Imperial College London, Department of Earth Science and Engineering

Nov 06-07, 2017

9:00 am - 4:30 pm

Instructors: Gerard Gorman, Nicolas Barral, Navjot Kukreja, Michael Lange

Helpers:

General Information

Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

For more information on what we teach and why, please see our paper "Best Practices for Scientific Computing".

Who: The course is aimed at graduate students and other researchers. You don't need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Royal School of Mines, Prince Consort Rd, Kensington, London SW7 2BP. Get directions with OpenStreetMap or Google Maps.

When: Nov 06-07, 2017. Add to your Google Calendar.

Contact: Please email michael.lange@imperial.ac.uk, n.barral@imperial.ac.uk for more information.


Schedule

Day 2

09:00 Version control with Git
12:00 Lunch break
13:30 Excercise and practice
16:00 Wrap up

Setup

Everything you need is already installed in the computer lab, and on the ESE student linux servers - student.ese.ic.ac.uk and student2.ese.ic.ac.uk [TODO?]. However, if you want to install any of the software on your own computer you can find instillation instructions below. Instructions on connecting to the student servers (using XMing and PuTTY) can be found below.

Connect to student servers from Windows

On the College computers, PuTTY and XMing should be already installed.

Start the XMing server, start PuTTY and type student.ese.ic.ac.uk in the Host Name field:

PuTTY Configuration

Make sure the option Enable X11 forwarding is ticked:

PuTTY X11 Configuration

Log in with your username and password and you will get a black window with a command prompt. This is called a terminal, and we will learn what to do with this in the next two days.

Connect to student servers from a Mac

If you don't have an X.Org X Window System running on your Mac, install XQuartz and reboot.

Start the Terminal app and connect to the student server with X11 forwarding, which means any graphical windows will be launched on your Mac:

ssh -Y <user>@student.ese.ic.ac.uk

Replace <user> with your username and login with your password. This gets you a terminal running on the remote server, which you can use in the same way as in the tutorial i.e. following the instructions above.

If you want to install everything yourself

To participate in a Software Carpentry workshop, you will need access to the software described below. In addition, you will need an up-to-date web browser.

We maintain a list of common issues that occur during installation as a reference for instructors that may be useful on the Configuration Problems and Solutions wiki page.

The Bash Shell

Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.

Windows

Video Tutorial
  1. Download the Git for Windows installer.
  2. Run the installer and follow the steps bellow:
    1. Click on "Next".
    2. Click on "Next".
    3. Keep "Use Git from the Windows Command Prompt" selected and click on "Next". If you forgot to do this programs that you need for the workshop will not work properly. If this happens rerun the installer and select the appropriate option.
    4. Click on "Next".
    5. Keep "Checkout Windows-style, commit Unix-style line endings" selected and click on "Next".
    6. Keep "Use Windows' default console window" selected and click on "Next".
    7. Click on "Install".
    8. 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:

      setx HOME "%USERPROFILE%"

    3. Press [Enter], you should see SUCCESS: Specified value was saved.
    4. Quit command prompt by typing exit then pressing [Enter]

This will provide you with both Git and Bash in the Git Bash program.

Mac OS X

The default shell in all versions of Mac OS X is Bash, so no need to install anything. You access Bash from the Terminal (found in /Applications/Utilities). See the Git installation video tutorial for an example on how to open the Terminal. You may want to keep Terminal in your dock for this workshop.

Linux

The default shell is usually Bash, but if your machine is set up differently you can run it by opening a terminal and typing bash. There is no need to install anything.

Git

Git is a version control system that lets you track who made changes to what when and has options for easily updating a shared or public version of your code on github.com. You will need a supported web browser (current versions of Chrome, Firefox or Safari, or Internet Explorer version 9 or above).

You will need an account at github.com for parts of the Git lesson. Basic GitHub accounts are free. We encourage you to create a GitHub account if you don't have one already. Please consider what personal information you'd like to reveal. For example, you may want to review these instructions for keeping your email address private provided at GitHub.

Windows

Git should be installed on your computer as part of your Bash install (described above).

Mac OS X

Video Tutorial

For OS X 10.9 and higher, install Git for Mac by downloading and running the most recent "mavericks" installer from this list. 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.

Linux

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

Text Editor

When you're writing code, it's nice to have a text editor that is optimized for writing code, with features like automatic color-coding of key words. The default text editor on Mac OS X and Linux is usually set to Vim, which is not famous for being intuitive. if you accidentally find yourself stuck in it, try typing the escape key, followed by :q! (colon, lower-case 'q', exclamation mark), then hitting Return to return to the shell.

Windows

Video Tutorial

nano is a basic editor and the default that instructors use in the workshop. To install it, download the Software Carpentry Windows installer and double click on the file to run it. This installer requires an active internet connection.

Others editors that you can use are Notepad++ or Sublime Text. Be aware that you must add its installation directory to your system path. Please ask your instructor to help you do this.

Mac OS X

nano is a basic editor and the default that instructors use in the workshop. See the Git installation video tutorial for an example on how to open nano. It should be pre-installed.

Others editors that you can use are Text Wrangler or Sublime Text.

Linux

nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.

Others editors that you can use are Gedit, Kate or Sublime Text.