Programming with Python: Setup

Install Python

In this lesson we will be using Python 3 with some of its scientific libraries. Although one can install a “plain vanilla” Python 3 and all required libraries “by hand”, we recommend installing Anaconda, a Python distribution that comes with everything we need for the lesson.

 

Obtain lesson materials

  1. Download python-novice-inflammation-data.zip and python-novice-inflammation-code.zip.
  2. Create a folder called swc-python on your Desktop.
  3. Move downloaded files into this newly created folder.
  4. Unzip the files.

You should now see two new folders called data and code in your swc-python directory on your Desktop.

 

If you’re using a Unix shell application, such as Terminal app in macOS, Console or Terminal in Linux, or Git Bash on Windows, execute the following command:

$ cd ~/Desktop/swc-python/data

On Windows, you can use its native Command Prompt program. The easiest way to start it up is by pressing Windows Logo Key+R, entering cmd, and hitting Return. In the Command Prompt, use the following command to navigate to the data folder:

$ cd /D %userprofile%\Desktop\swc-python\data

 

Option 1: Launch “plain vanilla” Python interpreter

To start working with Python, we need to launch a program that will interpret and execute our Python commands. To launch a “plain vanilla” Python interpreter, execute:

$ python

If you are using Git Bash on Windows, you have to call Python via winpty:

$ winpty python

 

Option 2: Start Jupyter Notebook

Jupyter Notebook provides a browser-based interface for working with Python. If you would like to use a notebook during the lesson, make sure to install Anaconda distribution.

To start a Jupyter server, execute:

$ jupyter notebook

Then create a new notebook by clicking “New” button on the right and selecting “Python 3” from the drop-down menu:

 

Option 3: Start IPython interpreter

IPython is an alternative solution situated somewhere in between the plain vanilla Python interpreter and Jupyter Notebook. It provides an interactive command-line based interpreter with various convenience features and commands. You should have IPython on your system if you installed Anaconda distribution.

To start using IPython, execute:

$ ipython