Detailed Installation Instructions

The following is addressed to an audience who is just getting started with Python and would benefit from additional guidance on how to install PyStan.

Installing PyStan requires installing:

  • Python
  • Python dependencies
  • PyStan

Prerequisite knowledge

It is highly recommended to know what bash is and the basics of navigating the terminal. You can review or learn it from the Software Carpentry bash lesson here: http://swcarpentry.github.io/shell-novice/.

Lessons 1 - 3 are proabably the most important.

Installing Python

The easiest way to install Python is to use the Anaconda distribution of python. It can be downloaded here: http://continuum.io/downloads.

This is because PyStan (and many python tools) require packages (aka modules) that have C dependencies. These types of dependencies are unable to be installed (at least easily) using pip, which is a common way to install python packages. Anaconda ships with it’s own package manager (that also plays nicely with pip) called conda, and comes with many of the data analytics packages and dependencies pre-installed.

Don’t worry about Anaconda ruining your current Python installation, can can be easily uninstalled (described below).

Anaconda is not a requirement

Anaconda is not an absolute requirement to get pystan to work. As long as you can get the necessary python dependencies installed, pystan will work. If you want to install Anaconda, follow the Windows, Macs, and Linux instructions below.

Windows

The Anaconda installer should be able to be double-clicked and installed. Use all of the defaults for installation except make sure to check Make Anaconda the default Python.

Macs

After downloading the installer, double click the .pkg file and follow the instructions on the screen. Use all of the defaults for installation.

Linux

After downloading the installer execute the associated shell script. For example, if the file downloaded were named Anaconda3-4.1.1-Linux-x86_64.sh you would enter bash Anaconda3-4.1.1-Linux-x86_64.sh in the directory where you downloaded the file.

Uninstalling Anaconda

The default location for anaconda can be found in your home directory. Typically this means it in in the ~/anaconda or ~/anaconda3 directory when you open a terminal.

Python dependencies

If you used the Anaconda installer, numpy and cython should already be installed, so additional dependencies should not be needed. However, should you need to install additional dependencies, we can use conda to install them as such:

  • open a terminal
  • type conda install numpy to install numpy or replace numpy with the package you need to install

Installing PyStan

Since we have the numpy and cython dependencies we need, we can install the latest version of PyStan using pip. To do so:

  • Open a terminal
  • type pip install pystan