ RECENT       │                                              │ ★★★★☆  ○ unread  ▲ medium       │
│ semaglutide… │ 36 results · 1 selected · sorted by newest   │ ── Abstract ────────────        │
├──────────────┴──────────────────────────────────────────────┴─────────────────────────────────┤
│ ⏎ Read  o Browser  a Annotate  space Select  e Export  f Filter  1-5 Rate  esc Back  ? Help   │
└───────────────────────────────────────────────────────────────────────────────────────────────┘
  • ✅ Results stream in per database, with a live preview of the highlighted paper
  • ✅ Rate with 1–5, annotate (status, priority, tags, notes) on one form
  • ✅ Library of everything you've annotated, filterable and searchable
  • ✅ Alerts view: see what's new for your saved alert searches
  • ✅ Export selected / shown / all results in 8 formats
  • ✅ Mouse support, command palette (Ctrl+P), themes, works on Linux, macOS and Windows
  • ℹ️ Enrichment, citation styles and PDF download are CLI flags for now

2️⃣ Command Line Mode - Direct Commands ✅ (Fully Production-Ready)

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 --zip

All 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.


🆕 What's New in Version 2.0

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-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

🎨 Full-screen TUI

Open any CLI search in the TUI to read, rate, select and export:

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

📬 Paper Alerts by Email, Telegram, Discord, Slack & more

Get new papers for your searches delivered on a schedule, run free by GitHub Actions. No server, no file edits:

  1. Fork this repo and enable workflows in the Actions tab.
  2. In Settings → Secrets and variables → Actions, add the variable LIXPLORE_QUERIES (one search per line), plus secrets for any channel: Email, Telegram, Discord, Slack, Microsoft Teams, Google Chat, Matrix, WeCom, Feishu, DingTalk, ntfy, Gotify, Pushover, PushPlus, ServerChan3, AstrBot or a custom webhook (n8n/Zapier for WhatsApp, SMS and more).
  3. Run Actions → Lixplore Alerts → Run workflow → test.

Each digest lists only papers new since the last one, with a CSV/BibTeX attachment. Full guide: docs/guide/alerts.md.

Prefer your own computer? pip install -U lixplore-cli, then lixplore --alerts init creates the settings file and lixplore --alerts schedule prints the cron / Task Scheduler line.


🚀 Quick Start

⚠️ Prerequisites

Before installing Lixplore, ensure you have:

Python 3.8 or higher:

python3 --version

Installation

Best for most users. Installs in an isolated environment, no virtual env needed.

# Install pipx if you don't have it
# Arch: sudo pacman -S python-pipx
# Ubuntu/Debian: sudo apt install pipx
# Fedora: sudo dnf install pipx
# macOS: brew install pipx

# Then install lixplore
pipx install lixplore-cli

# Upgrade
pipx upgrade lixplore-cli

Why pipx? Modern Linux distros (Arch, Fedora 38+, Ubuntu 23.04+, Debian 12+) block system-wide pip install (PEP 668). pipx handles this automatically by creating isolated environments per tool while keeping the lixplore command available globally.

Method 2: pip (in virtual environment)

# Create and activate a virtual environment
python3 -m venv ~/.venvs/lixplore
source ~/.venvs/lixplore/bin/activate

# Install
pip install lixplore-cli

# Upgrade
pip install --upgrade lixplore-cli

Method 3: Arch Linux (AUR)

# Using yay
yay -S lixplore-cli

# Using paru
paru -S lixplore-cli

Method 4: Homebrew (macOS & Linux)

brew install pryndor/lixplore/lixplore-cli

# Upgrade
brew update && brew upgrade lixplore-cli

Works on Apple Silicon and Intel Macs. Includes the full-screen TUI (lixplore --tui).

Method 5: From source

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

Optional: Full-screen TUI

For lixplore --tui (Textual, Python 3.9+; older Pythons get a simpler Rich TUI):

# With pipx (inject into existing install)
pipx inject lixplore-cli rich textual

# With pip
pip install "lixplore-cli[tui]"

# Arch Linux
sudo pacman -S python-rich

✅ Verify Installation

lixplore --version
lixplore --help

🐛 Troubleshooting

❌ Error: "externally-managed-environment" (Linux)

This means your distro blocks system-wide pip installs. Use pipx (Method 1) instead.

❌ Error: "command 'pip' not found"

# Use pip3 or python module syntax
pip3 install lixplore-cli
python -m pip install lixplore-cli

❌ Error: Permission denied (Linux/macOS)

# Use pipx (recommended) or install for current user
pipx install lixplore-cli
# or
pip install --user lixplore-cli

🖥️ TUI Mode Troubleshooting (Linux)

TUI mode requires the rich library (≥ 13.0.0). If it fails to launch, follow these steps:

Step 1 — Run the built-in diagnostics

lixplore --check-tui

This prints your Python version, Rich status, and exact fix instructions.

Step 2 — Install / inject Rich

Installation method Fix command
pipx (most common) pipx inject lixplore-cli rich
pip + venv pip install rich (activate venv first)
pip install 'lixplore-cli[tui]' installs Rich in one step
Arch Linux sudo pacman -S python-rich

pipx users — common gotcha: pipx creates an isolated environment per tool. Installing rich with plain pip or pacman puts it in a different Python environment that lixplore cannot see. Always use pipx inject lixplore-cli rich so Rich lands inside the same isolated env.

Step 3 — Check terminal compatibility

Rich needs a terminal that supports ANSI escape codes and Unicode. Verify yours:

# Should print "xterm-256color" or similar (not "dumb")
echo $TERM

# Quick Unicode/color test
python3 -c "from rich.console import Console; Console().print('[bold cyan]OK[/bold cyan]')"

Known-working terminals on Linux: GNOME Terminal, Konsole, Alacritty, Kitty, Tilix, Xfce4-terminal, WezTerm.

Step 4 — SSH / remote sessions

When connecting over SSH the TERM variable is sometimes lost, disabling Rich:

# On your local machine, connect with terminal forwarding
ssh -t user@host

# Or force 256-color on the remote side
export TERM=xterm-256color
lixplore --tui

Step 5 — Headless / container environments

Rich will not render correctly in Docker containers, CI runners, or terminals with NO_COLOR=1 set. In these environments, unset the variable if it was set unintentionally:

unset NO_COLOR
lixplore --tui

Step 6 — tmux / screen sessions

Multiplexers like tmux and screen sometimes set TERM=screen, which limits color support. Inside a tmux session:

# Quick fix for current session
export TERM=xterm-256color
lixplore --tui

# Permanent fix — add to ~/.tmux.conf
# set -g default-terminal "screen-256color"

For screen, launch it with: screen -T xterm-256color

Step 7 — Linux virtual console (tty without a desktop)

If you are logged in directly on a raw Linux console (not inside GNOME Terminal, Konsole, etc.) your TERM will be linux, which does not support 256 colors. Rich's TUI will look broken or fail to render.

Solution: Log in via SSH from a color-capable terminal, or start a desktop session and use a terminal emulator listed in Step 3 above. Alternatively, use CLI mode (all features work without a terminal emulator).

✅ If TUI still doesn't work — use CLI mode

All 95 flags work perfectly in CLI mode without any extra dependencies. CLI mode is fully production-ready and is what we recommend for scripting, automation, and SSH sessions:

# CLI equivalents for common TUI workflows
lixplore -P -q "your topic" -m 20          # search PubMed
lixplore -A -q "your topic" -m 50 -D       # search all + deduplication
lixplore -P -q "topic" -m 20 -X xlsx       # export to Excel
lixplore -P -q "topic" -m 20 -i            # interactive results browser (Rich optional)

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

📚 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
# 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

🎯 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

📊 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

🔧 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

🖥️ 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


📦 Installation Methods

Method Command Best for
pipx (recommended) pipx install lixplore-cli All Linux/macOS users
pip + venv pip install lixplore-cli Virtual environments
AUR yay -S lixplore-cli Arch Linux users
Homebrew brew install pryndor/lixplore/lixplore-cli macOS & Homebrew users
From source pip install -e . Development

See Quick Start above for detailed instructions.


🔍 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
  • openpyxl - Excel export support
  • rich (optional) - Enhanced TUI with colors and formatting

All core dependencies are automatically installed. For the enhanced TUI experience, install with pipx inject lixplore-cli rich or pip install "lixplore-cli[tui]".


📖 Man Page

After installation, install the man page using whichever method suits you:

Option 1 — built-in command (any install method):

lixplore --install-man
man lixplore

Option 2 — from a cloned repo:

bash docs/install_man_page.sh
man lixplore

The installer automatically finds the right directory, handles sudo when needed, and refreshes the man database. If man lixplore still fails after a user-local install, add this to your shell profile:

export MANPATH=$HOME/.local/share/man:$MANPATH

☕ Support the Project

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

Buy Me A Coffee

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

🚀 Development Roadmap

TUI Mode Enhancement (Active Development)

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.


🤝 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

📰 Reviews

Community write-ups, tutorials, and independent reviews of Lixplore:


📝 License

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


🙏 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

Reviews


📧 Support & Community



Made with ❤️ for the research community

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