Installation¶

⚠️ Prerequisites¶

Before installing Lixplore, ensure you have:

1. Python (Version 3.8 or Higher)¶

Check your Python version:

python --version
# or
python3 --version

If Python is not installed or too old: - Windows: Download from python.org - Mac: brew install python3 or download from python.org - Linux: sudo apt install python3 python3-pip (Ubuntu/Debian)

2. pip (Python Package Manager)¶

Check if pip is installed:

pip --version
# or
pip3 --version

Usually comes with Python. If missing:

python -m ensurepip --upgrade

3. Windows Only: Microsoft C++ Build Tools¶

⚠️ IMPORTANT FOR WINDOWS USERS:

If you're on Windows, you need Microsoft C++ Build Tools to avoid installation errors:

Option A: Build Tools Only (Recommended - ~6GB) 1. Download: Microsoft C++ Build Tools 2. Run the installer 3. Select "Desktop development with C++" 4. Click Install 5. Restart your computer after installation

Option B: Full Visual Studio (~20GB) 1. Download: Visual Studio Community 2. During installation, select "Desktop development with C++" workload 3. Restart your computer after installation

Why is this needed? The gensim package (a dependency of litstudy) requires C++ compilation on Windows. This is a one-time setup.

Installation Methods¶

Method 1: Install from PyPI (Recommended)¶

This is the simplest and recommended method:

pip install lixplore-cli

On Windows (after installing C++ Build Tools):

pip install lixplore-cli

Verify the installation:

lixplore --version
lixplore --help

Method 2: Install from Source¶

For the latest development version or to contribute:

# Clone the repository
git clone https://github.com/pryndor/Lixplore_cli.git
cd Lixplore_cli

# Install in development mode
pip install -e .

Method 3: Using pipx (Isolated Installation)¶

For an isolated installation that doesn't interfere with other Python packages:

# Install pipx if you don't have it
pip install pipx
pipx ensurepath

# Install lixplore
pipx install lixplore-cli

Dependencies¶

Lixplore automatically installs these core dependencies:

biopython - PubMed/NCBI API access
requests - HTTP library for API calls
litstudy - Literature study framework
openpyxl - Excel file generation

Optional dependencies: - rich - Enhanced TUI mode (install with: pip install lixplore-cli[all])

Note: Total installation size is approximately 150-200MB including all dependencies.

Upgrade¶

To upgrade to the latest version:

pip install --upgrade lixplore-cli

Uninstall¶

To remove Lixplore:

pip uninstall lixplore-cli

Verify Installation¶

After installation, verify it works:

# Check version and help
lixplore --help

# Run a simple test search
lixplore -P -q "test" -m 5

Troubleshooting¶

❌ Error: "Failed to build gensim" (Windows)¶

This is the most common error on Windows:

Error Message:

Building wheel for gensim (pyproject.toml) ... error
Failed to build gensim
error: Microsoft Visual C++ 14.0 or greater is required

Solution 1 (Recommended): 1. Install Microsoft C++ Build Tools (see Prerequisites section above) 2. Restart your terminal/PowerShell completely 3. Try installing again:

pip install lixplore-cli

Solution 2 (Alternative):

# Upgrade pip and try installing gensim first
pip install --upgrade pip setuptools wheel
pip install gensim --no-cache-dir
pip install lixplore-cli

Solution 3 (If still failing):

# Install from pre-built wheels
pip install --only-binary :all: gensim
pip install lixplore-cli

Still having issues? Report at: https://github.com/pryndor/Lixplore_cli/issues

❌ Error: "command 'pip' not found"¶

Solution:

# Try pip3 instead
pip3 install lixplore-cli

# Or use Python module syntax
python -m pip install lixplore-cli
# or
python3 -m pip install lixplore-cli

❌ Error: "command 'lixplore' not found" (After Installation)¶

On Linux/macOS:

# Add pip's bin directory to PATH
export PATH=$PATH:~/.local/bin

# Make it permanent
echo 'export PATH=$PATH:~/.local/bin' >> ~/.bashrc
source ~/.bashrc

On Windows: - The Scripts directory should be in PATH automatically - If not, add: C:\Users\YourName\AppData\Local\Programs\Python\Python3X\Scripts

❌ Error: Permission denied¶

On Linux/Mac:

# Install for current user only (no sudo needed)
pip install --user lixplore-cli

On Windows: - Right-click Command Prompt → "Run as administrator" - Then run: pip install lixplore-cli

❌ Error: Python version too old¶