7. Running Python

They are several ways to work with Python, each of which is best adapted to a certain type of task:

  • To write reusable python scripts, use a code editor (e.g. subl` (Sublime Text)), or an Integrated Development Environment (e.g. spyder), save the script and run it from a shell command line inside a Terminal.

  • To quickly test short pieces of code in an interactive manner, or to access the documentation of some functions or mudles, open a terminal and run ipython

  • To write a data analysis report use jupyter notebook

7.1. Running a python script from the command line

To run a python script, that is, a text file containing python code, you need to:

  1. Open a Terminal

  • MacOSX: Search for terminal in Spotlight.

  • Windows: Launch Git Bash (This assumes that you have installed

    Git for windows as described in Instructions for software installation)

  • Linux: Launch Terminal from your application menu or use

    Ctrl-Alt-T in Gnome, Xfce or Win+Return in i3.

  1. If the script is not located in your home directory, use the cd command to navigate to the directory that contains the script (to learn about this, read Navigation in the shell).

  2. Type python followed by the script’s filename, then press the return/enter key.

For example, let us suppose that you want to execute a script named matches.py located in a subdirectory PCBS/games of your home directory. Open a terminal and type:

cd PCBS/games
python matches.py


  • When the script has run to completion, you will be back to interacting with the shell.

  • It you need to interrupt a running python script, you can press Ctrl-C in the Terminal.

  • You can specify absolute or relative pathnames to specify the location of the script:

    python ~/PCBS/games/matches.py

Note: The directory from which you started the script is the current working directory: it will be the root for any relative path names that may be used within the script.

  • A good practice is to systematically take a glance to the code before running it. Depending on your system, you might be able to do this with the commands cat filename.py or less filename.py or micro filename.py.

7.2. Testing a short piece of python code

To quickly test some Python code, type ipython (“interactive Python”) on a command line.


Then press ‘Return’; you should obtain a should display like the following:


A blinking cursor after [1]: indicates that ipython is ready and waiting for you to enter a Python statement that it will execute as soon as you press the “Return” key. For example, try:

2 ** 5
2 ** 64
import turtle

import matplotlib.pyplot as plt
import numpy as np
t = np.linspace(0, 30, num=3001)
plt.plot(t, np.sin(t))

A Window should open with a graphical representation of the sine function, You can press ‘q’ in this Window to close it.

It is possible to execute a python script from within ipython. While in ipython, try:

cd PCBS/games
%run matches.py

Finally, To quit ipython, type quit() or press Ctrl-D .

This approach is fine if you need to quickly test an idea. But as soon as you quit ipython, you lose all what you have done.

To keep track of your work, you need to use a code editor and the Edit-Run approach.

7.3. Write code with a text editor (Edit-run cycle)

A script is nothing but a pure text file, that is, a sequence of characters.

A Python script is written with a text editor, saved on the disk, and then executed.

  1. Open a Text-Editor (e.g. Sublime Text) and a Terminal window side-by-side:

Using Atom and a Terminal side by side
  1. Create a New File in the Editor and enter the following text:

import turtle
  1. Using ‘File/Save as’, save the this text under the filename myscript.py in your personal (home) directory

  • run with a python interpreter, by typing python myscript.py on a command line of the Terminal. Try it now.

Important: you must make sure that the current working directory of the terminal is the same directory where the file myscript.py has been saved. Otherwise, you will get an error message such as ‘No such file or directory’. To fix this problem, you must use the cd command to navigate the directory structure.


  • You can learn more about Turtle graphics by reading the documentation at https://docs.python.org/2/library/turtle.html

  • WINDOWS Only: To be able to start ‘Sublime Text’ from the command line by just typing subl, copy the following command:

    export PATH=”/c/Program Files/SublimeText 3/”:”$PATH”

in the file $HOME/.bash_profile (create it if necessary)

7.4. Using an Integrated Development Environment (IDE)

Some people like to work within a single application and avoid going back and forth from the text editor to the terminal. The Anaconda Python distribution comes with and integrated development environment (IDE), Spyder, which provides an environment somewhat similar to the MATLAB IDE. PyCharm and Microsoft Visual Code are two other popular (and more powerful) IDEs.

The “spyder” Integrated Development Environment

The “Spyder” Integrated Development Environment

Visual Code, PyCharm, Spyder… are very nice IDEs but you should not use them to run python scripts that open new graphics windows (e.g. scripts using tkinter, pygame, …) because, when such scripts crash, they can leave the IDE in an unstable state. It is always safer to run a script directly from the command line in a terminal windows.

One commendable approach is to use an IDE to edit python code, but use the command line to run the scripts.

7.5. Perform an interactive data analysis with jupyter-notebook or jupyter-lab

To perform data analyses and produce nicely formatted reports, one can use jupyter-notebook or jupyter-lab (see https://jupyter.org/).

In practice, launch Jupyter Notebook from the Start Menu/Anaconda3 (in Windows) or type jupyter notebook in a terminal (Linux, MacOS). The “Jupyter homepage” should then open in your browser:

Jupyter homepage

Clicking New and selecting Python [root] will open a new tab containing a notebook where you can enter python code inside so-called ‘cells’. To execute the code in a cell, just move the cursor there and press Ctrl+Enter

Jupyter notebook

A nice feature of the Jupyter notebooks is persistence, i.e. they are saved automatically (in .ipynb files) and you can go on working on the same notebook whn you reopen it. This is also very handy, for example, to send a data analysis report by email.

Jupyter’s documentation is available at http://jupyter.readthedocs.io/en/latest/index.html

7.6. Developping in Python with Emacs




Comment or Uncomment cleverly









Navigate the function definitions

C-c C-j


Move backward to block



Move forward to block



Checking for errors, etc.


Checking for errors, etc.


Reformat code to best practices


Launch the Python Debugger (Pdb)