This lesson is being piloted (Beta version)

Intermediate Research Software Development in Python: Setup

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.

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.

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

GitHub Account

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.

Python Distribution

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.

We recommend using at least Python version 3.8+ but any supported version should work (i.e. 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:

Python 3.8.2

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

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-1205.0.22.11)] 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