How to access Python for doing scientific computing

 

 

 

This chapter is taken from the book A Primer on Scientific Programming with Python by H. P. Langtangen, 5th edition, Springer, 2016.

How to write and run a Python program

You have basically three choices to develop and test a Python program:

  1. use the IPython notebook
  2. use an Integrated Development Environment (IDE), like Spyder, which offers a window with a text editor and functionality to run programs and observe the output
  3. use a text editor and a terminal window
The IPython notebook is briefly descried in the section Writing IPython notebooks, while the other two options are outlined below.

The need for a text editor

Since programs consist of plain text, we need to write this text with the help of another program that can store the text in a file. You have most likely extensive experience with writing text on a computer, but for writing your own programs you need special programs, called editors, which preserve exactly the characters you type. The widespread word processors, Microsoft Word being a primary example, are aimed at producing nice-looking reports. These programs format the text and are not acceptable tools for writing your own programs, even though they can save the document in a pure text format. Spaces are often important in Python programs, and editors for plain text give you complete control of the spaces and all other characters in the program file.

Spyder

Spyder is a graphical application for developing and running Python programs, available on all major platforms. Spyder comes with Anaconda and some other pre-built environments for scientific computing with Python. On Ubuntu it is conveniently installed by sudo apt-get install spyder.

The left part of the Spyder window contains a plain text editor. Click in this window and write print 'Hello!' and return. Choose Run from the Run pull-down menu, and observe the output Hello! in the lower right window where the output from programs is visible.

You may continue with more advanced statements involving graphics: 

import matplotlib.pyplot as plt
import numpy as np
x = np.linspace(0, 4, 101)
y = np.exp(-x)*np.sin(np.pi*x)
plt.plot(x,y)
plt.title('First test of Spyder')
plt.savefig('tmp.png')
plt.show()

Choosing Run - Run now leads to a separate window with a plot of the function \( e^{-x}\sin (\pi x) \). Figure 1 shows how the Spyder application may look like.

Figure 1: The Spyder Integrated Development Environment.

The plot file we generate in the above program, tmp.png, is by default found in the Spyder folder listed in the default text in the top of the program. You can choose Run - Configure ... to change this folder as desired. The program you write is written to a file .temp.py in the same default folder, but any name and folder can be specified in the standard File - Save as... menu.

A convenient feature of Spyder is that the upper right window continuously displays documentation of the statements you write in the editor to the left.

Text editors

The most widely used editors for writing programs are Atom, Sublime Text, Emacs, and Vim, which are available on all major platforms. Some simpler alternatives for beginners are

We may mention that Python comes with an editor called Idle, which can be used to write programs on all three platforms, but running the program with command-line arguments is a bit complicated for beginners in Idle so Idle is not my favorite recommendation.

Gedit is a standard program on Linux platforms, but all other editors must be installed in your system. This is easy: just google the name, download the file, and follow the standard procedure for installation. All of the mentioned editors come with a graphical user interface that is intuitive to use, but the major popularity of Atom, Sublime Text, Emacs, and Vim is due to their rich set of key commands so that you can avoid using the mouse and consequently edit at higher speed.

Terminal windows

To run the Python program, you need a terminal window. This is a window where you can issue Unix commands in Linux and Mac OS X systems and DOS commands in Windows. On a Linux computer, gnome-terminal is my favorite, but other choices work equally well, such as xterm and konsole. On a Mac computer, launch the application Utilities - Terminal. On Windows, launch PowerShell.

You must first move to the right folder using the cd foldername command. Then running a python program prog.py is a matter of writing python prog.py. Whatever the program prints can be seen in the terminal window.

Using a plain text editor and a terminal window

  1. Create a folder where your Python programs can be located, say with name mytest under your home folder. This is most conveniently done in the terminal window since you need to use this window anyway to run the program. The command for creating a new folder is mkdir mytest.
  2. Move to the new folder: cd mytest.
  3. Start the editor of your choice.
  4. Write a program in the editor, e.g., just the line print 'Hello!'. Save the program under the name myprog1.py in the mytest folder.
  5. Move to the terminal window and write python myprog1.py. You should see the word Hello! being printed in the window.