Essential Software Engineering for Researchers: Setup

Completing this course requires you to have access to computer with some software prerequisites installed. If you are attending a delivery of this course in person through the Graduate School you have the option of using your own laptop or an ICT managed PC at the workshop venue. For instructions on setting up your own Laptop please see below. All attendees should join the Imperial Research Software Community Slack workspace before the workshop.

Joining The Imperial Research Software Community Slack Workspace

Slack is a commonly used tool for teams and communities to keep in touch. The Research Software Community at Imperial has a dedicated Slack workspace for discussing issues related to research software. We will use this as an area to share links and information and for you to ask questions and request help. We hope that longer term you will find the Community a valuable asset in your work.

Using Your Own Laptop

The below instructions can be used to setup the required software for your own laptop. For ICT managed PC’s setup steps will be covered during the workshop. Please note that due to time constraints we are unable to support you in setting up your laptop if you come to the workshop without the below prerequisites installed and working. In this case you will need to use one of the PC’s provided.

Conda

Conda is a Python distribution and package manager. We use both features to provide the version of Python that is used in these materials and to setup self-contained environments.

You can choose to install the full version of anaconda or the more minimal miniconda. Either is suitable but make sure to choose the Python 3.* version. If prompted, choose to install only for your user account and do not install PyCharm.

To test that the installation was successful follow the instructions for your operating system below.

Windows

# conda environments:
#
base                  *  C:\Users\ccaveayl\AppData\Local\Continuum\anaconda3\

Mac and Linux

# conda environments:
#
base                  *  /home/ccaveayl/anaconda3

Visual Studio Code

This course will use Visual Studio (VS) Code as an integrated development environment (IDE). You may already have a preferred IDE that you use regularly, however we strongly suggest that you use VS Code for this course and afterwards replicate the setup as you choose. If you already have VS Code installed please make sure it is updated to the latest version.

To install VS Code follow the instructions here.

You should then be able to launch VS Code and see something like: Screenshot of VS code

Git

Please follow the relevant instructions depending on your operating system.

Windows

  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps below:
    1. Click on “Next” four times (two times if you’ve previously installed Git). You don’t need to change anything in the Information, location, components, and start menu screens.
    2. From the dropdown menu select “Use the nano editor by default” and click on “Next”.
    3. Ensure that “Git from the command line and also from 3rd-party software” is selected and click on “Next”. (If you don’t do this Git Bash will not work properly, requiring you to remove the Git Bash installation, re-run the installer and to select the “Git from the command line and also from 3rd-party software” option.)
    4. Ensure that “Use the native Windows Secure Channel library” is selected and click on “Next”.
    5. Ensure that “Checkout Windows-style, commit Unix-style line endings” is selected and click on “Next”.
    6. Ensure that “Use Windows’ default console window” is selected and click on “Next”.
    7. Ensure that “Enable file system caching” and “Enable Git Credential Manager” are selected and click on “Next”.
    8. Click on “Install”.
    9. Click on “Finish”.
  3. If your “HOME” environment variable is not set (or you don’t know what this is):
    1. Open command prompt (Open Start Menu then type cmd and press [Enter])
    2. Type the following line into the command prompt window exactly as shown:
    3. setx HOME "%USERPROFILE%"
    4. Press [Enter], you should see SUCCESS: Specified value was saved.
    5. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash via the program Git Bash. You should be able to launch Git Bash from the Start Menu. Within the window that launches enter the command git --version and press enter. You should see output similar to the below:

git version 2.23.0.windows-1

MacOS

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent “mavericks” installer from this list. Because this installer is not signed by the developer, you may have to right click (control click) on the .pkg file, click Open, and click Open on the pop up window. After installing Git, there will not be anything in your /Applications folder, as Git is a command line program. For older versions of OS X (10.5-10.8) use the most recent available installer labelled “snow-leopard” available here.

To check the installation was successful open the “Terminal” app. In the window that launches enter the command git --version and press enter. You should see output similar to the below:

git version 2.25.0

Linux

If Git is not already available on your machine you can try to install it via your distributions package manager. For Debian/Ubuntu run sudo apt-get install git and for Fedora run sudo dnf install git.

To check the installation was successful open a new terminal. In the window that launches enter the command git --version and press enter. You should see output similar to the below:

git version 2.25.0