You will need the following software installed and working correctly on your system to be able to follow the course.
- Command line tool (such as Bash, Zsh or Git Bash)
- Git version control program
- GitLab account
- Python 3 distribution
- PyCharm integrated development environment (IDE)
Common Issues & Tips
If you are having issues installing or running some of the tools below, check a list of common issues other course participants encountered and some useful tips for using the tools and working through the material.
Command Line Tool
You will need a command line tool (shell/console) in order to run Python scripts and version control your code with Git.
- On Windows, it is strongly recommended to use Git Bash (which is included in
Git For Windows package - see the Git installation section below). The use of
Windows command line tool
cmdis not suitable for the course. We also advise against using Windows Subsystem for Linux (WSL) for this course as we do not provide instructions for troubleshooting any potential issues between WSL and PyCharm. - On macOS and Linux, you will already have a command line tool available on your system. You can use a command line tool such as Bash, or any other command line tool that has similar syntax to Bash, since none of the content of this course is specific to Bash. Note that starting with macOS Catalina, Macs will use Zsh (Z shell) as the default command line tool instead of Bash.
To test your command line tool, start it up and type:
$ date
If your command line program is working - it should return the current date and time similar to:
Wed 21 Apr 2021 11:38:19 BST
Git Version Control Tool
Git is a program that can be accessed from your command line tool.
- On Windows, it is recommended to use Git Bash, which comes included as part of the Git For Windows package and will install the Bash command line tool as well as Git.
- On macOS, Git is included as part of Apple’s Xcode tools and should be available from the command line as long as you have Xcode. If you do not have Xcode installed, you can download it from Apple’s App Store or you can install Git using alternative methods.
- On Linux, Git can be installed using your favourite package manager.
To test your Git installation, start your command line tool and type:
$ git help
If your Git installation is working you should see something like:
usage: git [-v | --version] [-h | --help] [-C <path>] [-c <name>=<value>]
[--exec-path[=<path>]] [--html-path] [--man-path] [--info-path]
[-p | --paginate | -P | --no-pager] [--no-replace-objects] [--bare]
[--git-dir=<path>] [--work-tree=<path>] [--namespace=<name>]
[--config-env=<name>=<envvar>] <command> [<args>]
These are common Git commands used in various situations:
start a working area (see also: git help tutorial)
clone Clone a repository into a new directory
init Create an empty Git repository or reinitialize an existing one
work on the current change (see also: git help everyday)
add Add file contents to the index
mv Move or rename a file, a directory, or a symlink
restore Restore working tree files
rm Remove files from the working tree and from the index
examine the history and state (see also: git help revisions)
bisect Use binary search to find the commit that introduced a bug
diff Show changes between commits, commit and working tree, etc
grep Print lines matching a pattern
log Show commit logs
show Show various types of objects
status Show the working tree status
grow, mark and tweak your common history
branch List, create, or delete branches
commit Record changes to the repository
merge Join two or more development histories together
rebase Reapply commits on top of another base tip
reset Reset current HEAD to the specified state
switch Switch branches
tag Create, list, delete or verify a tag object signed with GPG
collaborate (see also: git help workflows)
fetch Download objects and refs from another repository
pull Fetch from and integrate with another repository or a local branch
push Update remote refs along with associated objects
'git help -a' and 'git help -g' list available subcommands and some
concept guides. See 'git help <command>' or 'git help <concept>'
to read about a specific subcommand or concept.
See 'git help git' for an overview of the system.
When you use Git on a machine for the first time, you need to configure a few things:
- your name,
- your email address (the one you used to open your GitLab account with, which will be used to uniquely identify your commits),
- preferred text editor for Git to use (e.g.
nanoor another text editor of your choice), - whether you want to use these settings globally (i.e. for every Git project on your machine).
This can be done from the command line as follows:
$ git config --global user.name "Your Name"
$ git config --global user.email "name@example.com"
$ git config --global core.editor "nano -w"
GitLab Account
GitLab is an online host for Git repositories that you will use during the course to store your code in. You will need a GitLab account with which you have access to TNOs GitLab instance. Please contact us if you do not have such an account.
Secure Access To GitLab Using Git From Command Line
In order to access GitLab using Git from your machine securely, you need to set up a way of authenticating yourself with GitLab through Git. The recommended way to do that for this course is to set up SSH authentication - a method of authentication that is more secure than sending passwords over HTTPS and which requires a pair of keys - one public that you upload to your GitLab account, and one private that remains on your machine.
GitLab provides full documentation and guides on how to on this page. Please follow the instructions to setup an SSH connection.
To check that everything works, run:
ssh -T git@gitlab.example.com
returning (something similar to):
Hi [username]! You've successfully authenticated, but GitLab does not provide shell access.
Connection to gitlab.com closed.
Python 3 Distribution
To download the latest Python 3 distribution for your operating system, please head to Python.org.
If you are on Linux, it is likely that the system Python 3 already installed will satisfy the requirements of this course (the material has been tested using the standard Python distribution version 3.11 but any supported version should work).
The course uses venv for virtual environment management and pip for package management.
The material has not been extensively tested with other Python distributions and package managers,
but most sections are expected to work with some modifications.
For example, package installation and virtual environments would need to be managed differently, but Python script
invocations should remain the same regardless of the Python distribution used.
Recommended Python Version
We recommend using the latest Python version but any supported version should work. Specifically, we recommend upgrading from Python 2.7 wherever possible; continuing to use it will likely result in difficulty finding supported dependencies or syntax errors.
You can test your Python installation from the command line with:
$ python3 --version # on Mac/Linux
$ python --version # on Windows — Windows installation comes with a python.exe file rather than a python3.exe file
If you are using Windows and invoking python command causes your Git Bash terminal to hang with no error message or output, you may
need to create an alias for the python executable python.exe, as explained in the troubleshooting section.
If all is well with your installation, you should see something like:
Python 3.11.4
To make sure you are using the standard Python distribution and not some other distribution you may have on your system, type the following in your shell:
$ python3 # python on Windows
This should enter you into a Python console and you should see something like:
Python 3.11.4 (main, Jun 20 2023, 17:23:00) [Clang 14.0.3 (clang-1403.0.22.14.1)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>>
Press CONTROL-D or type exit() to exit the Python console.
venv and pip
If you are using a Python 3 distribution from Python.org,
venv and pip will be automatically installed for you. If not, please make sure you have these
two tools (that correspond to your Python distribution) installed on your machine.
PyCharm IDE
We use JetBrains’s PyCharm Python Integrated Development Environment for the course. PyCharm can be downloaded from the JetBrains website. The Community edition is fine, though if you are developing software for the purpose of academic research you may be eligible for a free license for the Professional edition which contains extra features.