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Installation

PMCGrab supports Python 3.10+ and can be installed via uv or from source.

For adding to an existing project:

uv add pmcgrab

For standalone installation:

uv pip install pmcgrab

This installs the latest stable version from PyPI along with all required dependencies.

From Source

If you want the latest development version or need to modify PMCGrab:

git clone https://github.com/rajdeepmondaldotcom/pmcgrab.git
cd pmcgrab
uv pip install -e .

Development Installation

For development work, install with development dependencies:

git clone https://github.com/rajdeepmondaldotcom/pmcgrab.git
cd pmcgrab

# Install with all development dependencies
uv sync --dev --all-groups

Verify Installation

Test your installation:

import pmcgrab
print(pmcgrab.__version__)

Or use the command line:

uv run python -m pmcgrab --help

Dependencies

PMCGrab requires the following packages:

  • beautifulsoup4 (≥4.13.4) - HTML parsing
  • biopython (≥1.83) - Biological data structures
  • lxml (≥4.9.0) - XML processing
  • numpy (≥1.24.0) - Numerical operations
  • pandas (≥2.0.0) - Data manipulation
  • requests (≥2.28.0) - HTTP requests
  • tqdm (≥4.64.0) - Progress bars

Optional Dependencies

For development and documentation:

uv add "pmcgrab[dev]"    # Development tools
uv add "pmcgrab[docs]"   # Documentation tools
uv add "pmcgrab[test]"   # Testing dependencies

System Requirements

  • Python: 3.10, 3.11, 3.12, or 3.13
  • Operating System: Windows, macOS, or Linux
  • Memory: Minimum 512MB RAM (2GB+ recommended for batch processing)
  • Network: Internet connection required for PMC article retrieval

Common Issues

ImportError with lxml

If you encounter issues with lxml installation:

# On Ubuntu/Debian
sudo apt-get install libxml2-dev libxslt-dev python3-dev

# On macOS
brew install libxml2 libxslt

# Then reinstall
uv pip install --force-reinstall lxml

Permission Errors

If you get permission errors during installation:

uv pip install --user pmcgrab

uv automatically manages virtual environments, but you can create one explicitly:

uv venv pmcgrab-env
source pmcgrab-env/bin/activate  # On Windows: pmcgrab-env\Scripts\activate
uv pip install pmcgrab

Next Steps

Once installed, proceed to Quick Start to begin using PMCGrab.