Summary and Setup
In this section we will focus on setting up the computer to get started with Python.
Python 3
It is sometimes claimed that biologist should use Python 2, because most biology related libraries in Python are written for that version. This is wrong. The reason why Python 2 is still out there is that following the release of Python 3.0 in December 2008, the CPython interpreter sustained several problems, and was not backward compatible. This meant that, any code written in Python 2, could not be run using Python 3 without modifications. By now, Python 2 is obsolete. Do not use it.
Why Anaconda?
For the purpose of this course, we recommend the Anaconda distribution of Python released by the Python Software Foundation, and maintained by the Anaconda Cloud.
Anaconda automatically installs many packages needed for scientific purposes (over 250 automatically installed). It is easy to install, and it takes care of dependencies between packages. This is particularly important because some of Python’s scientific libraries require Fortran– and C–based libraries, which may be challenging to install for beginners.
Installation
To install the Anaconda distribution of Python, please visit the installation instructions as outlined in the Anaconda documentations, and follow the instructions for your operating system. Ensure that you use the Python 3.x graphical installer for Windows and MacOSX (there is no graphical installer for Linux). Once downloaded, you can proceed to install the distribution as you would any other application on your computer.
Anaconda Navigator is a desktop graphical user interface (GUI) included in Anaconda distribution that allows users to launch applications and manage conda packages, environments and channels without using command-line commands. Navigator can search for packages on Anaconda Cloud or in a local Anaconda Repository, install them in an environment, run the packages and update them. It is available for Windows, macOS and Linux.
The following applications are available by default in Navigator:
JupyterLab
Jupyter Notebook
QtConsole
Spyder
Glue
Orange
RStudio
Visual Studio Code
We recommend using JupyterLab for writing and practicing your codes.