Python for ecologists

Short Introduction to Programming in Python

Overview

Teaching: 0 min
Exercises: 0 min
Questions
  • What is Python?

  • Why should I learn Python?

Objectives
  • Describe the advantages of using programming vs. completing repetitive tasks by hand.

  • Define the following data types in Python: strings, integers, and floats.

  • Perform mathematical operations in Python using basic operators.

  • Define the following as it relates to Python: lists, tuples, and dictionaries.

The Basics of Python

Python is a general purpose programming language that supports rapid development of scripts and applications.

Python’s main advantages:

Interpreter

Python is an interpreted language which can be used in two ways:

user:host:~$ python
Python 3.5.1 (default, Oct 23 2015, 18:05:06)
[GCC 4.8.3] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> 2 + 2
4
>>> print("Hello World")
Hello World
user:host:~$ python my_script.py
Hello World

Introduction to Python built-in data types

Strings, integers and floats

Python has built-in numeric types for integers, floats, and complex numbers. Strings are a built-in textual type.:

text = "Data Carpentry"
number = 42
pi_value = 3.1415

Here we’ve assigned data to variables, namely text, number and pi_value, using the assignment operator =. The variable called text is a string which means it can contain letters and numbers. Notice that in order to define a string you need to have quotes around your text. To print out the value stored in a variable we can simply type the name of the variable into the interpreter:

>>> text
"Data Carpentry"

However, in a script, a print function is needed to output the text:

example.py

# A Python script file
# Comments in Python start with #
# The next line assigns the string "Data Carpentry" to the variable "text".
text = "Data Carpentry"
# The next line uses the print function to print out the text string
print(text)

Running the script

$ python example.py
Data Carpentry

Tip: The print function is a built-in function in Python. Later in this lesson, we will introduce methods and user-defined functions. The Python documentation is excellent for reference on the differences between them.

Operators

We can perform mathematical calculations in Python using the basic operators +, -, /, *, %:

>>> 2 + 2   #  addition
4
>>> 6 * 7   #  multiplication
42
>>> 2 ** 16  # power
65536
>>> 13 % 5  # modulo
3

We can also use comparison and logic operators: <, >, ==, !=, <=, >= and statements of identity such as and, or, not. The data type returned by this is called a boolean.

>>> 3 > 4
False
>>> True and True
True
>>> True or False
True

Sequential types: Lists and Tuples

Lists

Lists are a common data structure to hold an ordered sequence of elements. Each element can be accessed by an index. Note that Python indexes start with 0 instead of 1:

>>> numbers = [1, 2, 3]
>>> numbers[0]
1

A for loop can be used to access the elements in a list or other Python data structure one at a time:

>>> for num in numbers:
...     print(num)
...
1
2
3
>>>

Indentation is very important in Python. Note that the second line in the example above is indented. Just like three chevrons >>> indicate an interactive prompt in Python, the three dots ... are Python’s prompt for multiple lines. This is Python’s way of marking a block of code. [Note: you do not type >>> or ....]

To add elements to the end of a list, we can use the append method. Methods are a way to interact with an object (a list, for example). We can invoke a method using the dot . followed by the method name and a list of arguments in parentheses. Let’s look at an example using append:

>>> numbers.append(4)
>>> print(numbers)
[1, 2, 3, 4]
>>>

To find out what methods are available for an object, we can use the built-in help command:

help(numbers)

Help on list object:

class list(object)
 |  list() -> new empty list
 |  list(iterable) -> new list initialized from iterable's items
 ...

Tuples

A tuple is similar to a list in that it’s an ordered sequence of elements. However, tuples can not be changed once created (they are “immutable”). Tuples are created by placing comma-separated values inside parentheses ().

# tuples use parentheses
a_tuple= (1, 2, 3)
another_tuple = ('blue', 'green', 'red')
# Note: lists use square brackets
a_list = [1, 2, 3]

Challenge - Tuples

  1. What happens when you type a_tuple[2]=5 vs a_list[1]=5 ?
  2. Type type(a_tuple) into python - what is the object type?

Dictionaries

A dictionary is a container that holds pairs of objects - keys and values.

>>> translation = {'one': 1, 'two': 2}
>>> translation['one']
1

Dictionaries work a lot like lists - except that you index them with keys. You can think about a key as a name for or a unique identifier for a set of values in the dictionary. Keys can only have particular types - they have to be “hashable”. Strings and numeric types are acceptable, but lists aren’t.

>>> rev = {1: 'one', 2: 'two'}
>>> rev[1]
'one'
>>> bad = {[1, 2, 3]: 3}
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
TypeError: unhashable type: 'list'

In Python, a “Traceback” is an multi-line error block printed out for the user.

To add an item to the dictionary we assign a value to a new key:

>>> rev = {1: 'one', 2: 'two'}
>>> rev[3] = 'three'
>>> rev
{1: 'one', 2: 'two', 3: 'three'}

Using for loops with dictionaries is a little more complicated. We can do this in two ways:

>>> for key, value in rev.items():
...     print(key, '->', value)
...
1 -> one
2 -> two
3 -> three

or

>>> for key in rev.keys():
...     print(key, '->', rev[key])
...
1 -> one
2 -> two
3 -> three
>>>

Challenge - Can you do reassignment in a dictionary?

  1. First check what rev is right now (remember rev is the name of our dictionary).

    Type:

    >>> rev
    
  2. Try to reassign the second value (in the key value pair) so that it no longer reads “two” but instead reads “apple-sauce”.

  3. Now display rev again to see if it has changed.

It is important to note that dictionaries are “unordered” and do not remember the sequence of their items (i.e. the order in which key:value pairs were added to the dictionary). Because of this, the order in which items are returned from loops over dictionaries might appear random and can even change with time.

Functions

Defining a section of code as a function in Python is done using the def keyword. For example a function that takes two arguments and returns their sum can be defined as:

def add_function(a, b):
    result = a + b
    return result

z = add_function(20, 22)
print(z)
42

Key points about functions are:

Key Points