Nov 16-18, 2015
9:30 am - 17:00 pm
Instructors: Alexander Konovalov (University of St Andrews), Kwasi Kwakwa (Imperial College London), Leighton Pritchard (James Hutton Institute)
Helpers: Nick Loughlin (University of Newcastle), Michael Torpey (University of St Andrews)
Software Carpentry's mission is to help scientists and engineers get more research done in less time and with less pain by teaching them basic lab skills for scientific computing. 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 PhD students and other researchers from UK institutions. You don't need to have any previous knowledge of the tools that will be presented at the workshop.
This workshop constitutes the initial part of the First CoDiMa Training School in Computational Discrete Mathematics which runs until Friday November 20th. By registering for this workshop you will automatically register for the whole School. Please see the School's page for further details.
Contact: Please mail firstname.lastname@example.org for more information.
|09:30||Automating tasks with the Unix shell|
|13:30||Automation with Make|
|09:00||Coffee - at Alan Turing Building, Atrium Bridge Level 1|
|09:30||Version control with Git|
|11:20||Version control with Git - continued|
|13:00||Lunch break (room 2.220)|
|14:00||Programming with GAP|
|15:30||School activities (see schedule here)|
|09:30||Programming in GAP|
|13:30||School activities (see schedule here)|
We will use this Etherpad for chatting, taking notes, and sharing URLs and bits of code.
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.
Bash is a commonly-used shell that gives you the power to do simple tasks more quickly.
Download the Git for Windows installer. Run the installer. Important: on the 6th page of the installation wizard (the page titled `Configuring the terminal emulator...`) select `Use Windows' default console window`. 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. This will provide you with both Git and Bash in the Git Bash program.
The default shell in all versions of OS X is bash, so no
need to install anything. You access bash from the Terminal
/Applications/Utilities). You may want to keep
Terminal in your dock for this workshop.
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
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).
Git should be installed on your computer as part of your Bash install (described above).
For OS X 10.9 and higher, install Git for Mac
by downloading and running the most recent "mavericks" installer from
After installing Git, there will not be anything in your
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"
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.
GAP is a system for discrete computational algebra. It provides a programming language, a library of thousands of functions implementing algebraic algorithms written in the GAP language as well as large data libraries of algebraic objects. Its latest version may be found on the GAP Downloads page.
From the GAP Downloads page,
.exe installer and double click on the file to run it. When you
will be asked for the installation path, note that it should not contain spaces.
For example, you may install GAP in
C:\Math\GAP\gap4r7, but you must not
install it in a directory named like
C:\Program files\gap4r7 or
C:\Users\alice\My Documents\gap4r7 etc.
On OS X, we suggest to install GAP using Homebrew.
After installing Homebrew, open the Terminal and call
brew install homebrew/science/gap --with-InstPackages.
Please be patient - this may take a while. If Homebrew is already installed
on your Mac, you may have to call
brew update first.
Alternatively, you may also install GAP from source as explained at the GAP Downloads page. The BOB installer, suggested in the next column for Linux, is also available for OS X.
We suggest to use an alternative GAP source installer BOB which will first check whether everything it needs from your system is installed and if not it will warn you and tell you what is needed. Please see BOB page for further instructions. To be able to compile GAP you may need to install some tools as described here. Alternatively, you may also install GAP from source as explained at the GAP Downloads page.
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 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.
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.
nano is a basic editor and the default that instructors use in the workshop. It should be pre-installed.