You will need the following software installed and working correctly on your system to be able to follow the course.
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 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.
- 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:
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.
- For AstraZeneca-managed computers (where you may not have admin permissions), you can obtain Git For Windows package from the AstraZeneca Software Store.
- 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 [--version] [--help] [-C <path>] [-c name=value] [--exec-path[=<path>]] [--html-path] [--man-path] [--info-path] [-p | --paginate | --no-pager] [--no-replace-objects] [--bare] [--git-dir=<path>] [--work-tree=<path>] [--namespace=<name>] <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 reset Reset current HEAD to the specified state 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 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 checkout Switch branches or restore working tree files commit Record changes to the repository diff Show changes between commits, commit and working tree, etc merge Join two or more development histories together rebase Reapply commits on top of another base tip 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. $ git help
For the purposes of the course, you will also need a GitHub account. GitHub is a free, online host for Git repositories that you will use during the course to store your code in. You can create an account at GitHub for free if you don’t already have one.
The material has been developed using the standard Python distribution version 3.8
and is using
venv for virtual environments 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.
To download a Python distribution for your operating system, please head to Python.org.
For AstraZeneca-managed computers, you can obtain Python 3.9.7 from the AstraZeneca Software Store. Please make sure not to use Anaconda as it is not free for commercial use.
Recommended Python Version
We recommend using at least Python version 3.8+ but any supported version should work (i.e. version 3.7 onward. 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
If all is well with your installation, you should see something like:
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:
This should enter you into a Python console and you should see something like:
Python 3.8.2 (default, Jun 8 2021, 11:59:35) [Clang 12.0.5 (clang-1126.96.36.199)] on darwin Type "help", "copyright", "credits" or "license" for more information. >>>
CONTROL-D or type
exit() to exit the Python console.
If you are using a Python 3 distribution from Python.org,
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.
For AstraZeneca-managed computers, PyCharm Community Edition is available from the AZ Software Store.