Why Python?

Overview

Teaching: min
Exercises: min

Questions

Objectives

Why Python?

• Free, well-documented, runs almost everywhere
• Large (and growing) user base among researchers and scientists
• Simple, readable, flexible, powerful language and easier for beginners to grasp
• Great for team working
  • Python aim - only one way to do something
  • Programs look very similar, easy for others to read
• Want to teach basic programming concepts that can be applied to other programming languages

What can you use it for?

• Almost anything - it’s general purpose!
• Used in many fields
  • Bioinformatics, Biology, Data visualisation, Engineering, Software development, etc.
• Used for processing data, general scripting, mapping, web applications, frameworks, numerical processing, education, HPC, at Google, …

Python is up and coming!

• Based on Southampton PhD students software usage survey conducted by SSI’s Policy researchers:

We’ll be teaching Python 3

• Python 3 is currently the standard version
• We’ll teach using version 3!
• Python 3 has many advantages over Python 2
  • Many consistency improvements - removing redundancy
  • In places, simply more sensible e.g. integer division
  • Python 2 support will end in 2020
  • ‘Short version: Python 2.x is legacy, Python 3.x is the present and future of the language’
• For new projects, seriously consider Python 3!

Learning objectives

• how to assign values to variables, simple operations
• how to repeat actions with loops
• how to make choices using conditionals
• why we should divide programs into small, single-purpose blocks of code
• how to build a program, step by step, to do basic analysis on some climate data
• how we should analyse and fix errors in our programs
• how to read and analyse patient data using libraries
• how to visualise data using libraries

Turning on Python Interpreter

• The interpreter provides an interactive environment to play with the language
• Mac/Linux: Open a terminal window and type python3
• Windows: Open Git Bash and type python
• At the prompt type ‘hello world!’

Why indentation?

• Studies show that’s what people actually pay attention to + Every textbook on C or Java has examples where indentation and bracing don’t match
• Doesn’t matter how much indentation you use, but the whole block must be consistent
• Python Style Guide (PEP 8) recommends 4 spaces
• And no tab characters

Indexing a List Example I

Indexing a List Example II

Slicing a List Example I

Slicing a List Example II

NumPy Arrays

• NumPy arrays and operations on arrays of data

  

Indexing in a NumPy 2D array

• The indices are (row, column) instead of (column, row).
• Example Patient inflammation data who were given treatment for arthritis:
  • Rows: Hold information for a single patient
  • Columns: Represent successive days

Cont..

Wrap-up Challenge: Connecting the dots

Write a python script (function) for Fahrenheit to Celsius temperature conversion and stores the output in a file.

• Hint (Tools to be used):
  • Unix pipes and filters
  • Python functions
  • Command-line programs
  • Using Fahr_to_kelvin() and Kelvin_to_celsius() functions

Thank You!

Key Points