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COMP0233: Research Software Engineering With Python

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Windows

Python

We recommend installing a complete scientific python distribution. One of these is Anaconda.

Please download and install Anaconda (Python 3.7 version).

Sophos

To use the Jupyter lab or notebook on a Windows computer with Sophos anti-virus installed it may be necessary to open additional ports allowing communication between the notebook and its server. The solution is:

  • open your Sophos Endpoint Security and Control Panel from your tray or start menu
  • Select “configure” > “Anti-virus” > “Authorization” from the menu at the top
  • Select the websites tab
  • click the “Add” button and add 127.0.0.1 and localhost to the “Authorized websites” list
  • restart computer (most likely not needed, just restart the Jupyter notebook)
  • output works now :)

Git

Install the GitHub for Windows client. This comes with both a GUI client as well as the Git Bash terminal client which we will use during the course. You should register with Github for an account and sign into the GUI client with this account. This will automatically set-up SSH based authentication for the terminal client. The terminal client comes in 3 different flavours based on Windows CMD (DOS like), Windows Powershell, and BASH. We will use the BASH client as this most closely resembles the Linux and OS X terminal used by other students. In order to configure this open the Github client. Sign in with your credentials and:

  • Select tools
  • Options
  • Default Shell
  • Git Bash
  • And Press Update to save.

Verify that this is working by opening Git Bash. The Shell window should have a title that starts with MINGW64.

Editor

Unless you already use a specific editor which you are comfortable with we recommend using Visual Studio Code. Check their setup page for detailed instructions.

Using VSCode to edit text files including code should be straight forward but in addition you could configure Git Bash and python prompt.

For a better git integration we suggest the git graph plugin.

Testing your install

Check this works by opening the git bash shell. Once you have a terminal open, type

which code

which should produce readout similar to /c/Program Files (x86)/Code/Code.exe

Also verify the typing:

code

opens the editor and the close it again.

which git

which should produce /bin/git. The which command is used to figure out where a given program is located on disk.

Telling Git about VS Code

Now we need to update the default editor used by Git.

git config --global core.editor "code --wait"

Note that it is not obvious how to copy and paste text in a Windows terminal including Git Bash. Copy and paste can be found by right clicking on the top bar of the window and selecting the commands from the drop down menu (in a sub menu).

Testing python

Confirm that the Python installation has worked by typing:

python -V

Which should result in details of your installed python version.

This should print the installed version of the python and git confirming that both are installed at working correctly.

You should now have a working version of git, python, and code, all accessible from your shell.