Chapter 2: Getting started with Anaconda and Spyder

The Integrated Development Environment (IDE)

“IDE” what? Wikipedia defines it as follows:

An integrated development environment (IDE) is a software application that provides comprehensive facilities to computer programmers for software development. An IDE normally consists of at least a source code editor, build automation tools and a debugger. An IDE normally consists of at least a source code editor, build automation tools and a debugger.
en.wikipedia.org

Hence, an IDE mainly consists of a source code editor, build automation tools (e.g., integrated in a terminal/console) and a debugger.

Available are all-in-one Python-specific solutions, e.g., Spyder via Anaconda, PyCharm, Visual Studio Code and many more. You can find a broader overview here ꜛ.

The Spyder IDE, included in Anaconda. (own screenshot)

there are also online solutions like Google Colab ꜛ:

But in principle, you can use any text editor and the terminal/console of your operating system (with an installed Python version).

A text editor a terminal and a Python installation is already everything, what you need to program in Python. (own screenshot)

Anaconda

In this course, we will use Anaconda:

it is free and open-source,
comes with Python and R,
has an easy to use editor with integrated console (Spyder),
has a simplified package management, and
it can be installed on MacOS, Windows and Linux.
https://www.anaconda.com/products/individual

We will install some additional packages first, which we will need throughout our course:

Please, follow the instructions on the slides above and install the following additional packages – either during the course or in preparation of part II at home (also see voluntary homework):

matplotlib
numpy
pandas
openpyxl
xlrd
pingouin (requires the conda-forge channel to be added!)

Some of these packages will not be listed at first glance. If this happens, you need to add the additional channel conda-forge. Also here, please follow the instruction on the slides

Spyder

Let’s launch Spyder:

Spyder will open up and it should look like something like the screenshot:

Spyder IDE explained

Module	Description
Console	code execution, either directly (by typing your commands right into this window) or from your script
Editor	here you will write your script, in principal a text file (with the file ending “.py”), which contains line-by-line your code, that will then be executed in the console
Variable explorer tab	an overview of all your currently defined variables
File explorer tab	like your Windows Explorer or MacOS Finder, navigate through your files
Plots tab	by default, all your plots are displayed in this tab
Current folder path	view and change the current folder
Run file button	run your script (the first execution of a new script displays a command prompt to save the script)
Run current cell button	executes your currently selected cell (cells will be introduced later)

Our first commands

Type your first Python commands into the console:

  5+5
  print("Hello world.")

Click on the Variable explorer and define your first variables in the Console:

  a=5
  b=10
  print(a+b)          # this is the default print command
  print(f"a+b={a+b}") # this is a formatted print command

Type the following code into the editor and hit the Run file button:

  a=5
  b=10
  print(a+b)
  print(b**a)

Change b to 20 and re-run your script.

  b=20

Note, that the variable b will be updated in the Variable explorer

You can also define variables with text (“strings”):

  text_A = "Hello, my name is "
  text_B = "Gandalf."
  print(text_A)
  print(text_B)
  print(text_A + text_B)

Comments

In Python, you have two options to add comments to your code:

use # followed by you comment text, to add a line comment
- can be placed anywhere in your script
- good for, e.g., quick annotations
- every new line needs to be initialized with a new #

# This is a line comment placed at the line beginning:
print(f"Some text")

# Line comments can be written one after another
# and as many as you want to

print(f"Some more text")  # they can be arbitrarily placed

use ''' your block comment text ''', to add a block comment (also called dockstring when, e.g., used within functions or classes)
- good for, e.g., longer comments (it accepts line breaks within the comment block)

""" This is a block comment """

""" You can insert line breaks into block comment, which
    useful e.g., for longer comments, as you
    don't have to write # for each new line.
"""

General usage suggestions for comments: Where appropriate, use as many comments as possible: comment you changes and add-ons to your code, explain your code (to yourself and to colleagues and potential other users of your code), describe the units of the variables that you use, note down to-do’s and infos, if something is not working yet, etc. Your future self will thank you for that.

Code Cells

Besides comments, we can further structure our code by introducing code cell:

use #%% at the beginning of a line, to introduce a new code cells
an additional #%% afterwards will define the code cell’s end and the beginning of a new cell
after #%% you can even write some text to describe the purpose of your cell
you can execute code cells cell-by-cell by hitting the Run current cell button (instead of always running your entire script)

#%% My first code cell
a=5
b=20
print(a+b)
print(b**a)

#%% My second code cell
text_A = "Hello, my name is "
text_B = "Gandalf."
print(text_A)
print(text_B)
print(text_A + text_B)

General suggestions for code cell: You can use code cells to separate, e.g., the variable definition part, your main algorithm and a potential plot command section from each other.