| title |
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Setup |
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
- GitHub account
- Python 3 distribution
- PyCharm integrated development environment (IDE)
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. {: .callout}
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
{: .language-bash}
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
{: .output}
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
{: .language-bash}
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.
{: .output}
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 GitHub 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 "[email protected]"
$ git config --global core.editor "nano -w"
{: .language-bash}
GitHub is a free, online host for Git repositories that you will use during the course to store your code in so you will need to open a free GitHub account unless you do not already have one.
In order to access GitHub using Git from your machine securely, you need to set up a way of authenticating yourself with GitHub 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 GitHub account, and one private that remains on your machine.
GitHub provides full documentation and guides on how to:
A short summary of the commands you need to perform is shown below.
To generate an SSH key pair, you will need to run the ssh-keygen command from your command line tool/GitBash
and provide your identity for the key pair (e.g. the email address you used to register with GitHub)
via the -C parameter as shown below.
Note that the ssh-keygen command can be run with different parameters -
e.g. to select a specific public key algorithm and key length;
if you do not use them ssh-keygen will generate an
RSA
key pair for you by default.
GitHub now recommends that you use a newer cryptographic standard (such as EdDSA variant algorithm Ed25519),
so please be sure to specify it using the -t flag as shown below.
It will also prompt you to answer a few questions -
e.g. where to save the keys on your machine and a passphrase to use to protect your private key.
Pressing 'Enter' on these prompts will get ssh-keygen to use the default key location (within
.ssh folder in your home directory)
and set the passphrase to empty.
$ ssh-keygen -t ed25519 -C "[email protected]"
{: .language-bash}
Generating public/private ed25519 key pair.
Enter file in which to save the key (/Users/<YOUR_USERNAME>/.ssh/id_ed25519):
Enter passphrase (empty for no passphrase):
Enter same passphrase again:
Your identification has been saved in /Users/<YOUR_USERNAME>/.ssh/id_ed25519
Your public key has been saved in /Users/<YOUR_USERNAME>/.ssh/id_ed25519.pub
The key fingerprint is:
SHA256:qjhN/iO42nnYmlpink2UTzaJpP8084yx6L2iQkVKdHk [email protected]
The key's randomart image is:
+--[ED25519 256]--+
|.. .. |
| ..o A |
|. o.. |
| .o.o . |
| ..+ = B |
| .o = .. |
|o..X *. |
|[email protected] |
|+*XOoOo+ |
+----[SHA256]-----+
{: .output}
Next, you need to copy your public key (not your private key - this is important!) over to
your GitHub account. The ssh-keygen command above will let you know where your public key is saved (the file should have the
extension ".pub"), and you can get its contents (e.g. on a Mac OS system) as follows:
$ cat /Users/<YOUR_USERNAME>/.ssh/id_ed25519.pub
{: .language-bash}
ssh-ed25519 AABAC3NzaC1lZDI1NTE5AAAAICWGVRsl/pZsxx85QHLwSgJWyfMB1L8RCkEvYNkP4mZC [email protected]
{: .output}
Copy the line of output that starts with "ssh-ed25519" and ends with your email address (it may start with a different algorithm name based on which one you used to generate the key pair and it may have gone over multiple lines if your command line window is not wide enough).
Finally, go to your GitHub Settings -> SSH and GPG keys -> Add New page to add a new SSH public key. Give your key a memorable name (e.g. the name of the computer you are working on that contains the private key counterpart), paste the public key from your clipboard into the box labelled "Key" (making sure it does not contain any line breaks), then click the "Add SSH key" button.
Now, we can check that the SSH connection is working:
$ ssh -T [email protected]
{: .language-bash}
While using passwords over HTTPS for authentication is easier to setup and will allow you read access to your repository on GitHub from your machine, it alone is not sufficient any more to allow you to send changes or write to your remote repository on GitHub. This is because, on 13 August 2021, GitHub has strengthened security requirements for all authenticated Git operations. This means you would need to use a personal access token instead of your password for added security each time you need to authenticate yourself to GitHub from the command line (e.g. when you want to push your local changes to your code repository on GitHub). While using SSH key pair for authentication may seem complex, once set up, it is actually more convenient than keeping track of/caching your access token. {: .callout}
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.
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. {: .callout}
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
{: .language-bash}
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
{: .output}
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
{: .language-bash} 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.
>>>
{: .language-bash}
Press CONTROL-D or type exit() to exit the Python console.
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.
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.
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