Getting Started with Python

We will be using Python throughout the course. Why Python and not another language like Julia or R? While Julia and R have a lot to bring to the table, Python has been a de facto choice for many data scientists. And for good reason, Python’s ecosystem is mature; there are countless libraries that you can use in your daily work. Inevitably, we will introduce some of these libraries ourselves. Python is also not limited to data analysis. If ever you would like to explore applications outside of data science, Python is not a bad initial choice.

Side Note:
if you are interested other languages, you are in good company. Jacob is a big fan of Haskell and Todd loves Rust and still appreciates C. We can’t include all of the languages we care about in this course, but if you would like to know how you can use another language over the course of your PhD, let us know! We can get you connected with people that would also like to use your language of choice (especially if it is Haskell or Rust). There are people at the lab that use R, and there are people who are interested in pushing things further with Julia.

Anaconda

We will start by using Anaconda, a distribution of Python including a package manager with many of the packages commonly used in data science, and a way to manage programming environments. While not the only way to get started with Python, this is one of the most common approaches. Many collaborators at ORNL will be familiar with Anaconda, and it is an easy way to quickly get people on the same page when setting up their compute environments.

Installation

As of Fall 2020, the Anaconda is distributing Python 3.8. Don’t worry if you find that you need to use a different version of Python. Anaconda can help you manage multiple versions of Python within conda environments. Just don’t use Python 2. It is no longer supported by the Python Foundation, the governing body of Python.

Side Note:
For much of this book we are assuming that you are using a Unix like operating system (Linux, MacOS, BSD). If you are using Windows, please let us know! We can help you sort out some potential issues you may have. For much of the computing at ORNL, particularly when it comes to the supercomputers, Linux is the default. We do not demand that you use a Unix like OS, but you may have to do some extra leg work.

Graphical Installer

For a graphical installer of Python, follow the download instructions here.

Command Line Installation

If you prefer to work on the command line, you can find various versions of bash install scripts in the Anaconda archive. Make sure that you grab the appropriate 64 bit installer for you operating system in the archive, then download it using wget:

wget https://repo.anaconda.com/archive/<Filename>

where <Filename> is the name of the bash script found in the archive. For example, if you are on a 64 bit Linux system, use

wget https://repo.anaconda.com/archive/Anaconda3-2020.07-Linux-x86_64.sh

Once you have that install script, follow the steps outlined after running the installer:

bash <Filename>

Verifying our Installation

Once you have installed Anaconda, let’s check to see that everything is working well. Let’s start by checking where Python is installed:

which python

This will give you a path to where Python is installed. For example, my Python is installed in the following path:

which python
>>> /home/yngtodd/.local/opt/anaconda3/bin/python

We will discuss paths and the Linux filesystem a bit later on. For now, Let’s make sure that the path you get from which python includes anaconda3/bin/python. If instead you see /usr/bin/python, then we need to do some debugging as you are using what is known as system Python instead of Anaconda.

Side Note:
You may wonder what which is. This is a Unix program that is installed in Unix-like operating systems by default. It tells you the path to where any program you run on the command line lives. Knowing more about the command line environment will be useful for us, but we need to get up and running with Python first! If you are curious and want to look further into this, try man which to see the manual page for which (man is another default Unix program). What happens if you run which which?

Resources

1. Corey Schafer’s YouTube video on installing Anaconda
2. Anaconda Docs