Installation

Quick Install

Install scPPIN-py directly from GitHub:

pip install git+https://github.com/shahrozeabbas/scppin-py.git

Note

The package is not yet available on PyPI. Install from GitHub using the command above.

Development Install

If you want to contribute or build documentation:

  1. Clone the repository:

git clone https://github.com/shahrozeabbas/scppin-py.git
cd scppin-py

  1. Create a virtual environment (recommended):

python -m venv venv
source venv/bin/activate  # On Windows: venv\Scripts\activate

.. note::
   On Windows, use ``venv\Scripts\activate`` instead.

  1. Install in development mode:

pip install -e ".[all]"

This installs the package with all optional dependencies including documentation tools.

Dependencies

Core Dependencies (required)

These are automatically installed with scPPIN-py:

  • numpy >= 1.20.0,<2.0

  • scipy >= 1.7.0

  • igraph >= 0.11.0

  • matplotlib >= 3.3.0

  • pandas >= 1.3.0

  • pcst-fast >= 1.0.0

Optional Dependencies

Install these for additional functionality:

  • scanpy: For scanpy integration and AnnData support .. code-block:: bash

    pip install “scppin[scanpy]”

    This installs:

    • scanpy >= 1.8.0

    • anndata >= 0.8.0

  • dev: For development and testing .. code-block:: bash

    pip install “scppin[dev]”

    This installs:

    • pytest >= 7.0.0

    • pytest-cov >= 3.0.0

    • black >= 22.0.0

    • flake8 >= 4.0.0

    • mypy >= 0.950

  • docs: For building documentation .. code-block:: bash

    pip install “scppin[docs]”

Installing pcst-fast

The pcst-fast package is required for solving the Prize-Collecting Steiner Tree problem. It should install automatically, but if you encounter issues:

pip install pcst-fast

If compilation fails, you may need to install build tools:

On Ubuntu/Debian

sudo apt-get install build-essential python3-dev

On macOS

xcode-select --install

On Windows

Install Visual Studio Build Tools from https://visualstudio.microsoft.com/downloads/

Verifying Installation

Run this simple test to verify your installation:

from scppin import scPPIN

# Run a simple test
model = scPPIN()
model.load_network([('A', 'B'), ('B', 'C')])
model.set_node_weights({'A': 0.001, 'B': 0.005, 'C': 0.01})
module = model.detect_module(fdr=0.01)

print(f"Module detected: {module.vcount()} nodes")

If this runs without errors, installation is successful!

Platform-Specific Notes

macOS (Apple Silicon M1/M2)

  • May need to install Rosetta for some dependencies

  • Use native ARM Python if possible

Windows

  • May need Visual Studio Build Tools

  • Use Anaconda for easier dependency management

Linux

  • Should work out of the box on most distributions

  • May need python3-dev package

sudo apt-get install python3-dev  # Ubuntu/Debian
sudo yum install python3-devel     # CentOS/RHEL

Next Steps

Now that you have scPPIN-py installed, check out the Quick Start guide to get started!