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Python for ecologists

Short Introduction to Programming in Python

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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. As a consequence, we can use it 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

The most basic data types in Python are strings, integers and floats:

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 scripts we must use the print function:

# Comments start with #
# Next line will print out text
print(text)
"Data Carpentry"

Operators

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

>>> 2 + 2
4
>>> 6 * 7
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. This is Python’s way of marking a block of code.

To add elements to the end of a list, we can use the append method:

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

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. 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

  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}
...
TypeError: unhashable type: 'list'

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? Give it a try.

  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 part of a program in Python as a function 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 here:

Key Points

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