pyspi: Statistics for Pairwise Interactions
pyspi GitHub
  • Welcome to pyspi
    • Citing pyspi
  • Installing and using pyspi
    • Installation
      • Alternative Installation Options
      • Troubleshooting
    • Usage
      • Walkthrough Tutorials
        • Getting Started: A Simple Demonstration
        • Neuroimaging: fMRI Time Series
        • Finance: Stock Price Time Series
        • Distributing Calculations
      • Advanced Usage
        • Creating a reduced SPI set
        • Distributing calculations on a cluster
      • FAQ
  • Information about pyspi
    • SPIs
      • Glossary of Terms
      • Table of SPIs
      • SPI Descriptions
        • Basic Statistics
        • Distance Similarity
        • Causal Inference
        • Information Theory
        • Spectral
        • Miscellaneous
      • SPI Subsets
    • API Reference
      • pyspi.calculator.CorrelationFrame
      • pyspi.calculator.Calculator
      • pyspi.data.Data
      • pyspi.calculator.CalculatorFrame
      • pyspi.utils.filter_spis
    • Publications using pyspi
    • Related Packages
  • Development
    • Development
      • Incorporating new SPIs
      • Contributing to pyspi
      • Code of Conduct
    • License
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On this page
  • 1. Local Installation
  • 2. pyspi Docker Image
  • Using the pyspi Docker Image
  1. Installing and using pyspi
  2. Installation

Alternative Installation Options

PreviousInstallationNextTroubleshooting

Last updated 1 year ago

For users encountering issues with installing pyspi, we recommend you first consult the troubleshooting guide. If your issue has not been addressed, we offer three alternative installation options.

1. Local Installation


To install pyspi using a local pip install, download or clone the from GitHub, unpack and install:

git clone https://github.com/DynamicsAndNeuralSystems/pyspi
cd pyspi
pip install .

2. pyspi Docker Image


Why should I use a Docker Image?

By using a Docker image, you're not just simplifying the initial setup of pyspi, you're also setting the stage for a more reliable and reproducible workflow. Here are some reasons why we recommend users work with a Docker image:

  1. Ease of Setup:

Configuration issues, operating systems compatibility problems, and dependency conflicts are a just a few of the hurdles you may encounter when trying to install any software package locally. A Docker image eliminates these hassles by providing you with a pre-configured, read-to-run container that has everything the software needs. Just download the image, and you're ready to go!

  1. Reproducibility:

Docker images encapsulate the entire runtime environment - the software, the exact versions of all packages and the necessary configurations. This ensures that the software runs identically, no matter where or when it's executed, and that your results are reproducible each time.

Using the pyspi Docker Image

To get started with using a pyspi docker image, follow these steps:

  1. Download the Docker Desktop Application

  2. Create a Docker Account

  3. Pull and Run the pyspi Docker Image

    With the Docker Desktop application running in the background, open the terminal or command prompt and run the following command:

    $ docker pull jmoo2880/pyspi:v1.0

    Now, to run the Docker image:

    $ docker run -it jmoo2880/pyspi:v1.0

This should start a python session with pyspi installed and ready to import.


Install Docker Desktop from the . This application runs Docker on your machine.

Register for an account on if you haven't already. This account is needed to download ('pull') Docker images.

latest version
official Docker website
Docker Hub
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