Skip to content

Installation

This guide covers the installation and setup of NullStrike for structural identifiability analysis.

Prerequisites

NullStrike requires Python 3.8 or higher and has the following dependencies:

System Requirements

  • Python: 3.8+
  • Operating System: Linux, macOS, or Windows
  • RAM: 4GB minimum (8GB+ recommended for large models)
  • Storage: 500MB for installation + space for results

Required Python Packages

The core dependencies include:

  • SymPy: Symbolic mathematics and computation
  • NumPy: Numerical arrays and linear algebra
  • Matplotlib: Visualization and plotting
  • NetworkX: Graph analysis and visualization
  • SciPy: Scientific computing utilities

Installation Methods

For development and customization, install from the source repository:

# Clone the repository
git clone https://github.com/vipulsinghal02/NullStrike.git
cd NullStrike

# Install in development mode
pip install -e .

This method allows you to:

  • Modify the source code and see changes immediately
  • Add custom models and options easily
  • Contribute to the project development
  • Access the latest features and bug fixes

Method 2: Direct Installation

For production use or if you don't need to modify the code:

# Install directly from the repository
pip install git+https://github.com/vipulsinghal02/NullStrike.git

Method 3: Local Installation

If you have a local copy of the source code:

cd /path/to/NullStrike
pip install .

Verification

After installation, verify that NullStrike is working correctly:

1. Check Installation

# Verify the command is available
nullstrike --help

Expected output: 

usage: nullstrike [-h] [--parameters-only] model_name [options_file]

NullStrike: Structural identifiability analysis with nullspace analysis

positional arguments:
  model_name         Name of the model to analyze
  options_file       Configuration file (optional)

optional arguments:
  -h, --help         Show this help message and exit
  --parameters-only  Run parameters-only analysis

2. Run Test Analysis

Test with a built-in example:

# Run analysis on the two-compartment model
nullstrike C2M

This should:

  1. Create a results/ directory
  2. Generate analysis files including visualizations
  3. Display progress information in the terminal
  4. Complete without errors

3. Check Python API

Test the Python interface:

# Test in Python interpreter
from nullstrike.cli.complete_analysis import main

# This should work without import errors
print("NullStrike successfully installed!")

Troubleshooting

Common Installation Issues

Problem: ModuleNotFoundError when importing NullStrike

Solutions: 

# Ensure you're in the correct environment
which python
which pip

# Reinstall in development mode
pip uninstall nullstrike
pip install -e .

Problem: Permission denied during installation

Solutions: 

# Use user installation
pip install --user -e .

# Or use virtual environment (recommended)
python -m venv nullstrike_env
source nullstrike_env/bin/activate  # Linux/macOS
# nullstrike_env\Scripts\activate   # Windows
pip install -e .

Problem: Slow symbolic computation or memory errors

Solutions: - Increase system RAM or use smaller models for testing - Check that SymPy version is compatible (≥1.8) - For large models, consider using --parameters-only flag

Problem: Matplotlib plots not displaying or saving

Solutions: 

# For headless systems, ensure proper backend
export MPLBACKEND=Agg

# Install additional backends if needed
pip install PyQt5  # or tkinter support

Platform-Specific Notes

# If using Homebrew Python
brew install python@3.9

# Ensure pip is up to date
python -m pip install --upgrade pip

# Install Python development headers
sudo apt update
sudo apt install python3-dev python3-pip

# Install build tools if needed
sudo apt install build-essential

Use Windows Subsystem for Linux (WSL) or ensure: 

# Install Visual C++ Build Tools if compilation errors occur
# Use Anaconda/Miniconda for easier dependency management
conda install sympy numpy matplotlib networkx scipy
pip install -e .

For isolated installation:

# Create virtual environment
python -m venv nullstrike_env

# Activate environment
source nullstrike_env/bin/activate  # Linux/macOS
# nullstrike_env\Scripts\activate   # Windows

# Install NullStrike
pip install -e .

# Deactivate when done
deactivate

Development Dependencies

For contributing to NullStrike development:

# Install development dependencies
pip install -e ".[dev]"

# Or manually install testing/docs tools
pip install pytest pytest-cov sphinx mkdocs mkdocs-material

Next Steps

After successful installation:

  1. Quick Start Guide: Get started with immediate examples
  2. First Analysis: Step-by-step tutorial
  3. User Guide: Learn about model definition and configuration
  4. Examples: Explore practical use cases

Getting Help

If you encounter issues:

Installation Complete

If you can run nullstrike C2M successfully, you're ready to start analyzing your own models!